1 CENTRAL SERICULTURAL RESEARCH & TRAINING INSTITUTE

BIOINFORMATICS CENTRE

Dr. C. K. Kamble Director & Coordinator Central Silk Board (Ministry of Textiles – Govt. of India) Srirampura, Manandavadi Road, Mysore – 570 008 Ph. 0821-2362547 Fax : 2362845 E-mail : [email protected]

Introduction

Ever since the human genome has been deciphered, it has emerged that bioinformatics will become increasingly important for many areas in the life sciences. This era has seen an explosion of information discovered from the areas of molecular biology and genetics. The focus of bioinformatics is dealing with this flood of information turning it into useful knowledge. The flow of information has revolutionized many fields of biosciences. It is also important for the improvement of genomes of economically important crops and animals. Full understanding and application of this new data requires a large and growing body of intelligent, creative and experienced scientists with strong understanding of both computation and biology. The post- genomic era has thrown great challenges for the scientists to create, manage and interpret the massive sets of complex biological data. Rapid advances in information technology, computer science, structural biology and development of sophisticated computational software and tools have played a key role in deciphering the structure and function of biological molecules, which has great relevance to agriculture, human health and environment. It is befitting to state that the increased significance of bioinformatics can no longer be overemphasized.

The Department of Biotechnology, Govt. of India has reacted to this development with the establishment of a special research focus on bioinformatics. The department has established a nation wide network of bioinformatics centres spread across the country even the farthest corners. This network has established a link between diverse groups of scientists working in various R & D institutions and universities engaged in specified areas of biotechnology. I am proud to state that Central Sericultural Research & Training Institute, Mysore, which is the premier research institute for sericulture in the country, is a part of this prestigious network. The bioinformatics centre of this institute was established in 1999 to primarily support biotechnological research in sericulture.

The annual meeting of the coordinators of BTISnet is held to review the progress and activities of all the centres. It is highly overwhelming to host such an important event of this year in this institute. The progress reports of all the centres compiled in this volume is a valuable document for taking stock of the activities and achievements of the BTISnet. I earnestly foresee that these two days’ congregation of ignited brains will provide an excellent platform for meaningful interaction, exchange of valuable ideas and new thoughts, which will lead to new breakthroughs. I am confident that this will further enable us to conquer greater heights in the field of Bioinformatics.

Dr. Chandrakant K. Kamble DIRECTOR

2 CONTENTS

1. Advanced Centre for Treatment, Resarch, & Education in Cancer, 01 Mumbai 2. Aligarh Muslim University, Aligarh 05 3. All India Institute of Medical Sciences, New Delhi 09 4. Anna University, Chennai 12 5. Assam Agricultural University, Jorhat 16 6. Banaras Hindu University, Varanasi 21 7. Banasthali Vidyapith, Banasthali 27 8. Barkatullah University, Bhopal 32 9. Bharathidasan University, Tiruchirappalli 38 10. Biotech – Consortium India Limited, New Delhi 43 11. Biotech Park, Lucknow 50 12. Birla Institute of Scientific Research, Jaipur 56 13. Birla Institute of Technology, Mesra, Ranchi 61 14. Bose Institute, Kolkata 66 15. Central Agricultural Research Institute, Port Blair 72 16. Central Drug Research Institute, Lucknow 77 17. Central Institute of Freshwater Aquaculture, Bhubaneswar 84 18. Central Institute of Medicinal and Aromatic Plants, Lucknow 89 19. Central Plantation Crops Research Institute, Kasaragod, Kerala 94 20. Central Sericultural Research and Training Institute, Mysore 99 21. Centre for Cellular & Molecular Biology, Hyderabad 104 22. CSK Himachal Pradesh Krishi Vishvavidyalaya, Palampur 110 23. Devi Ahilya University, Indore 114 24. Dr.Y S Parmar University of Horticulture and Forestry, H.P. 119 25. G. B. Pant University of Agriculture & Technology, Pantnagar 125 26. Guru Nanak Dev University, Amritsar 129 27. Himachal Pradesh University, Summer Hill, Shimla 134 28. Indian Agricultural Research Institute, New Delhi 138 29. Indian Institute of Science, Bangalore 143 30. Indian Institute of Spices Research, Calicut, Kerala 148 31. Indian Institute of Technology, New Delhi 152 32. Indian Institute of Technology, Kharagpur 157 33. Indian Veterinary Research Institute, Izatnagar 162 34. Indian Institute of Advanced Research, Gandhinagar, Gujarat 167 35. Indian Institute of Integrative Medicine, Canal Road, Jammu 171 36. Indian Institute of Chemical Biology, Kolkata 176 37. Institute of Bioresources and Sustainable Development, Imphal 180 38. Institute of Microbial Technology, Chandigarh 184 39. Karnataka Veterinary, Animal & Fisheries Sciences University, Mangalore 192 40. Kerala Agricultural University, Thrissur 201 41. Madurai Kamaraj University, Madurai 205 42 Mahatma Gandhi Institute of Medical Sciences, Sevagram (Wardha) 211 43. M.S. University of Baroda, Baroda 217 44. National Brain Research Centre, Manesar, Haryana 223 45. National Dairy Research Institute, Karnal 229 46. National Institute of Immunology, New Delhi 233 47. National Institute of Oceanography, Goa 237 48. National Institute for Plant Genome Research, New Delhi 241 49. National Institute of Technology, Raipur 243 50. North-Eastern Hill University, Shillong 246 3 51. Pondicherry University, Pondicherry 255 52. Punjab Agricultural University, Ludhiana 262 53. Rajiv Gandhi Centre for Biotechnology, Trivandrum 268 54. State Council of Science & Technology for Sikkim 273 55. T. M. Bhagalpur University, Bhagalpur 278 56. Tamilnadu Veterinary and Animal Sciences University, Chennai 283 57. Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu 288 58. Tropical Botanic Garden and Research Institute Palode, Kerala 293 59. University of Calcutta, Kolkata 299 60. University of Kashmir, Hazratbal, Srinagar, J&K 303 61. University of Pune, Pune 307

Bioinformatics Infrastructure Facility Centres (BIFs)

1. Assam Agricultural University, Khanapara, Guwahati 320 2. Alagappa University, Karaikudi, Tamil Nadu 323 3. Bharathiar University, Coimbatore 328 4. CCS Haryana Agricultural University, Hisar 330 5. Dr. B. R. Ambedkar Center for Biomedical Research, 333 Delhi 6. Fakir Mohan University, Balasore, 337 7. Forest Research Institute - Dehradun 339 8. Guru Jambheshwar University of Science & Technology, 343 Hisar 9. HNB Garhwal University, Garhwal 347 10. Holy Cross College, Tiruchirappalli, Tamil Nadu 350 11. Indira Gandhi Krishi Vishwavidyalaya, Raipur 354 12. Indian Institute of Technology, Madras 357 13. Jamia Millia Islamia, New Delhi 360 14. Jiwaji University, Gwalior 364 15. Kannur University, Kannur 367 16. Karnatak University, Dharwad 371 17. Kumaun University, Nainital 373 18. Lady Doak College, Madurai 375 19. Lucknow University, Lucknow 378 20. Madras Christian College, Chennai 381 21. Maharani’s Science College for Women, Bangalore 384 22. Maulana Azad National Institute of Technology, Bhopal 387 23. Narendra Deva University of Agriculture & Technology, 391 Faizabad 24. National Institute of Pharmaceutical Education and 396 Research, Chandigarh 25. Orissa University of Agriculture and Technology, 399 Bhubaneswar 26. Presidency College, Chennai 402 27. Presidency College, Kolkata 406 28. Sardar Vallabh Bhai Patel University of Agriculture & 409 Technology, Meerut 29. Sant Gadge Baba Amravati University, Amravati 411 30. Sanjay Gandhi Postgraduate Institute of Medical 414 Sciences, Lucknow 31. Shri Mata Vaishno Devi University (SMVDU), Katra, 418 Jammu 4 32. Sri Padmavati Mahila Visvavidyalayam, Tirupati 422 33. Sri Venkateswara College, (University of Delhi) 425 34. Sri Venkateshwara Institute of Medical Sciences, 428 Tirupati 35. Tezpur University, Tezpur 432 36. University of Allahabad, Allahabad 435 37. University of Bangalore, Bangalore 438 38. University of Calicut, Kerala 441 39. University of Hyderabad, Hyderabad 443 40. University of Jammu, Jammu 446 41. University of Kalyani, Kalyani, West Bengal 451 42. University of Madras, Chennai 455 43. University of North Bengal 458 44. University of Rajasthan, Jaipur 461 45. Vidyasagar University, Midnapur, West Bengal 464 46. West Bengal University of Technology, Kolkata 469 47. COE, Jawaharlal Nehru University, New Delhi 472

5 Advanced Centre for Treatment, Research, & Education in Cancer, Mumbai. Coordinator : Robin Mukhopadhyaya

1. Summary of the progress made by the centre from its inception.

The Department of Biotechnology (DBT), Government of India, funded the establishment of a Biotechnology Information Service (BTIS)/Bioinformatics Centre at the Cancer Research Institute in 1989. Since then DBT has maintained its support and TMC has also provided necessary inputs as and when required for gradual maturation of the facility.

Along with expansion of the institutional infrastructure, advanced data/information dissipation with higher level of security to increasing number of users is an ongoing process. During this period quite a few hardware additions took place.

BTIS organizes every year a two-day workshop primarily targeting College/University faculties/Ph.D. students (15-16 nos) to provide basic knowledge of applications in bioinformatics using data/information on cancer biology and proteomics, gene expression analysis using Micro arrays etc along with lectures on computer basics, literature mining followed by hands on training sessions. A bioinformatics expert usually is invited from other national institute to deliver a special lecture. BTIS staff supports the scientists/students for all bioinformatics/biostatistics related queries and additionally was also responsible for initial development, updating and maintenance of the website that is hosted on our server. ‘Computerized repository of cell line maintenance’, a small software, was developed (available on the ACTREC web site) by a basic research scientist in association with BTIS staff.

2. Major research activities in Biotechnology and its related fields at your institution: Focus is on basic and translational research in cancer biology. All details are available at www.actrec.gov.in/Research/Basic Research. In relation to use of bioinformatics thrust is on genomics and proteomics of oral cancer, cervical cancer and a hematological malignancy in keeping with the wet lab thrust areas.

3. Area of Specialization of the centre. Cancer Biology: Basic and Translational.

4. Major activities of the centre during the year 2007-08: Significant addition of computational infrastructure contributed by the institute; Organization of training course; Training new Ph.D. students in use of bioinformatics resources; Uploading of a new database developed in-house.

Infrastructure facilities in the Bioinformatics Centre i. Computer & Communication facility: Two Linux based IBM servers, purchased on DBT grant, and are used as the Internet and mail servers. The high end X-225 server is configured as mail server and X-205 is the proxy+web server and the Trend Antivirus is being used on the gateway as well as mail server. The old ACER PII server, procured long back also through DBT, is being used for deploying MS security patches as well as anti-virus software at

6 desktop level (recently switched from Symantec corporate edition to Trend Micro client-server messaging security). A Linux based IBM Intellistation Z Pro workstation for a molecular modelling study was acquired in recent times. Hundred- user license patch-easy software was deployed for patch management and additional 40-user license of MS Office 2003 was also procured. To ease net connectivity on demand avoiding additional civil work, Wi-Fi facility was implemented in certain areas with high volume users/laptop users within the institute and a NAS server (1 TB capacity) was deployed for online back up. We have a 1Mbps shared (1/4) leased line from VSNL through MTNL OF connectivity. Additionally a 250 Kbps last mile wire less internet connectivity from M/S Tulip Inc has recently been commissioned. Internet is connected to ~150 PC terminals.

ii. Scientific Software packages: None iii. Databases & other information resources: Database on oral cancer genes and chromatin ( See 11 below) 5. Details about staff members working in the centre (Name of the staff, Designation, Specialization and period of working. Please indicate their absorption status)

All staff on DBT funding was absorbed by the institute way back in 1994. The centre has one Scientist C, Mr. NK Gadewal, with a post graduate degree in Biotechnology and a diploma in Bioinformatics; the facility is actively supported by staff from IT and biostatistics personnel who are permanent staff of the Centre.

6. Types of services provided: Training in basics of bioinformatics to scientific staff/doctoral students; special emphasis is to train scientific staff, and post graduate students of biology from resource poor academic institutes in the state.

7. Educational activities with details of placement: Nil 8. Initiative to validate the outcome of bioinformatics resources: Each year there are about 40 short term trainees from different parts of the country who undertake their M Sc dissertation with faculty at ACTREC and utilize these facilities. Fairly good numbers of students/academic staff members from Mumbai and nearby institutes also regularly access the facility/take suggestions relevant to their work from BTIS staff.

9. Collaborative works/ initiatives: Nil

Databases/ Software packages developed:

A major focus of this group, in keeping with the wet lab thrust area, is to develop meaningful database related to genomics/ proteomics of oral cancer. A new database was developed here and uploaded on our website (URL- http://www.actrec.gov.in/oralcancer/GeneHome.htm). This year a new Histone database was uploaded on our website (URL http://www.actrec.gov.in/histone/infobase.htm)

Papers published or presented in the conferences with reference: 7 Database and interactome map of genes involved in oral cancer. Gadewal NS, Zingde SM. Online J Bioinfo 8: 41-44, 2007.

Initiation of R&D activities in Bioinformatics: Bioinformatics is now an integral component of several queries in this centre. It is required for analysis of the genomics and proteomics related programs on oral cancer, cervical cancer, brain cancer and hematological malignancies. In 2007 Structural Biology has been introduced as a thrust area at the Centre. The scientific inquiries in this include proteosomal dynamics, structure activity relationships of apoptotic proteins and X-ray crystallography of cancer- associated proteins all of which will require extensive mining of data from different bases using relevant bioinformatics software. Structure-based drug design and molecular modeling.

10. Details of Training/ Workshop organized and total no. of user trained.

A DBT sponsored workshop on Bioinformatics was held on 22-23 March 2007 at this centre. The 11 participants from other institutes were lecturers as well as doctoral students. The Workshop included lectures on different topics like Applications in bioinformatics, Cancer biology and proteomics, Micro array data analysis, Computer/networking basics, Database concept and usage followed by hands on training sessions. Dr. Surekha Zingde, Dr. Chandan Kumar, Mr. N. Gadewal, Mrs. S. Kannan, and Mrs O. Upasani delivered the lectures; the “Hands-on Training session” involved the members of the Bio- informatics/Biostatistics section and one doctoral student, Mr. Santhosh VC, explained genome sequencing/annotation. All course materials were provided to the participants on CD. A guest lecture was delivered during the workshop by Dr. Urmila Kulkarni-Kale from Bioinformatics Centre, University of Pune. One student was provided short term training on Database development (Meenakshi Sharma, M.Sc Bionformatics, Banasthali Vidyapith, Rajasthan, January 8-June 7). 11. Impact shown by your centre on the growth of biotechnology and allied areas. Papers published from the center-45; Invited lectures by the staff of BTIS in neighboring institutes. There is a growing demand from many city colleges/institutes to hold the bioinformatics workshop twice in a year. 12. Future activities: Infrastructure and expertise development in molecular modeling.

Additional Details: Nil

Name of the Coordinator: R. Mukhopadhyaya

Postal Address: Bioinformatics Centre, Advanced Centre for Treatment, Research & Education in Cancer (ACTREC), Kharghar, Navi Mumbai - 410 210. Phone Number: 022-2740 5000 Fax No.: 022-2740 5085

Email: [email protected] Website: www.actrec.gov.in

Name of Contact Person: Dr. Ashok Varma. Email: [email protected] 8 Aligarh Muslim University, Aligarh Coordinator : Professor M. Saleemuddin

1. Summary of the progress made by the centre from its inception The Distributed Information Sub-Centre was established by the DBT, New Delhi at Aligarh Muslim University, Aligarh in the academic session 1988-89. The main function of the Centre is to act as a member of Bioinformatics Network System for providing information to the interested users on topics pertaining to the relevant areas of Biotechnology specially protein folding and design, protein structure and protein engineering. The functions of the Centre include, among others, acquisition, creation and development of programmes and databases needed by the users. For the last several years, Centre is contributing significantly for the manpower development by organizing workshops and courses in the field of bioinformatics. Since its inception the Centre has organized 14 national level bioinformatics workshops and trained more than 325 participants from different universities and institutions. Centre is regularly organizing seminar lecture for the benefit of students, researchers and scientists working the area of biotechnology or in the areas related to biotechnology. Centre is regularly providing Internet facility for its users since 1994. Recently a dedicated 512 kbps BSNL leased line and a 2 mbps broadband connection has been installed and is functioning satisfactorily in providing online literature search etc.

2. Major research activities in Biotechnology and its related fields at your institution Right from its establishment, the unit has been concentrating on research in various aspects of protein biotechnology and efforts continue in this direction, in addition to those in immunology and molecular biology. One aspect that is being actively pursued is the stabilization of enzymes with the help of polyclonal antibodies. Attempts are currently being made to identify regions of the enzyme that are crucial for enzyme stability and raise antibodies against the regions in experimental animals. Another group is actively engaged in the study of pathways leading to various folding intermediate of proteins, which involves the characterization of various intermediates. Moreover development of liposome-based vaccines to project against various antifungal diseases are also in pipeline. Studies on isolation of T4 nrdB mutants for the investigation of the structure-function relationship in RNA splicing of group I introns on a model with view to understand the requirement of secondary and tertiary structure of RNA in the autocatalytic splicing of intron is also being investigated. Molecular Biology and Yeast genetics exploring Transcription factors and their interaction with 3’ RNA processing machinery. Transcription regulation and gene silencing versus histone methylation .

3. Area of Specialization of the centre : Basic Biotechnology

4. Major activities of the centre during the year 2007- 08 Distributed Informatics Sub-center is involved in bioinformatics research in the fields of genome and proteome analysis. The genome of Arabidopsis thaliana was analyzed to determine the position and frequency of simple sequence repeats (SSRs). Simple sequence repeats or microsatellite repeats are defined as regions within DNA sequences where short sequences (1-6 bp; monomers to hexamers) are repeated in tandem array. We have developed a perl program (SSRscanner) for this 9 analysis. The work was published in the journal Bioinformation (Anwar, T & Khan, A.U., 2005. Mapping and analysis of Simple Sequence Repeats in the Arabidopsis thaliana Genome. Bioinformation 1(2):64-68.) At present research work is going on the in silico analysis of proteome of a deadly virus i.e., Influenza A virus (Bird flu virus). This program will be very helpful to Influenza researchers who wish to do analysis of Influenza sequences or any other sequence by comparison of two sequences. Workshops on Bioinformatics : Workshop on ” Genome analysis: A bioinformatics” was organised during February 24-25, 2007 in which 22 participants were trained. E-Mail and Internet Facility : The Centre is regularly providing INTERNET facility to the users through BSNL dedicated 512 kbps leased line and BSNL 2 mbps Broad Band Connection which has recently been procured by the Centre. CD-ROM Databases Facility : The CD-ROM databases facility of the Centre is being regularly used by the students, researchers and teachers of this University for the retrieval of scientific information. Scientific Software Facility : Among others, Centre has procured few scientific softwares like Sigma Plot, DTMM, Reference Manager, Enzfitter, Instat, Peakfit, which are being regularly used by the students and researchers of this University. Bioinformatics teaching: A paper entitled “Computational methods and bioinformatics” has been introduced in the curriculum offered to M.Sc. Biotechnology and the bioinformatics part is being taught by the BTIS staff of this Centre. Inhouse Databases: These are Proteolytic enzyme database, Immobilized metal affinity chromatography database, Human Vaccine database.

5. Infrastructure facilities in the Bioinformatics Centre: i. Computer & Communication facility The Bioinformatics Centre is now fully equipped with BSNL dedicated 512 kbps leased line and BSNL 2 mbps Broad Band Connection, One servers, fourteen Pentium IV systems, three Pentium 2 systems and one Pentium 1 system with two dot matrix printers, three laser printers, two scanners, one photocopier and a fax machine. ii. Scientific Software packages iii. Databases & other information resources Medline, Biotechnology Abstracts, Agricola, and Life Science Collection Journals: European Journal of Biochemistry, Science, New Scientist, Trends in Biochemical Sciences and Trends in Biotechnology, Nature, New Scientist, Nature Biotechnology etc.

6. Details about staff members working in the centre (Name of the staff, Designation, Specialization and period of working. Please indicate their absorption status) Name of the staff Designation Period of Work S. Faisal Maqbool Sr. Scientific Officer 18 years Parveen Salahuddin Sr. Res. Assistant 17 years S. Aqtedar Husain Data Entry Operator 17 years All above have already absorbed by the University

7. Types of services provided Workshops on Bioinformatics, E-Mail and Internet Facility, CD-ROM Databases Facility, Scientific Software Facility,In-house Databases. The following databases have been developed and upgraded regularly for the routine use of the biotechnologists. (a) Proteolytic enzyme database (b) Immobilized metal affinity chromatography database (c) Human Vaccine database

8. Educational activities with details of placement • Bioinformatics teaching: 10 • Multimedia and E-learning initiatives:

9. Initiative to validate the outcome of bioinformatics resources • Organizing workshop in bioinformatics for manpower development. • Providing online services through BSNL dedicated 512 kbps leased line and BSNL 2 mbps Broad Band Connection for literature search etc. • Providing offline services using CD-ROM database (Medline, Life Science Collection and Biotechnology Abstracts). • Providing scientific softwares like Sigma plot, Grafit, Reference Manager, DTMM, Instat, Buffer Maker and a number of word processing softwares for the routine use of researchers and teachers.

10. Collaborative works/ initiatives Nil

11. Databases/ Software packages developed Databases: (i) Proteolytic enzyme database (ii) Immobilized metal affinity chromatography database (iii) Human Vaccine database Software: AMACAN: An hydrophobicity analysing software for protein and amino acid sequences developed in visual basic and MS-Access for the routine use of students and teachers.

12. Papers published or presented in the conferences with reference During the year (2007-2008) years more than 35 papers were published using bioinformatics facilities

13. Initiation of R&D activities in Bioinformatics: Nil

14. Details of Training/ Workshop organized and total no. of user trained The centre has organized 14 workshops since 1994 and has trained more than 325 users so far.

15. Impact shown by your centre on the growth of biotechnology and allied areas. In this you may highlight the details like number of paper published/ number of papers published with the help of your centre, how your centre is promoting various activities of your organization and neighboring institutions, manpower trained, tools developed, patents & copyrights acquired and other services offered etc.

Centre is involved in bioinformatics research in the fields of genome and proteome analysis. The genome of Arabidopsis thaliana was analyzed to determine the position and frequency of simple sequence repeats (SSRs). Simple sequence repeats or microsatellite repeats are defined as regions within DNA sequences where short sequences (1-6 bp; monomers to hexamers) are repeated in tandem array. We have developed a perl program (SSRscanner) for this analysis. At present research work is going on the in silico analysis of proteome of a deadly virus i.e., Influenza A virus (Bird flu virus). The avian influenza (bird flu) caused by Influenza virus is an infectious disease of birds, ranging from a mild to a severe form of illness. Influenza viruses pose significant challenges to both human and animal health. Highly pathogenic avian influenza virus infection can result in huge economic loss. The proteins Nucleoprotein (NP), Neuraminidase (NA) and Hemagglutinin 11 (HA) of Influenza A Virus (Bird flu virus) sub-type A/Hatay/2004/(H5N1) from chicken are being analyzed to check the mutations and to find out the protein that is responsible for causing the disease, secondary structure prediction, etc. A perl program MAPMUTATION that compares two sequences and report the exact location of mutation in the sequence and change in amino acid/nucleotide was also developed for this study. This program will be very helpful to Influenza researchers who wish to do analysis of Influenza sequences or any other sequence by comparison of two sequences. More than 38 papers have been published using bioinformatics facilities(see attached list).

16. Future activities • Analysis of eukaryotic genomic DNA and its organization using gene finder program. • Development of databases in the areas actively investigated at this University such as on vaccines against human diseases, chemokines, Enzyme immobilisation. etc. • Organising workshops on bioinformatics. • Organising seminar lecture programmes in the areas of bioinformatics and biotechnology • Online access to E-journals, softwares etc.

Additional details: Name of the Coordinator:Professor M. Saleemuddin Postal Address: Coordinator, Distributed Information Sub-Centre, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh – 202 002. Phone: 0571-2720388, Fax: 0571-2721776 E-mail: [email protected]

12 All India Institute of Medical Sciences, New Delhi Co-ordinator: Prof. Y.D. Sharma

1. Summary of the progress made by the centre from its inception The progress made by BTIS is reflected in modern methods of M.Biotech. teaching and ready access of bioinformatics tools The research scholars and students in our department have become more adept in handling various scientific packages and their efforts in this direction have led to the development of two software packages Spectral Repeat Finder and My Pattern Finder. The manpower trained by us has found placement in government and private sectors both in India and abroad.

All our research labs are connected through a local area network afforded by BTIS and provided with internet connectivity. The BTIS facility provides strong support to all research projects of the department and 24hours of internet connectivity is utilized effectiviley for accessing various online databases and for online submission of manuscripts and sequences.

2. Major research activities in Biotechnology and its related fields at your institution.

The research laboratories in the department of biotechnology at AIIMS are carrying out active research in the fields of molecular and immunological aspects of infectious diseases like Malaria and Tuberculosis, tumor biology and cardiac diseases. PCR based diagnostic methods have been developed for TB and closely related mycobacteria and they have also been patented. Research is also being carried out to identify potential drug and vaccine target antigens for TB and Malara. Basic research is being carried out to decipher the role of DevR-DevS signal transduction system in pathogenesis and virulence of M. tuberculosis. Mutations in cytokine genes and their receptors are also being studied in different categories of cancer patients for providing a better diagnostic tool. In the field of cardiac diseases, modulation of endothelin in blood plasma of patients undergoing coronary artery bypass surgery imparted with relaxation therapy in the form of meditation is being studied.

3. Area of Specialization of the centre: Infectious diseases, tumor biology, cardiac diseases.

4. Major activities of the centre during the year 2007-08. BTIS provided support for three major activities of our department namely (i) Teaching: The bioinformatics module for M.Biotech. students was further strengthened to a 3.0 credit point course (ii) Research: Active research was carried out in the field of infectious diseases including malaria & tuberculosis, cancer and cardiac diseases culminating in (iii) Publications, diagnostics and patents. 5. Infrastructure facilities in the Bioinformatics Centre Computer & Communication facility Tetronix color laser printer (1), laser Printers (5), Deskjet Printer (1), Modem (2), UPS (1), Fax Machine (2), Modi Xerox (1), Electronic Type Writer (1), Server Netfinity (1), Windows NT Server (1), CD Writer (2), Zip

13 Drive (2), Router DI-1162 (1), HP Scanners (2), OHP (1)Lap Top & LCD Projector (1), Gel Doc System (1).

Scientific Software packages (procured): • Labwork for Gel Analysis on UVP system • Graph Pad • End Note Version 7.0

Databases & other information resources: NIL 6. Details about staff members working in the centre (Name of the staff, Designation, Specialization and period of working. Please indicate their absorption status)

Name Of The Designation Specialization Working Absorption Staff Since Status Shalini Narang Data entry M.Sc. Computer April 2000 AIIMS operator Science ( 7 yrs.) employee

7. Types of services provided. Access to computers and accessories including round the clock internet facility for teaching, scientific research and publication to students, research scholars, office staff and faculty

8. Educational activities with details of placement. A 3.0 credit point course module in bioinformatics is being run for M.Biotech. students. The students are imparted with hands on training in the use of various bioinformatics tools and packages. Experts are invited from other departments, institutes (TCGA) and universities (JNU). The details of the placement of individual candidates may be viewed in Appendix-I

9. Initiative to validate the outcome of bioinformatics resources. The two-software packages developed by us are being used by students for in silico analysis of research hypotheses and are finding support in experimental results.

10. Collaborative works/ initiatives. Interactions with Other Institutions/Centres: Experts are invited from various academic institutes/centres for delivering lectures on various topics in Bioinformatics to M.Biotech. students. Some of the collaborating institutes/centres include IGIB, New Delhi, SIT, JNU New Delhi, IIT Delhi, Deptt. of Biophysics, AIIMS, Deptt. of Computer facility, AIIMS and Deptt. Of NMR, AIIMS. 11. Databases/ Software packages developed. Two software packages developed by us are 1. Spectral Repeat Finder 2. My Pattern Finder 12. Papers published or presented in the conferences with reference In 2007 16 papers have been published in peer-reviewed (Pub-Med indexed) journals. (See Appendix-II for references).

13. Initiation of R&D activities in Bioinformatics. 14 In silico analysis of wet-lab. Data and hypothesis formulation using bioinformatics tools available on-line is an integral part of all R&D activity being carried out in our department.

14. Details of Training/ Workshop organized and total no. of user trained. BTIS is providing support to the M.Biotech. Teaching Programme, PhD scholars, MD/MS trainees, WHO fellows, DBT Associates and summer trainees. The total strength of manpower trained is, therefore, greater than 332.

15. Impact shown by your centre on the growth of biotechnology and allied areas. No. of M.Biotech students trained: > 168 No. of PhD scholars passed out 27 No. of PhD scholars enrolled currently 18 No. of Post MD/MS professionals trained > 15 No. of summer trainees > 90 No. of WHO fellows trained 14 No. of papers published in 2007 16 No. of patents 14

16. Future activities The conditions for learning and teaching of Bioinformatics shall be optimized based on the articulated needs and concerns of the students carrying out research in the field of biomedical sciences. Upgradation Infrastructure Facility shall be carried out for teaching purposes

Additional Details: Name of the Coordinator: Prof. Y.D.Sharma Postal Address: Department of Biotechnology, All India Institute of Medical Sciences Ansari Nagar, New Delhi -110029 Phone Number: 26594609 Mobile: 9868397964 Fax: 26589286 Email: [email protected] Website: www.aiims.edu/aiims/departments/biotech.

15 Anna University, Chennai Coordinator : Prof. P. Gautam

1. Summary of the progress made by the centre from its inception The Distributed Information Centre, Centre for Biotechnology, Anna University has good infrastructure facility with a Apple cluster for parallel computing, a high end SGI Server and SGI Fuel Workstations and IBM PCs. These facilities are used for research activities in Molecular dynamics, Molecular modeling, Docking, Cluster computing, Database creation, Protein Structure Studies, Genomics and Systems Biology. A three Credit course in bioinformatics is offered to the Undergraduate students and a 3 Credit course in Computational Biology is offered to Postgraduate and Doctoral students of the University. We also provide guidance on Projects in Bioinformatics for our Undergraduates, Postgraduates and students from other Universities. Information dissemination and training is one of the mandates of the centre. Regular workshops and training programmes are conducted by the centre for familiarizing College Professors and Lecturers with the latest trends in Bioinformatics and Computational biology. 2. Major research activities in Biotechnology and its related fields at your institution Tissue Culture and Drug Discovery, Immunotechnology, Bioorganic Chemistry and Bioremediation, Computational Biology & Bioinformatics, Protein Biotechnology, Molecular Biology, Bioprocess engineering. 3. Area of Specialization of the centre Areas of specialization of the BTIS DIC, CBT, Anna University include Molecular Dynamics, Molecular modeling and docking, Cluster Computing, Protein Structure Prediction and Genomics. 4. Major activities of the centre during the year 2007-08 Research at the Centre is mainly focused in the areas of Molecular dynamics, Molecular modeling, Protein structural analyses, Genomics and Systems Biology.

16 Infrastructure facilities in the Bioinformatics Centre A High End SGI Origin Server with the following specification: Dual R14000 @600 MHz, 1GB ECC Ram, 18GB Ultra SCSI Internal hard disk Silicon Graphics Fuel Systems - 2 Nos. IBM Intel Pentium IV 2.4GHz with 512cache 256MB RAM, 40GB HDD - 4 Nos. in Cluster and 2 Nos. as Workstations Dual 2GHz PowerPC G5 Apple Mac - 1 No. IBM Netvista Pentium III 88 MhZ, 20 GB HDD - 7 Numbers HP 24 port 100Mbps Switch Colour Laserjet Printers - 1 no. Apple Mac - 1 No Apple G5 64Bit Cluster Computing System With Accessories- 1 No. B. Scientific Software packages Oracle Database 10g and Internet Application Server, GROMACS (Parallel Molecular Dynamics), AutoDock, Dock, Whatif, Delphi, VectorNTI Ver 4.0, Matlab, EMBOSS, Rasmol, Molscript, Phylip, Dotter, ClustalW, 5. Details about staff members working in the centre (Name of the staff, Designation, Specialization and period of working. Please indicate their absorption status) Protein Structure Prediction, Dr. Sharmila Member Research 2003 onwards Comparative Anishetty Staff Contract Basis Genomics, Databases, Systems Biology Member Research Molecular Dynamics 1996 onwards Ms. T.Kothai Staff Simulation Contract Basis Mrs. Documentation 2006 Onwards Vijaylakshmi Digital Library Officer Contract Basis Narayanan

Types of services provided Educational activities with details of placement Teaching Bioinformatics to the Undergraduate B.Tech Industrial Biotechnology, Postgraduate M.Tech Biotechnology and Doctoral students. We also provide Summer term Projects and Curriculum Based Projects for Undergraduates and students from other Universities.

Initiative to validate the outcome of bioinformatics resources We are working on protein protein interaction networks. The results obtained in this study will be validated through single molecule studies using FRET. 17 Papers published or presented in the conferences 1) FEBS Lett. 2007 Sep 18;581(23):4377-83. Epub 2007 Aug 14. Activation of Candida rugosa lipase at alkane-aqueous interfaces: a molecular dynamics study. James JJ, Lakshmi BS, Seshasayee AS, Gautam P.

2) Protein Pept Lett. 2007;14(6):552-6. Distribution of tripeptides in MHC binding peptides. Sharmila Anishetty, Gautam Pennathur

3) Bioinformatics. 2007 Feb 1;23(3):267-71. In silico identification of putative metal binding motifs. Thilakaraj R, Raghunathan K, Anishetty S, Pennathur G.

Initiation of R&D activities in Bioinformatics: B. Tech and M. Tech Projects: Areas of Research: Molecular dynamics simulations of phospholipases and lipases, Respiratory tract pathogens, Molecular level studies of multidrug resistance, Protein protein interactions, Alpha beta hydrolases, Metalloproteins, Quorum sensing pathways, Metabolic flux analysis of aromatic amino acid pathways, Modeling of phenylketonuria. Ph.D. students: We have six Ph.D. students in Computational Biology working on Modeling quorum sensing pathways in Pseudomonas aeruginosa, Cell wall biosynthetic pathway inhibitors in pathogenic bacteria, Protein protein interactions, Comparative genomics and systems biology studies of marine organisms, Molecular dynamics simulations of lipases and acetylases. Details of Training/ Workshop organized and total no. of user trained No. Workshop Title Period No.of Participants 1. Workshop on Sequence Analysis and 5th – 8th Molecular Simulation December 2007 15 Impact shown by your centre on the growth of biotechnology and allied areas. In this you may highlight the details like number of paper published/ number of papers published with the help of your centre, how your centre is promoting various activities of your organization and neighboring institutions, manpower trained, tools developed, patents & copyrights acquired and other services offered etc In the last three years we have published about eight papers in bioinformatics. One person has finished a Ph.D. in Computational Biology and one person has completed a 18 M.S. degree. Currently six students are registered for a Ph.D. in Computational Biology. The facilities of the center are used by students from different colleges in and around Chennai.

Future activities Research: 1) Molecular Dynamics simulation of enzymes immobilized on surfaces. 2) Understand Quorum sensing in Pathogens through a Systems Biology and a Comparative genomics approach 3) Understand the mechanism of metal ion transport in bacteria by optical imaging and develop tools for the process. 4) We are in the process of developing an algorithm for identification of conserved protein interaction network motifs. 5) Systems Biology approach to model phenylalanine metabolism related disorders. Education: We would like to start a M.Sc. ( Computational Biology ) Course with the bioinformatics Centres of Madurai Kamaraj University and Pondicherry University.

Additional Details: Name of the Coordinator: Prof. P. Gautam, Centre for Biotechnology, Anna University, Chennai – 600025. Phone Number:091-44-22350772 Fax No.: 091-44-22350299 Email: [email protected], [email protected] Website: http://www.annauniv.edu/biotech/boc/ Name of Contact Person(s): Dr. Sharmila Anishetty, Ms.T.Kothai Email: [email protected], [email protected]

19 Assam Agricultural University, Jorhat Coordinator : Dr. Mahendra K. Modi

1. Summary of the progress made by the centre from its inception : The Assam Agricultural University is a Premier University in the North-East- India engaged in teaching, research and extension activities of Agricultural and Allied Sciences. At present the university has four faculties viz. Agriculture, Veterinary, Home Science and Fisheries with six constituent colleges. The center successfully bridged the interdisciplinary gaps on information and links in the area of Agricultural Biotechnology in the North- East India. The center is also providing information via Reference Retrieval system and facilities like computational analysis of the research data, Internet/Email facilities and imparting teaching and organizing training programmes on Bioinformatics for the teachers and researchers involved in different Universities, educational institutes and R & D centers of North-east India. The centre since its inception, have been organizing regular National Workshops/Training on Bioinformatics to make entry and mid-level scientist familiar to the basic fundamentals of bioinformatics as well as ways of utilizing Information Technology in Life Science Research. A two hour credit course on “Application of Computers in Biotechnology” has been introduced for the Post Graduate students of this University since 1990. This course was found very useful and effective for the students. From 2004-05 a new post- graduate course on “Introduction to Bioinformatics” has been introduced, in which the students are exposed to various softwares and techniques in Bioinformatics. The Centre also actively engaged in the preparation of different databases and successfully completed database like 1. “Citrus Germplasm Database” which include citrus germplasm available in India along with their detaled morphological and biochemical characteristics. 2. “Tea germplasm database” which include different tea gerplasm available in north-east India along with their detailed morphological and biochemical characteristics.

2. Major research activities in Biotechnology and its related fields in your institution

The major research activities in Biotechnology are :

a. Development of an EST library in Tea (camellia sinensis) b. Genetic transformation of chickpea mediated through Agrobacterium for development transgenic chickpea against stored grain pest. c. Genetic transformation of black gram mediated through Agrobacterium for development transgenic chickpea against pod borer. d. Genetic transformation of Citrus mediated through Agrobacterium for development of transgenic Citrus reticulata cv. Khasi mandarin and Citrus limon cv Assam lemon against stem/trunk borer. e. Genetic transformation of rice mediated through Agrobacterium for development of transgenic indica rice varieties of Assam. 3. Area of Specialization of the centre : a. Broad : Agricultural Biotechnology

20 b. Specific : Plant Tissue Culture, Plant Molecular Biology, Plant Genetic Engineering and Microbial Biotechnology.

4. Major activities of the centre during the year 2007-08: No major activity could be taken up during this year as the Information Officer has gone on a years’ study leave. The databases on citrus and tea are being converted from ‘stand-alone’ to ‘network’ mode and efforts are being made to publish the databases once the conversion is completed.

5. Infrastructure facilities in the Bioinformatics Centre

A. Computer & Communication facility :

i. Computer Hardware : LAN Server, 2 Unit; PC-Pentium II, III & IV, 10 Units; Workstation 1 Unit, Notebook, 1 Unit; Multimedia Projector, 2 Unit; Network Printer 1 Unit Other Inkjet & Laser Printer, 7 Unit, various UPSs, Scanners, Networking equipments etc.

ii. Communication Facilities : 1. 512 Kbps dedicated leased line Internet Port facility has been obtained from BSNL. 2. SCPC VSAT link (256 Kbps) from ERNET – subscribed by the university and ICAR. The facility is shared by the center through a fibre- optic campus LAN – However This link is being upgraded to 2 MBPS leaswed line 3. FAX /Telephone

B. Scientific Software packages SPSS 12.0.1, Vector NTI Advance for PC version 9.1, EMBOSS software suit, BioEdit, Rapidistance, Phylip, DNASIS, pDRAW, DNAClub, ClustalW etc, Exome, Exome-ED, PDQuest Gel analysis software

C. (i) Databases & other information resources Name of Broad Subject Broad Developed Status of Network Database area functional or acquired completion Availa- area bility Agricola Agricultural Bibliographical Acquired Yes Science database Agris Agricultural Bibliographical Acquired Yes Science database CABCD Agricultural Bibliographical Acquired Yes Science database Citrus Morphological, Research/ Developed Completed No Germplasm biochemical and Teaching Database molecular biological information Tea Varietal Research/ Developed Completed No Germplasm information, Teaching Database Tissue culture and Molecular biology Rice Varietal Research/ Developed Under No Germplasm information, Teaching Progress 21 Breeding Weed Morphological, Research/ Developed Under No Database biochemical and Teaching Progress molecular biological information ii. Journals and other information sources

Name of Broad Subject Network Online/Pri Remarks Journal/ area Availability nt based Online service Blackwell- Plant Science Yes Online ≈40 journals are Synergy available. Acquired from DBT resources Springer-Link Agricultural Yes Online ≈180 journals are Sciences available. Acquired through university resources (ICAR) Science Plant Science Yes Online ≈160 journals are Direct available. Acquired through university resources (ICAR) Print Related to No Print 8 journals from Journals Biotechnology, NISCAIR and few other Bioinformatics & journals are subscribed Computer Science by the center.

6. Details about staff members working in the centre (Name of the staff, Designation, Specialization and period of working)

Sl. Designation Num- Educational Area of Status of Anticipated No. ber qualification specialization manpower future absorption requirement 1. Salvinder 1 M.Sc. (Agri) Agricultural Filled - Singh Biotechnology Information Officer 2. Technical 1 B.Sc. Biology Vacant 1 Asstt. 3. Data Entry 1 Graduate English Vacant 1 Operator 4. Research 1 Graduate & B.Sc. and Filled - Associate Diploma in Diploma in Computer Computer Sc. Sc.

22 7. Types of services provided :

Analysis of Research Data; Retrieval of bibliographic information, both online and offline; Training in the field of Bioinforamtics etc.

8. Educational activities with details of placement : Our Centre has not introduced one year Advanced Post Diploma or M.Tech courses. Alternatively, a two-hour credit course on, “Application of Computers in Biotechnology” was introduced for the Post-graduate students of this University since 1990.The present course for the PG students shall be continued. A separate course on Bioinformatics, viz. “Introduction to Bioinformatics”, was introduced for the Post-Graduate students in 2004-05.

9. Initiative to validate the outcome of bioinformatics resources: No initiatives have been taken to validate outcome of bioinformatics resources

10. Collaborative works/ initiatives The centre has collaboration with the Department of Plant Breeding & Genetics, Biochemistry & Agricultural Chemistry, Horticulture, Tea Husbandry & Technology, Agronomy and Regional Agricultural Research Station, Titabar of Assam Agricultural University for the development of Databases. We have also initiated collaboration with the Bioinformatics Facility (BIF) established at College of Veterinary Sciences, Khanapara, Guwahati. The centre is also collaborating with the Agricultural Research Information System (ARIS) programme of this University, which is being supported by ICAR, Govt. of India, New Delhi. The Centre is also associated with the scientists of North Eastern Institute of Technology (Formerly Regional Research Laboratory), Jorhat; Tocklai Experimental Station, Jorhat; Rain Forest Research Institute, Jorhat and Central Muga & Eri Research Institute, Jorhat.

11. Databases/ Software packages developed : Same as mentioned above in section 5(c)

12. Papers published or presented in the conferences with reference: Nil

13. Initiation of R&D activities in Bioinformatics: The center is developing of an expert system for detection of Weed seeds in the field. The system will have a detailed database detailing the morphological attributes with photographs and DNA fingerprints. This system will help the seed certification agencies and quarantine agencies to identify contaminating weed seeds in seed lots of crop plants.

14. Details of Training/ Workshop organized and total no. of user trained

1993 : National workshop on “Bioinformatics”.* 1995 : National workshop on “Bioinformatics and its application in Life Sciences”.* 1996 : National workshop on “Computers in Scientific Communication”.* 1997 : National workshop on “Applications of Computers in Biological Sciences”.* 23 1999 : National workshop on “Application of Computers in Agriculture and Allied Sciences”. * 2000 : National workshop on “Application on Computers in Scientific Communications”. * 2001 : National workshop on “Bioinformatics in Agriculture”. * 2003 : National Workshop on “Use of Computers and Internet in Biological Sciences “* 2004 : National workshop on Use of Linux in Bioinformatics”.* 2005 : National Workshop on “Bioinformatics – Tools and Applications”.* 2006 : National Workshop on “Basics of Bioinformatics and its application in Biological Sciences * Number of Participants in each Workshop : 30 (Thirty). The deta

15. Future activities: 1. To provide services to the scientific community of NE India 2. Organize National Workshop on Bioinformatics for teachers, scientists and research scholars of this region. 3. To complete the databases under progress. 4. A new database with the parentages of modern rice varieties is proposed and work will be initiated in the near future. The database will allow the breeders to know the parentages of varieties quickly and help in planning breeding programmes. 5. The existing databases will be converted to web-accessible format so that these can be made available online.

16. Additional Details:

Name of the Coordinator: Dr. Mahendra K. Modi Postal Address: Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat-785013 Phone Number:0376-2340095 Fax No.: 0376-2340001 Email: [email protected] [email protected] Website: http://www.aau.ac.in, http://www.aau.ac.in/btis

Name of Contact Person(s): 1. Dr. M.K. Modi, Coordinator, Bioinformatics Sub-Centre, Department of Agricultural Biotechnology, AAU, Jorhat-785013, Email: [email protected], [email protected]

24 Banaras Hindu University, Varanasi Coordinator : Prof. Ashok Kumar

1. Summary of the progress made by the Centre from its inception: The Bioinformatics Centre was setup in 1989 at the School of Biotechnology, Faculty of Science, Banaras Hindu University, Varanasi, as one of the Distributed Information Sub-Centres (Sub-DICs) under the Biotechnology Information System (BTIS). The main function of the Centre is to act as a member of Bioinformatics Network System for providing information to the interested users in the area of Bioinformatics and Biotechnology. A separate room attached to the School of Biotechnology was built in 1998 which had been housing all the facilities of the Bioinformatics Centre. Now the Centre has got additional two rooms (12ftX28ft and 9ftX15ft). The posts of Data Entry Operator (grade II) and Programmer (grade II) were filled up in 1995 and the employees appointed have been absorbed by University in 2005 and made permanent. The Internet facility through VSAT became operational during the year 1997. In addition Fiber optics connectivity has also been provided by the University and is functioning for providing online literature search. The Centre has been providing internet, data search and other facilities to all the users of the university and neighboring institutes. The facilities of the centre are utilized for teaching of M.Sc. Biotechnology courses in general and one course namely Computer Applications, Bioinformatics and Biostatistics is taught and covered by the staff of the centre. The centre has become an independent unit under Faculty of Science since August 1998. The posts of Information officer and Data Entry Operator are yet to be filled. For the last several years, the centre has been organizing various training courses regularly for the manpower development in the area of Bioinformatics and Biotechnology. The Centre has acquired a number of software and databases for the use of researchers.

2. Major research activities in Biotechnology and its related fields at your institution: The faculty members of the School are focusing their efforts in the following areas:

A. Development of Regional Biofertilizer Strain Collection and Research Centre: Our School has developed the facilities and competence in the molecular and applied aspects of Biofertilizer technology. On molecular side, the genes responsible for nitrogen fixation, dicarboxylate transport, osmoregulation in the plant growth promoting bacterium, Azospirillum were cloned and characterized. On applied side, the technology for large scale production and field application of cyanobacterial biofertilizer were developed and demonstrated to farmers. We have collected a number of bacterial isolates which could be used for biofertilizer purposes.

B. Environmental Microbiology and Enzyme Technology: The School has demonstrated its ability to address some of the environmental problems via bioremediation. Several bacterial strains have been isolated and characterized for their ability to degrade sodium dodecyl sulphate, acrylamide, tannins and recalcitrant carbon compounds present in distillary and explosive factory effluent. Some of the isolates seem to be potential for

25 bioremediation studies. With the success in application of PCR fingerprinting techniques on clinically important bacteria such as Salmonella typhi and Helicobacter pylori, the School plans to develop programme for surveillance and forecasting of bacterial and viral (infectious/epidemic) isolates causing diseases. The School has also developed competence in enzyme technology and is capable of producing industrially and clinically important enzymes such as urease, β-galactosidase and α-amylase.

C. Development of insect resistant chickpea and pigeonpea: Attempts have been made to develop a regeneration protocol amenable to genetic transformation for insect resistant chickpea and pigeonpea. Decapitated embryo axis has been used to develop a genotype-independent high frequency and highly reproducible shoot regeneration protocol. These regeneration systems were used for genetic transformation mediated by Agrobacterium tumefaciens.

D. Cellular & Molecular immunology, and Tumour immunology: The School has excellent expertise in the area of animal cell culture and immunology. The main focus of research in these disciplines has been the study of the mechanisms of anti-cancer defense operating in the body and the study of the tumor growth dependent immuno-suppression with an aim to generate effective immuno-therapeutic strategies for locating cancer.

3. Area of Specialization of the Centre: Bioinformatics & Agriculture.

4. Major activities of the centre during 2007-2008: The major activities of the Centre during the year 2006-2007 are; a. 512 kbps leased line connection has been installed in the Centre for providing the better connectivity of internet. b. The University has also provided a Optical Fiber connectivity to the centre for access of free online important Journals related to biotechnology and bioinformatics. c. Networking (Local Area Network) of Internet facility to all the teachers and their research laboratory has been completed. d. Imparted regular theory and practical classes to the M.Sc. Biotechnology students on “Computer Applications, Bioinformatics and Biost” course. e. Provided literature searches online and through CD (Medline Abstract and Biotechnology Abstract) to Teaching staff and Research Scholars.

5. Infrastructure facilities in the Bioinformatics Centre: A. Computer and Communication facility: Sl. NO. Particulars Quantity 1. 512 kbps Leased Line connection 1 No. 2. HP Proliant ML 350 Server 1 No. 3. Optical Fiber Internet Connection (University) 1.No. 4. Xeon based 2.4 GHz Server with color monitor 1 No. 5. Lap top Computer System 1 No. 6. Pentium IV Computer System with color monitor 13 Nos. 7. Pentium III Computer System with color monitor 2 No. 26 8. HP Laser Jet Color Printer 1 No. 9. HP Laser Jet Printer 3 Nos. 10. Dot matrix Printer 3 No. 11. Hp Laserjet (all in one) 1 No. 12. Fax (Samsung SF 4500) 1 No. 13. Telephone /Fax (STD/ISD) 1 No. 14. UPS 10KVA, 5KVA 2 No.

B. Scientific Software packages: The Centre has acquired software packages viz., Windows-95, Windows-98,MS Windows NT4, Windows –XP, MS Office 2000 Professional, MS Office 2007, Norton Anti Virus 2007, MS Visual Studio 2005, Sigma Plot 10, Sigma State 3.5, SPSS, WIN/ISIS, “Exome” Version 1.3, Accelrys Gene 2.5 for various types of analysis related to bioinformatics

C. Databases and other information resources: Sl. No. Name of Data base Acquired/Developed 1. Medline Abstracts Acquired 2. Biotechnology Abstracts Acquired

6. Details about staff members working in the centre (Name of the staff, Designation, Specialization, and period of working. Please indicate their absorption status): Name of the staff Designation Specialization Period of working Mr.Dinesh Data Entry Data Entry March- 1995 to till date* Chaudhary Operator Mrs. Savita Rani Programmer Programming June – 1995 to till date* * The post of Data Entry Operator Gr.II and Programmer Gr.II has been absorbed by the University in June 2005.

7. Types of services provided: The following types of services are provided by the centre: a. E-Mail and Internet Services: Provided to all the Teaching staff, Research Scholars and other scientific staffs for their R& D works. b. Databases Services: The Bioinformatics Centre provides database accessibility online and through CD (Medline Abstracts and Biotechnology Abstracts) to all the interested users. c. Communication Services: The Centre provides the communication facilities like Internet, Fax and Phone etc. to all the staff, students and other members belonging to Faculty of Science/other faculties of the university. d. Other services: Xerox facility.

8. Educational activities with details of placement: Ongoing teaching programmes: A course on Computer Applications, Bioinformatics and Biostatistics for M.Sc. Biotechnology students.

9. Initiative to validate the outcome of Bioinformatics resources: Attempts are being made to have Industry- University collaboration. 27

10. Collaborative works/initiative: Mahila Mahavidlaya, BHU, has started two years course in Bioinformatics where our centre is getting involved in organization of the course. Furthermore Faculty of Science, BHU, is also going to start PG and Diploma course in Bioinformatics involving our centre. The centre has established collaborations with other institutions such as IIVR, Varanasi and IIT, Roorkee.

11. Databases/software packages developed: Sl. No. Name of Data base Acquired/Developed 1 Cytokine Developed 2. Plant Growth Promoting Rhizobacteria Developed

12. Papers published or presented in conferences with reference: „ Jha, P.N. and Kumar, A. (2007). Endophytic colonization of Typha australis by a plant growth – promoting bacterium klebsiella oxytoca Strain GR -3. Journal of Applied Microbiology (Published on-line June 2007). „ Nagarajan, T., Vanderleyden, J. and Tripathi, A.K. (2007). Identification of salt stress induscible genes that control cell envelope related functions in Azosplreillum brasilense SP 7. Molecular Genetics and Genomics 278: 43-51. „ Tripathi, P., Leggio, L.L., Mansfeld, J., Ulbrich-Hofmann, R., and Kayastha, A.M. (2007). α-amylase from mung beans (Vigna radiata)- Correlation of biochemical properties and tertiary structure by homology modelling. Phytochemistry 68:1623-1631. „ Sebnem Unlu, Kumar Arvind, Wayne R. Waterman, Junichi Tsukada, Kent Z. Q. Wang, Deborah L Galson, Philip E. Auron (2007). Phosphorylation of IRF8 in a pre – associated complex with Spi-1/ PU. 1 and non- phosphorylated Stat 1 is critical for LPS induction of the ILI1B gene. Molecular Immunology 44: 3364-3379. „ Alahari, A., Tripathi, A.K. and Le Rudulier, D. (2006) Cloning and characterization of a fur homolog from Azospirillum brasilense Sp7. Current Microbiology 52:123-127. „ Tripathi, A. K., Verma, S.C., Paul Chowdhury, S., Lebuhn, M., Gattinger, A. and Schloter, M. (2006) Ochrobacterum oryzae sp. nov, a novel endophytic bacterial species isolated from deep-water rice in India. International Journal of Systematic and Evolutionary Microbiology 56:1677-1680. „ Paul Chowdhury, S., Schmid, S., Hartmann, A. and Tripathi, A.K. (2006) Identification of diazotrophs in the culturable bacterial community associated with roots of Lasiurus sindicus, a perennial grass of Thar Desert, India. Microbial Ecology 54: 82-90.

13. Initiation of R&D activities in Bioinformatics: The School has acquired an Automated DNA Sequencer, which has been linked to the internet facility of the Bioinformatics centre. This has facilitated and speed up direct analysis of the nucleotide sequence data for comparison with databases such as GenBank, swissprot etc. Recently, researches have been initiated on comparative and functional genomics of plant growth promoting bacteria (Azospirillum and Rhizobium). 28 Genome of Azospirillum brasilense is being analyzed by random mutagenesis and transposon flanking regions have been sequenced to identify the genes and their promoters. Identification of genes by database searches gives an idea about the function/phenotype of the mutated genes.

14. Details of Training workshop organized and total no. of users trained: A I. Organized a Short Training Course on L TEX for Ph.D. students and M.Tech. students from Feb. 17, to March 5, 2005. Total No. of participants: 34. II. Organized a short training course on “Computer Application on Office Automation” from 4-9th July, 2005 for technical and administrative staff of Mahila Mahavidlaya of the University. Total No. of participants: 16. A III. Organized a Short Training Course on L TEX for Ph.D. students and M.Tech. students from September 26 to October 1, 2005. Total No. of participants: 18. A IV. Organized a Short Training Course on L TEX for Ph.D. students and M.Tech. students from February 6 to Feabruary 11, 2007. Total No. of participants: 16.

15. Impact shown by your centre on the growth of biotechnology and allied areas. The centre has provided excellent facilities in literature survey, getting accession number and online submission of research papers. Sequence homology search, primer designing etc. are routinely done with the facilities available in the Centre. More than 20 research papers have been published in Journals of repute with the tools available in the Centre. A number of teachers and research scholars both from this university and other neighboring institutions have been trained in the training programs organized by the Centre for collecting and generating data bases

16. Future activities: The Centre proposes to organize at least four short training and one workshop annually for the benefits of researchers involved in biotechnological research. It is planed to develop teaching package in biology with particular reference to the courses of M.Sc. Biotechnology. Attempts are also being made to start two years M.Sc. teaching course in Bioinformatics under the Faculty of Science, utilizing the facilities available at the Centre. The Centre also plans to develop more databases in Agricultural Biotechnology and other.

Additional Details:

Name of the Coordinator:Prof. Ashok Kumar Postal Address: School of Biotechnology, Faculty of Science Banaras Hindu University, Varanasi 221 005 Phone Number: 0542-2368364 Fax No.0542- 2368693/2368174 Email: [email protected] Website: http://bioinformaticsbhu.tripod.com Name of Contact Person(s): Prof. Ashok Kumar 29 Email: [email protected]

30 Banasthali Vidyapith, banasthali Coordinator : Dr. Vinay Sharma

1. Summary of the progress made by the centre from its inception The Centre for Bioinformatics at Banasthali University is being extensively used by PG students in Biotechnology & Bioscience, Ph.D. students, faculty of the Department of Bioscience & Biotechnology. In addition, the research students, teachers/scientists of many other departments, especially Home Science, Chemistry, Krishi Vigyan Kendra etc. The services of the Centre for Bioinformatics include analysis of biological data, bibliographic references to published literature in science and technology (including databases and patents). Some of the important databases and softwares of biological importance are acquired as well as developed for the users. Training programmes are also organized to train manpower. 2. Major research activities in Biotechnology and its related fields at your institution The Ph.D. students carry out research in various disciplines of Biotechnology, Bioscience and Bioinformatics. There are sponsored research projects with teaching faculty of the department. Some of the Agricultural Biotechnology related research topics are: Phytoalexins; Immobilization of enzymes; Fluoride toxicity; Reclamation of desert soils using plants; Tissue culture of arid zone species etc. Collaborative work with local/nearby institutions as Krishi Vigyan Kendra, Banasthali University, Durgapura (Jaipur) Agriculture Research Station and others is being carried out. A research collaboration of a few faculty members with laboratories in Germany and USA. Prof. Vinay Sharma has been a Visiting Professor at the Department of Molecular Biology and Microbiology, University of Florida, USA (January to May, 2006). Dr. Bhumi Nath Tripathi lecturer was awarded the prestigious DBT Young Scientist Overseas Associateship and visited the laboratory of Prof. Karl- Josef Dietz, University of Bielefeld, Germany (July to November, 2006) Dr. Bhumi Nath Tripathi Senior Lecturer is a Visiting Scientist at the Research institute of Bioresources, Okayama University, Japan (October 07-March 08).

3. Area of Specialization of the centre • Information Dissemination in Biotechnology • Bioinformatics Education & Human Resource Development • Environment and Diversity 4. Major activities of the centre during the year 2007-08 The Major activities of the Centre of Bioinformatics at Banasthali: • The total number of users utilizing the bioinformatics facilities has increased, currently, it is more than 500. • To cater the regional and national needs, the Centre has also developed databases on “Biotechnological Industries of Rajasthan”, SSR Database of Citrus sinensis, Database for Simple Sequence Repeats of Takifugu rubripus and Database of Diterpene Synthase Gene. The work on the other database, “Flora of Indian Desert” and “Plant Host-Pathogen Interaction” is in progress. • The Centre has a website link at (website of the institution).

31

5. Infrastructure facilities in the Bioinformatics Centre A. Computer & Communication facility Servers & PCs :HP Proliant DL 385 G2 Server 1 No.; HP NET E60 Server 1 No.; HP Proliant ML 150 Server 1 No.; Wipro super genius 6100 2 Nos. ; Vinitron Celeron @300A MHz 2 Nos.; HP Brio Celeron @300A MHz 2 Nos.; Zenith P-IV 1 No.; Ingram Micro VESTA PC 5 Nos.; IBM Thinkcentre P-IV 13 Nos.; IBM ThinkPad 2 Nos.; HP scanner 6300c 1 No. Printers :HP Laserjet (color) 2550 1 No; HP Laserjet (color) 2500 1 No; HP Laserjet 4200n 1 No; HP LaserJet 2100m 1 No; HP Deskjet 5160 1 No; HP Deskjet 3500c 1 No; HP LaserJet 1015 2 No; TVSE MSP345 1 No UPS : Vinitek 3 KVA UPS 1 No.; Vinitek 5 KVA UPS 1 No.; Vinitek 10 KVA UPS 1 No. Communication Facilities :Modem 56.6 KBPS 1 No.; Sony LCD Projector 1 No.; Desktop Photocopier Model K-1212 1 No.; External CD Writer 1 No.; Kodak 6330 Digital Camera 1 No.; Creative Web Camera 2 Nos.; Switch 8 port 2 Nos ; Switch 16 port 2 Nos.; Switch 24 port 1 No. B. Scientific Software packages Insight II (Homology); Genocluster ver 1.0; Chrome Circle Application; HPLC Software; TLC Manual; Crash Proof Instant Data Recovery Software C. Databases & other information resources Biotechnology Abstract; Medline; Indian Forester Information System; Agris; Agricola 6. Details about staff members working in the centre (Name of the staff, Designation, Specialization and period of working. Please indicate their absorption status) Sr. Name of the Designation Educational Period of Absorption No Staff Qualification/ Working Status Specialization 1) Ms. Saroj Information M.Sc. 1 Year ---- Yadav Officer Bioinformatics (Contract) 2) Mrs. Kiran Technical P.G.D.C.A. 11 Years ---- Shanti Assistant (Permanent) 3) Mr. S. R. Computer A.D.C.A., 7 Years ---- Choudhary Operator P.G.D.C.T.A. (Contract) I.T. 4) Mr. K. M. Computer ‘A’ Level 3 Years ---- Jangid Operator C++ (Contract) 5) Mr. Amit Data Entry ‘O’ Level, 3 Years ---- Goyal Operator MCSE, CCNA (Contract)

7. Types of services provided Please also see S.No. 4 • The services of the Centre for Bioinformatics include analysis of biological data, bibliographic references to published literature in Science and Technology (including databases and patents) and access to Internet. • Some of the currently available important databases in Biological sciences are: Medline Standard, Agris, Agricola, Chrome Circle Application, Biotechnology Abstracts and Indian Forester Information System. • To generate trained manpower in Bioinformatics, National Workshops with participation of University level teaching faculty/ Scientists are regularly organized by the Centre. 32 8. Educational activities with details of placement • Educational activities: To generate trained manpower in Bioinformatics, National Workshops with participation of University level teaching faculty / Scientists are regularly organized by the Centre. • Placement: -Not applicable- 9. Initiative to validate the outcome of bioinformatics resources The information on various hardware and the related equipments, software, databases; both acquired and developed that are available with this Bioinformatics Centre is available on the web site of this institution and these facilities are open to access by academic and para academic organizations. If the need be, the databases developed by the centre will be made available to the DBT for further suitable action. 10. Collaborative works/ initiatives ƒ Collaborative work with local/nearby institutions as Krishi Vigyan Kendra, Banasthali University, Central Sheep Wool Research Institute, Avikanagar, Durgapura (Jaipur) Agriculture Research Center and others is being carried out. ƒ As in S.No. 2 11. Databases/ Software packages developed S. Name of Database Broad Subject Broad Developed/ Completion No Area Functional Area Acquired Status 1. Biotechnological Bioinformatics Biotechnology Developed Completed Industries of /Biotechnology Rajasthan 2. SSR Database of Bioinformatics Bioinformatics Developed Completed Citrus sinensis 3. Database for Simple Bioinformatics Bioinformatics Developed Completed Sequence Repeats of Takifugu rubripus 4. Database of Bioinformatics Bioinformatics Developed Completed Diterpene Synthase Gene 5. Database of Flora of Bioinformatics/ Biodiversity Developed In Progress Indian Desert Plant Science 6. Database of Plant Bioinformatics/ Biodiversity Developed In Progress Host-Pathogen Plant Science Interaction

12. Papers published or presented in the conferences with reference Research Papers published in peer reviewed journals by using Bioinformatics Support Ten Important Research Publications in 2006 & 2007 1. Anamika, Saxena J. and Sharma V. (2007). J. Pure & Applied Microbiology 1: 269-280. 2. Joshi G.K. and Sharma V. (2007). Research Journal of Biotechnology, 2: 50 - 56. 3. Joshi, G. K., Kumar, S. and Sharma V. (2007). Brazilian J. Microbiology, 38: 773-779. 4. Tripathi, A., Sharma, N. and Sharma, V. (2007). Biochemical and Cellular Archives (accepted, In Press) 5. Joshi G.K., Kumar S., Tripathi B.N. and Sharma V. (2006). Current Microbiology (Springer) 52: 354-358.

33 6. Tripathi B.N., Mehta S.K., Anshu Amar and Gaur J.P. (2006). Chemosphere 62: 538-544. 7. Shanker A., Bhargava A., Bajpai R., Singh S., Srivastava S. and Sharma V. (2007). Sci. Horti. 113: 353-361. 8. Shanker A., Singh A. and Sharma V. (2007). Microbiological Research 162: 250-256. 9. Grover A. and Sharma P.C. (2007). In Silico Biol. 7: 0021. 10. Grover A., Aishwarya V., and Sharma P.C. (2007). Mol Gen Genomics 277:469-480. Book Published: ƒ Tripathi B. N., Shekhawat G. S. and Sharma V. (2007). Applications in Biotechnology. Avishkar Publisher, Jaipur. ƒ Sharma V., Munjal A. and Shanker A. (2007). Textbook of Bioinformatics. Rastogi Publications, Meerut (in press).

13. Initiation of R&D activities in Bioinformatics • Bioinformatics related problems are regularly given to M.Sc. Biotechnology and M.Sc. Bioinformatics students for their project work. • The facilities of the Centre are regularly used for various R & D activities in Biotechnology carried in the Dept. of Bioscience & Biotechnology at this University. 14. Details of Training/ Workshop organized and total no. of user trained Workshops are regularly organized by the Centre to generate trained manpower in Bioinformatics. A three days workshop on “Biological Databases and Data Mining” was organized by the Centre for Bioinformatics, Dept. of Bioscience & Biotechnology from 22nd Dec. to 24th Dec., 2007 with 66 participants. 15. Impact shown by your centre on the growth of biotechnology and allied areas. • Number of publications is very high in Biotechnology and Bioinformatics as seen in column 12 (Appendix ‘A”). • Intensive use of the Centre by PG, PhD. Students and faculty. • Workshops are regularly organized by the Centre to generate trained manpower in Bioinformatics. Several databases have been developed/are being developed by the centre. • More than 200 teachers/scientists from Colleges, Universities and scientific institutions have been trained.

16. Future activities • To cater to the regional and national needs, the work on the developing specific databases being currently developed by the Center will continue. • The R & D activities will be strengthened in Bioinformatics. • The PG courses in Bioinformatics will be focalized towards offering specializations in future.

Additional Details:

34 Name of the Coordinator: Dr. Vinay Sharma Postal Address: Dr. Vinay Sharma Prof. & Head Department of Bioscience & Biotechnology Banasthali University P.O. Banasthali Vidyapith – 304 022 (Rajasthan) Phone Number: 01438-228302 (O) 01438-228533 (R) Email: [email protected] [email protected] Website: www.banasthali.org Name of Contact Person(s): Dr. Vinay Sharma Email: [email protected] [email protected].

35 Barkatullah University, Bhopal Coordinator: Dr. Anil Prakash

1. Summary of the progress made by the centre from its inception: 10 days Training was organized IN THE Department of Biotechnology and Bioinformatics Center during 9th Jan to 18th Jan 2008, which was sponsored by the Madhya Pradesh Council of Science and Technology. 21 participants were enrolled for this hand on training program. Total 4152 genes of Bacillus licheniformis are analyzed. 4 students will join the Center for dissertation to work further on the other species of Bacilli. Center has written one article title as “Bioinformatics and Personalized medicine” for the Industrial & Academic meet going to be held at BMHRC, Bhopal and one poster will be presented on the work done on Bacillus licheniformis. Fish diversity database is in progress and initiative has been taken to develop the database of Medicinal plant diversity database of Madhya Pradesh. 2. Major research activities in Biotechnology and its related fields at your institution i. Selection of Bio-inoculants for the growth promotion of J. curcus (MNES projects) ii. Inventorisation of Medicinal and Aromatic plant resources of selected areas of Madhya Pradesh iii. Secondary metabolites of Fluorescent Pseudomonads and other Rhizobacteria (Indo- German project) iv. Rhizobacterial inoculants for low input Wheet based cropping system. (Indo- Swiss Project) v. PGPR operative ISR in Soyabean (Glycine max)

3. Area of Specialization of the centre i. Sequence analysis and Annotations of Fungi and Bacterial Genome ii. Database creation: Fish biodiversity of Madhya Pradesh iii. Medicinal Plant diversity database of Madhya Pradesh 4. Major activities of the centre during the year 2006-07 i. Total 10 research publications and 3 oral presentations, during the 2007- 08 in the field of Biotechnology ii. One Article and one poster presentation in Bioinformatics iii. Three Bacilli species are analyzed for codon usage preferences. iv. Organized 10 days Hands on Training in Bioinformatics, title as “Bioinformatics Tool and data analysis” during 9 - 18 Jan 2008. 5. Infrastructure facilities in the Bioinformatics Centre Computer & Communication facility 2 Servers (DNA- Windows Server 2003 & RNA – Linux Fedora Core 4) of Intel Xeon Processor 400 GB, 4 GB SDRAM 1 Server (Cell – Fedora Core 4): Intel P-III, 40 GB, 512 RAM by Wipro Infotech Pvt. Ltd. 26 Clients Desktop: - 8 from Bioinformatics grant: Compaq – P IV, 40 GB and 256 DDRAM and 18 from Biotechnology grant: Wipro, P-IV, 20 GB, 128 RAM 36 2 Client Workstation for Hyperchem and ExomED of 40 GB HDD, 512 MB DDRAM Printer: 5 in No. (HP Laser Color 1, Laser HP 1200 series – 2, Dot-matrix Wipro– 2) Scanner: 3 No. External CD Writer: 1, Laptop: IBM ThinkPad (P IV, 20 GB), OHP (Over Head Projector): 1, LCD projector (In progress): 1 Networking Equipments Internet Facility: Router Cisco 1751 series with Interface cards, Switches: 1 manageable 24 port, 2 non-manageable- 16 port, Modem: 4 external (3 – 56 kbps Dialup, 1 – 128 kbps ISDN), 8 internal (56 kbps Dial up),. Internet Connection: a. 512 KBPS Leased Line Internet connection b. 64 kbps ISDN line separate for Web site updatation Uninterrupted Power Supply: UPS: 5 in no. (1 KVA – 2, 3 KVA – 1, 5 KVA – 2), Scientific Software packages Licensed Bioinformatics Software: Hyperchem Release 7.5 (1 user) and ExomED research (1 user) Free Software OS and Packages: Linux Fedora Core 4, MySQL Windows and Linux based Licensed Software OS and Packages: Windows server Standard 2003 (2 User) with CAL, Visual studio .NET (1 User), MS-Office 2003 (12 User), Adobe Creative Suite Premium (1 user), Macromedia Dreamweaver MX 2004 Education (1 user), SQL Server 2000(1 server & 5 client) Databases & other information resources Developed Database: 1. FISH Biodiversity database of Madhya Pradesh developed in collaboration with Limnology department of Barkatullah University 2. Library Book Database using E-Grantahalay Acquired Database: PDB Protein Structure database and EMBL Nucleotide Sequence database in CD form 6. Details about staff members working in the centre (Name of the staff, Designation, Specialization and period of working. Please indicate their absorption status) Name Designation Specialization Period of Absorption Working Status Mr. Kishor K. Information Bioinformatics & 4 years Not Shende Officer Biotechnology Absorbed Mr. Durgesh Technical Bioinformatics & Botany 2 years Not Assistant Absorbed Mrs. Archana Computer Windows OS and DBMS 2 years 6 Not Nema Professional (MS Access, SQL server months Absorbed 2000 and MySQL), Mr. Chandan Data Entry Data entry and Official 4 years & Not Bisht Operator Work 1 month Absorbed

7. Types of services provided • Phylogenetic analysis using Bioinformatics Tools as PHYLIP 37 • Training in Bioinformatics to students, research scholars and staff related with various field of bioinformatics like Sequence analysis, Structural analysis, molecular modeling, Database creation and front end designing and software development. • Providing the Internet and Library facility to the students, research scholars and staff of Life science department of Barkatullah University • Organizing a workshop in Bioinformatics • Solving the Hardware & Software related problems of the staff and research scholars of Life Science departments Barkatullah University

8. Educational activities with details of placement M.Sc. in Biotechnology: 2 year master degree course in Biotechnology divided in 4 semesters Ph.D. in Biotechnology Placements: Last year students are placed Government and Private Organizations Government Organization: Students are working as Lecturer, Research associates, project assistant or research fellow some of the following institutes 1. High Secure Animal Disease Laboratory, Bhopal 2. Jawaharlal Nehru University, New Delhi 3. Central Drug Research Institute, Lucknow 4. The Energy Resource Institute, New Delhi 5. Carrier college, Bhopal Most of the Students are doing their 6 months project from Government organizations 1. National Institute of Immunology 2. Institute of Genomics and Integrative Biology, New delhi 3. National Environmental Engineering and Research Institute, Nagpur 4. IIT, New Delhi 9. Initiative to validate the outcome of bioinformatics resources: Nil 10. Collaborative works/ initiatives Biotechnology: 1. Project through Indo-Swiss Collaboration in Biotechnology 2. Collaborative work CIMAP, Lucknow for the project on Medicinal Plants of Madhya Pradesh Bioinformatics: 1. Organizing the training in Bioinformatics in collaboration with the MPCST. 2. Department of Limnology, Barkatullah University, Bhopal for FISH Biodiversity database of Madhya Pradesh 11. Databases/ Software packages developed Database: i. FISH Biodiversity database of Madhya Pradesh ii. Medicinal Plant Databases 12. Papers published or presented in the conferences with reference Biotechnology:

38 1). D. K. Chaudhary and B. N. Johri, Anil Prakash; 2008; Volatiles as priming agents that induce plant growth and defense response; Current Science (Accepted) 2). D. K. Chaudhary, Anil Prakash and B. N. Johri; 2007; Induced systemic resistance (ISR) in plants: Mechanism of action”; Indian Journal of Microbiology, Vol 47, 289-297 3). B. N. Johri, D. K. Chaudhuri and S. Chaudhuri; 2007, Dr. U. Ashwathanarayana (Ed); How to use soil microorganisms to optimize soil productivity; Chapter in Book: Food and Water Security, page 51-62; Publication: Taylor & Francis, Netherland 4). Alok Sharma, A. Pathak, M. Sahgal, J. M. Meyer, V. Wrey and B. N. Johri; 2007; Molecular characterization of plant growth promoting rhizobacteria that enhance peroxidase and pheny-alanine ammonia lyase activity in chilly (Capsicum annum L.) and tomato ( Lycopersicon esculantum L.); Archive Microbiology Vol 188 : 887-894 5). Sharma, V. Wrey, and B. N. Johri; 2007; Rhizosphere Pseudomonas sp. Strain reduce occurrence of pre- and post emergence damping off in chilly and tomato in Central Himalayan Region; Archive Microbiology, Vol 187 : 321-335 6). P. K. Sharma, M. Kukreja, K. K. Sahu and Ragini Gothalwal; Texo-ethano- botanical value of some plants from Chattisgarh; Advances in Biological Sciences, Volume: 6 (102), page 37-38 7). Chakroborty, S. S. Nadi and Ragini Gothalwal; 2007; Periplasmic high level expression and single step purification of fusion MBP- Human ranulocyte colony stimulating factor protein in E. coli; Applied Microbiology and Biotechnology (on line version no ID AMB-07-14996.RI) 8). Sweta Sao, Ragini Gothalwal, L. K. Thetwar and N. D. Deshmukh; 2007; Effect of flyash and plant harmones treated soil on the increased protein and amino acid content in the seed of ground nut.; Asian Journal of Chemistry, Vol 19: 1017-1022 9). P. K. Sharma and Ragini Gothalwal; 2007; Supplimentation: Enhances the growth and biological efficiency of Pleurotus sajor-caju grown in different Lignocellulosic wastes; Advances in Biological Sciences, Vol 6: 19-23 10). P. K. Sharma and Ragini Gothalwal; 2007; Comparative study of grains on spawn development of two Pleurotus sp. Journal of Basic and Applied Mycology

Oral Presentation in Bhartiya Vigyan Sammelam 2007 held in Bhopal on 23- 25 Nov, 07 1. Atul V.Singh, Pavan K. Agarwal, Anil Prakash and B. N. Johri; 2007; Influence of Rhizobacteria and Arbuscular Mycorrhizal Fungi (AMF) on the soil and crop in Wheat- Legume Cropping System. 2. Rubina Begum and Anil Prakash; 2007; Diversity of endophytic fungi in Stevia rebaudiana Bartoni leaves 3. Puja Uppal and Anil Prakash; 2007; Effect of Bioinoculants on growth promotion of Jatropa caucas

Bioinformatics 1. Kishor Shende and Anil Prakash; Article, “Bioinformatics and Personalized Medicine” presentation in MEDBIO-2008 & 3rd Industry-Academia Meet, organized by BMHRC, Bhopal during 14th – 16th Feb 2008

39 2. Kishor Shende, Leena Agrawal, Priyanka Johri, Durgesh Gupta, Ragini Gothalwal and Anil Prakash; Poster presentation “Compositional bias in codon usage preferences among the 4152 genes of Bacillus licheniformis ATCC 14580” in National Symposium organized by School of Biotechnology, GGU, Bilaspur (Date 28-29 Jan 2008).

13. Initiation of R&D activities in Bioinformatics 1. Genome analysis of Bacterial Genome is in progress 2. Creation of Databases using the data made available by various Life Science departments

14. Details of Training/ Workshop organized and total no. of user trained Workshop Title of the Workshop Date No. Participants Workshop “Bioinformatics tools and 9 – 18 Jan 20 1 data analysis” 2008 Workshop “Structural Bioinformatics” 12-14 Feb 20 2 2008 Workshop “Proteomics and Drug 10-12 Mar 20 3 designing” 2008

15. Impact shown by your centre on the growth of biotechnology and allied areas. In this you may highlight the details like number of paper published/ number of papers published with the help of your centre, how your centre is promoting various activities of your organization and neighboring institutions, manpower trained, tools developed, patents & copyrights acquired and other services offered etc. 1. The Ph.D. students of Barkatullah University are using the Bioinformatics Center Library and the Internet connection and help for reference searching. Students are also using the Bioinformatics Center to learn the applications of Bioinformatics tools in basic research work in Life science and finding the study materials: 50 users per day 2. Bioinformatics awareness spread through the Departmental website and by organizing workshop and Training in Bioinformatics 16. Future activities 1. Web Sever development and Web site hosting at Departmental server. 2. Organizing the 15 days Training on Phylogenetic analysis using the various techniques in Wet Lab and Dry lab. 3. Two workshops will be organized in Bioinformatics 4. Development of FISH Biodiversity Database of Madhya Pradesh and making available online. 5. Task oriented six month training in Bioinformatics for students from other institute 6. Further analysis of Bacilli gene for the codon usage frequency and its role in gene regulations

Additional Details: 40 Name of the Coordinator: Dr. Anil Prakash Postal Address: Department of Biotechnology & Bioinformatics Center, Barkatullah University, Bhopal Phone Number: 755-2677748-102 Mobile: Email: [email protected] Website: http://bioinfobubpl.nic.in Name of Contact Person(s): Dr. Anil Prakash Email: [email protected]

41 Bharathidasan University, Tiruchirappalli Coordinator : Dr. L. Uma

1. Summary of the progress made by the centre from its inception : The Centre was launched in April 2001 as a special purpose centre meant for cyanobacteriology. The centre is equipped with Servers, an SGI Fuel Workstation, Desktops, LCD Projector, scanner, printers and photocopier with a small library. The centre has a round-the-clock 512 kbps leased line internet connectivity. A dozen ASM online journals, and the magazine PCQuest have been subscribed. Training workshops (Workshop On Bioinformatics for Cyanobacteriologists - WOBIC) on the basics of bioinformatics are being conducted every year during the month of February / March. A database on cyanobacteriology has been developed. News letter on cyanobacteriology with information about scientific meetings, research positions available is posted in the National Facility for Marine Cyanobacteria (NFMC) and University websites and the activities of the NFMC, is maintained online. The literature collection of more than three thousand reprints on cyanobacteriology available in NFMC has been digitized. The Centre assists the Facility and the Department of National Facility for Marine Cyanobacteria (DBT, Sponsored Facility) to all faculty and scholars by providing infrastructural facilities like internet, email, printing and also conducts bioinformatics theory and lab courses for M.Sc. programme. The Bioinformatics Centre at this institute, supported by DBT, has created awareness in cyanobacteria, the primordial organism. The Centre focuses on database generation, data mining and its application in wet lab research. 2. Major research activities in Biotechnology and its related fields at your institution Our Bioinformatics Centre research activities aids as a platform for our wet lab analysis. Our study is focused on superoxide dismutase, cytochrome P450 & CN splitting enzyme, toxin genes and sequencing of plasmid from Indian isolates. Our Centre is assisting the NFMC in the biotechnological exploitation of marine cyanobacteria through genome wide hunt for its biotechnological potential in the areas of food, feed, fertilizer, fuel, fine chemicals, colorant, pharmaceuticals and waste treatment. 3. Area of specialization of the centre Cyanobacteriology 4. Major activities of the centre during the year 2007-2008 The leased line internet facility has been upgraded to 512 kbps, and a pair of 2 mbps capable modems has been added to the centre. As part of human resource development, Workshop On Bioinformatics for Cyanobacteriologists and Workshop on Research Techniques in Cyanobacteria (WOBIC is conducted every year and this year between March 3rd to 7th 2008). The participants are made familiar with wet and dry hands on experiments. Bioinformatics exercise includes database search, analysis at nucleic acid and protein level and phylogeny analysis. Research in Cyanobacterial bioinformatics: 42 ¶ The Bioinformatics centre has paved way for multidisciplinary approach resulting in one of the esteemed chemistry journals “Journal of Chemical Society” along with Dept. of Chemistry, Bharathidasan University. ¶ DATA MINING At present our research areas include ƒ Superoxide dismutases - the first line of defense antioxidant against oxidative damage. ƒ Cytochrome P450 – known to play a role in xenobiotic degradation ƒ CN splitting enzymes – nitrilase, rhodanase and cyanate lyase involved in nitrile and cyanide degradation. ƒ PCD genes – unique with much similarity to eukaryotic caspases. ƒ Toxin gene as marker for cyanobacterial identification ƒ Comparison of plasmid genes ƒ Initiation of RNAi work. ¶ GENOMICS Cyanobacteria exhibit tremendous biotechnological potentials but one of the major hurdles in exploiting them for industrial application is the non- availability of multi-host expression systems. Vectors developed with Escherichia coli or other bacterial replicons are not functional in the cyanobacteria. As a preliminary step, the Centre has partially sequenced a marine cyanobacterial plasmid pbdu02 from Phormidium sp. of from our germplasm is submitted in NCBI (Genome Accession No: AAZV00000000). The genes identified are: hypothetical protein, P-loop linked to ATPase acetyltransferase, Aldo/keto reductase, hypothetical protein, NifZ, Pseudouridine synthase, Peptide deformylase, Pyrimidine regulatory protein, ATP-dependent Clp protease adaptor protein, 2-tRNA, and 1-rRNA. This sequence analysis of cyanobacterial plasmid has given an insight into their functional organization, and facilitates its possible use as cloning vectors. Our online database, Blue Green Database (BGBASE) is being updated constantly and is being accessed by cyanobacteriologists around the world. This searchable database contains information regarding literature, germplasm and scientists working on cyanobacteriology. An online newsletter, BGNEWS serves as a portal for cyanobacteriologists in providing information regarding the updates of our site, scientific meetings, conferences, workshops etc., conducted on cyanobacteriology, and research positions available in cyanobacteriology. The Centre is helping Marine Biotechnology students in conducting courses in Bioinformatics paper at the Post Graduate level. The students and scholars are given the facilities like email, internet on all 365 days. Online journals subscribed - 12 (American Society for Microbiology) Reprints on cyanobacteria - 3100 Website usage - @ 800 day-1 5. Infrastructure facilities in the Bioinformatics Centre A. Computer & Communication facility Alpha Servers - 2 Xeon Server - 1 SGI FUEL Workstation - 1 Pentium IV Computers - 16 43 Scanner - 1 Printers - 5 (4 + 1 Large format printer) 7.5 KVA UPS - 1 LCD Projector - 1 Photocopier - 1 Router - 1 Leased Line Modems - One Pair Further, 512 kbps Leased-line internet connection is available round the clock. B. Scientific software packages 1) CHROMOSOB : For identification of secondary metabolities C. Databases & other information resources Blue Green Database - BGBASE, a database on Cyanobacteriology has been developed at the centre and is available online at www.nfmc.res.in. The database is constantly being updated. A library with about 250 books on bioinformatics and computer science is available for the researchers. Twelve online journals of the American Society for Microbiology, and the magazine PC-Quest are also available in the library. 6. Details about staff members working in the centre Name and Specialization Period of Whether Designation working Absorbed Mr. K. Ganesan Cyanobacteriology Till June No Information Officer and Bioinformatics 2007 Mrs. R. Renganayagi Computer 3.3 yrs. No Technical Assistant Application Mr. B. Venkatesh Moorthy Computer Till June No Data Entry Operator Application 2007.

7. Types of services provided Internet access and Email facilities are provided round the clock to the needy. The facilities are also extended to other departments and colleges whenever required. Copies of the reprints available at the centre are made available to these researchers.

8. Educational activities & details of placement Human Resource Development – Cyanobacterial Bioinformatics

9. Initiative to validate outcome of bioinformatics resources - Our center is focusing on Cyanobacterial Bioinformatics and shares its knowledge with faculties, researchers and students. 10. Collaborative works / initiatives Initiated research on genome wide hunt on cyanobacteriology. 11. Databases / software packages developed An internationally accessible online database Blue Green Database – BGBASE (www.nfmc.res.in/bgbase/) has been developed at the Centre. The database is searchable

44 and consists information on culture collections, cyanobacteriologists, literature / publications in the field of cyanobacteriology. 12. Papers published / presented in conferences with reference

1. Saha K., Das R., Bora K.N., UMA. L. (2007) Biodiversity epilithic Cyanobacteria from freshwater streams of Kakoijana reserve forest, Assam, India. Indian Journal of Microbiology. 47: 219-232 2. Rajendiran V., Palaniandavar M., Swaminathan P., UMA L.. (2007) Cleavage of proteins by a mixed ligand copper (II)-phenolate complex: Hydrophobocity od diimine co-liand promotes cleavage. Inorganic Chemistry (communication). 3. Subramanian G., UMA L., Priya B., Prabaharan D (2007) Utilization of microalgae to address pollution problems. Indian Hydrobiology 10(2): 1- 25 4. Balakrishnan Priya, Jagadeesan Premanandh, Raman T Dhanalakshmi, Thangaraj Seethalakshmi, Lakshmanan Uma, Dharmar Prabaharan, Gopalakrishnan Subramanian (2007) Comparative analysis of cyanobacterial superoxide dismutases to discriminate canonical forms. BMC Genomics 8: 435 13. Initiation of R&D activities in bioinformatics Completed - Short term bioinformatics projects on the topics 1) Caspases, metal Transportors

On going: Superoxide dismutases, Cytochrome P450, Microcystin 14. Details of Training/ Workshop organized and total no. of user trained The Workshop is conducted as a continuation of a wet lab workshop on cyanobacteriology conducted by NFMC, enabling researchers to get trained in both in vitro and in silico methods. 15. Impact shown by your centre on the growth of biotechnology and allied areas a) Number of paper published/ presented. Three – presented at National conferences. Two international publications. b) Promoting various activities of your organization and neighboring institutions Infrastructure and expertise provided to the University for conducting the Bioinformatics Theory and Practicals to Marine Biotechnology courses. c) Manpower trained 14 researchers through workshops and 14 students are trained in the 2007 - 08. d) Tools developed Online database on cyanobacteriology – available at www.nfmc.res.in A database booklet for workshop. e) Patents & copyrights acquired - Nil f) Other services offered - Nil 16. Future activities Completion of whole plasmid sequencing ADDITIONAL DETAILS :

45 Coordinator : Dr. L. UMA Bioinformatics Centre, NFMC Bharathidasan University Tiruchirappalli – 620 024 Email: [email protected] Phone/Fax. : 0431 2407084 Website : www.nfmc.res.in

46 Biotech – Consortium India Limited, New Delhi Coordinator : Dr. Purnima Sharma

1. Summary of the progress made by the centre from its inception Since its inception in 1992, the Distributed Information Sub Centre (DISC) at Biotech Consortium India Limited (BCIL) has taken up various activities to facilitate commercialisation of biotechnology. It has brought out a number of publications and periodicals, databases and status reports and has organized several seminars/workshops, events, entrepreneurs’ meets etc. for promotion of commercial biotechnology. Current activities include compilation of databases and directories, preparation of industry specific status reports on different aspect of biotechnology and organizing national and international workshops, seminars, conferences and entrepreneurs’ meets to create awareness on issues relevant to commercialization of biotechnology.

The DISC also runs a Biotechnology Club. The biotech club membership is being offered on annual and life memberships basis to individuals, institutions and corporate bodies interested in biotechnology. Members receive BCIL’s publications and, participate in events organized by BCIL, either free of cost or at a discount.

2. Major research activities in biotechnology and its related fields in your institution: BCIL’s main objective is to provide linkages to facilitate commercialization of biotechnology. BCIL has been engaged in technology transfer, consultancy, fund syndication, information dissemination, and manpower training related to biotechnology. In these areas, it has assisted over 200 clients including scientists, technologists, research institutions, universities, first generation entrepreneurs, the corporate sector, government, banks and financial institutions.

3. Area of specialization of the centre: Technology assessment, valuation and transfer, preparation of commercial databases, biotechnology project specific updates, publication of journals and organization of national and international workshops, seminars, and training programmes.

4. Major activities of the centre during the year 2007-08 Focussing on commercial biotechnology, in the year under review, DISC continued to bring out publications and organize events primarily of relevance to industry. The major projects completed were:

I. Directory of Biotechnology industries and institutions in India-5th Edition The 5th edition of the Directory of Biotechnology Industries and Institutions in India covering profiles of more than 1000 industries and institutions has been compiled during the year. The directory is being received very well by industry, institutions and academia. The directory was circulated to all the bioinformatics centres (DICs and DISCs) on complementary basis. 47

II. Maintenance of following websites : The following websites containing value added information on R&D and commercialization of GMOs were developed during the previous year and are being continuously updated by DISC:

a) Indian Biosafety Clearing House (BCH) website (http://indbch.nic.in) as part of India’s commitment to the Cartagena Protocol on Biosafety b) Updation & Maintenance of DBT Biosafety websiteThe website (http://dbtbiosafety.nic.in) has a public domain for guidelines, acts and rules on GMOS as well as a confidential domain in providing online tracking of regulatory clearance of applications to RCGM and e-monitoring of 328 IBSCs on personalized web features. c) Web-based database on Indian GMO Research Information System (IGMORIS) (http://igmoris.nic.in) d) GEF- World Bank Website for MoEF (http://www.envfor.nic.in/divisions/csurv/biosafety/default.htm) e) BCIL website (parent organization) www.bcil.nic.in f) Website for National Certification Systems for Tissue Culture Raised Plants (NCS-TCP) was developed and maintained by DISC (http://dbtncstcp.nic.in/)

III. Conferences, workshops, seminar-cum-training programmes : DISC has played an important role by providing both manpower and information support to BCIL in organizing several national and international events. The events where DISC has assisted BCIL range from entrepreneurs development programmes in biotechnology, workshop on commercilisation of biotechnology, workshop on management of IPR in biotechnology, workshop on biosafety issues and investors meet on current topics of interest. Some of the important events organized during the year are highlighted as under:

a) Workshop on “Management of Intellectual Property Rights in Biotechnology”: DISC at BCIL under the sponsorship from the Department of Biotechnology (DBT) had organized 3 workshops on Management of IPR in Biotechnology at Chennai, Lucknow and Hyderabad. Around 350 participants from academia and research institutions attended these programmes.

b) Entrepreneurship Development Programme (EDP) in Biotechnology: Entrepreneurship Development Programmes (EDP) in Biotechnology sponsored by Department of Biotechnology (DBT), Ministry of Science and Technology, Government of India and the Office of the Development Commissioner, Ministry of Micro, Small and Medium Enterprises (MSME) were organized at Kolkata, Pune, Shimla, Indore, 48 Chennai and Agartala. The objective of these programmes was to train the prospective entrepreneurs on different aspects of business management in biotechnology and to encourage them to set up commercially viable biotech ventures in small and medium scale sector. Around 300 participants attended these events.

c) Workshop on Commercialisation of Biotechnology: As part of the DISC activity, a workshop on Commercialisation of Biotechnology was organized during the year with a focus on business opportunities, issues in biotechnology commercialization such as technology evaluation, valuation and financing, regulatory requirements and issues related to patenting of biotechnology products.

IV. Biotechnology club The Biotechnology Club managed by DISC at BCIL has more than 200 members including life members, annual members and VATIS Update subscribers. Many leading biotech companies are members of the club. The members of the club receive host of privileges such as complimentary copies of BCIL publications, discount on reference directories published by BCIL, participation in events organized by BCIL either free of cost or at discounted fees, copies of proceedings of various workshops and seminars organized by BCIL.

V. Publication The following periodicals and journals are being published by DISC:

a) Vatis Update: Biotechnology The Value Added Technology Information Services (VATIS) Update, Biotechnology a bimonthly publication in association with Asian and Pacific Centre for Transfer of Technology (APCTT) was continued during the year. b) Biotech Bulletin The in-house bimonthly publication from DISC, “Biotech Bulletin”, consisting of compilation of interesting news clippings on biotechnology from newspapers, magazines and journals for apprising industry on current national/international developments in the area of biotechnology was also continued. c) Biosafety Newsletter (Quarterly) The quarterly newsletter introduced in association with Ministry of Environment and Forests, Govt. of India to update on various developments and issues in the area of biosafety, was circulated to the Biotech Club Members of BCIL.

5. Infrastructure facilities in the Bioinformatics Centre

(i) Computer & Communication facility: The Centre has two servers, an IBM LAN server and Linux based proxy server. A 512 kbps Internet Lease Line (ILL) (wireless radio 49 link) has been installed at the centre from SIFY. Besides, the centre has Pentium 4 Laptops, Pentium 4 desktops, CISCO Router, HP color laser printer, HP scanner and related peripherals required for its functioning.

(ii) Scientific Software Packages: Nil

(iii) Databases and other information resources In-house databases developed as detailed under 11.

6. Details about staff members working in the centre:

Name Designation Specialization Period (years) Dr. Vibha Ahuja Dy. General Ph.D in industrial 14 Manager Biotechnology (Absorbed in BCIL) Dr. Jeevan Manager Ph.D. in Agri 2 Kumar Biotechnology (Absorbed in BCIL) Anita Sharma Deputy Management of Sub-DIC 13 Manager activities (Absorbed in BCIL) Dr. Vivek Dixit Sr. Project Ph.D. in Plant 6 months Executive Biochemistry Contractual (Information Officer) Vinod Kumar Assistant Management of BCIL 6 Manager Biotech Club & VATIS Absorbed Update (in BCIL) Arvind Kumar System Database Development, 2 Administrator Website Maintenance Contractual Deepanshu Computer Data processing, Data 2 Sharma Operator entry Contractual Mr. Mukesh Project Information collection and 2 months Raja Executive compilation Contractual

50 7. Types of Services provided DISC provided information to scientists, academia and industry through its website and various journals/publications on biotechnology. The publications include: a) Vatis Update: Biotechnology b) Biotech Bulletin c) Biosafety Newsletter (Quarterly) d) Organization of Workshops

In addition, the DISC continued to support the activities of BCIL by providing information support for preparation of various reports and publications.

8. Educational activities with details of placement : NA

9. Initiative to validate the outcome of bioinformatics resources: NA

10. Collaborative works/initiatives DISC at BCIL worked in close collaboration with Ministry of Environment and Forests (MoEF), Department of Biotechnology (DBT), Ministry of Agriculture and The Development Commissioner, Ministry of Micro, Small and Medium Enterprises, Government of India, for organizing various workshops on biotechnology issues, status studies, market surveys during the year.

11. Databases/Software packages developed The following databases were prepared to support ongoing activities of BCIL. (a) Database of IBSC members and DBT nominees (b) Directory of Biotechnology Industries and Institutions in India (5th Edition) (c) Online database (web-enabled) for accepting application from PG students across the country applying under Biotechnology Industrial Training Programme (BITP) of DBT for 6 months industrial training. (d) Online database for accepting feedback forms from students placed for training in industry and also from trainer industry. This database is capable for accessing individual information of the trainee student and trainers industry.

12. Papers published or presented in the conferences with reference: In almost all the workshops, conferences and training programmes, BCIL officers have been presenting papers on various issues related to biotech commercialization such as status of biotech industry in India, IPR issues in biotechnology, regulatory requirements, biosafety issues, business opportunities in biotechnology.

13. Initiation on R&D activities in Bioinformatics: NA

14. Details of Training / Workshop organized and total no. of user trained DISC at BCIL has organized the following workshops during the year.

S. Workshops/seminars organized Participants

51 No. 1. Workshop on “Management of Intellectual Property 350 Rights in Biotechnology” 2. Entrepreneurship Development Programme (EDP) in 300 Biotechnology 3. Workshop on Commercialisation of Biotechnology 100 Total 750

15. Impact shown by your centre on the growth of biotechnology The DISC at BCIL is promoting activities related to commercial biotechnology by organizing workshops in key issues related to commercialization of biotechnology, assisting (providing database support) in identifying suitable licensees for transfer of technologies and bringing out publications in biotechnology.

1) During the year more than 750 stake holders belonging to diverse background i.e. scientists, industry, academicians and students were trained on different aspects of commercial biotechnology. 2) A Plant extract based biopesticide formulation ‘Bollcure’ effective against cotton bollworm Helicoverpa armigera was transferred to a leading company 3) The Directory of Biotechnology Industries and Institutions in India- 5th Edition covering more than 1000 records was updated and released. 4) Provide support service to the parent organization in placing more than 400 post graduate students in biotechnology for 6 months industrial training in leading biotech companies under BITP of DBT.

16. Future activities The DISC at BCIL proposes to take up the following activities: i. Creation of Databases which can further promote and facilitate networking between the academia and the industry e.g. list of resource persons in biotechnology, sector specific databases etc. ii. Organizing workshops on Commercialisation of Biotechnology iii. Updation of technology profiles iv. Establishment and maintenance of websites v. Organizing technically intensive training programmes in the following areas such as technology transfer and licensing, management of ntellectual Property Rights, Biosafety issues, Enhancing skills of biotech industry vi. Providing value added services to the members of Biotechnology Club of DISC at BCIL

Additional Details Name of the Coordinator : Dr. Purnima Sharma Executive Director & CEO Postal Address : Biotech Consortium India Limited 5th Floor, Anuvrat Bhawan 210, Deen Dayal Upadhyaya Marg New Delhi – 110 002 52 Phone No. : 011-2321 9064/65/66/67 Fax No. : 011-2321 9063 Email : [email protected] Website : www.bcil.nic.in

Name of the contact person : Dr. Jeevan Kumar, Manager, BCIL [email protected]

53 Biotech Park, Lucknow Coordinator: Dr. P. K. Seth

1. Summary of the progress made by the centre from its inception :- The Bioinformatics Centre, Biotech City was set up in November 2001 at Industrial Toxicology Research Centre (ITRC), Lucknow as networking site. Subsequently it has started functioning since August 25th, 2003 from the site office of the Biotech Park at Sector-G, Jankipuram, Kursi Road, Lucknow from June 2006 from its Biobusiness Centre. The Major Objective of the Bioinformatics Centre is to showcase the R & D and academic strength of the Lucknow in the area of Biotechnology and serve as nodal point for industry- academia-U.P. Government interactions. The Centre is extensively involved in popularizing the application of Bioinformatics in R & D by providing training to the scientists Research Scholars and students. It has established a close network with the neighboring Academic and R&D institutions to provide information to industries, entrepreneurs and farmers regarding technologies, facilities and expertise available with them in the area of Biotechnology. The centre has 1 Mbps. Radio link internet connectivity through Software Technology Park of India (STPI), Lucknow. It proves to be a valuable resource in providing upto date information about expertise and facilities available in various local institutions for entrepreneurs through its website.

2. Major research activities in Biotechnology and its related field at your institution:- The Biotech Park offers common integration facilities for knowledge based bio-business and state of the art infrastructure facilities in the area of industrial biotechnology. The thrust areas are Health Care: Human and animal health care products including therapeutic aids, immunodiagnostics, and vaccines etc Agriculture: Micro propagation (Tissue Culture), biofertilizers and biopesticides, vermicompost, floriculture crops, Energy: Biofuel from Jatropha curcas, renewable energy resources. The Park has GLP/GMP compliant facilities for the startup companies in the area of industrial biotechnology which includes common instrumentation facilities, tissue culture facilities, diagnostic and drug delivery facilities, upscaling/ processing of plant based lead molecules, pilot plant for biofertilizers/biopesticides, hardening and macro propagation facilities.

3. Area of Specialization of the BTISnet centre:- Development of Interactive websites, Databases and Softwares.

4. Major activities of the centre during the year 2007-08:- • The centre has organized four DBT sponsored training programme/workshop and the total number of candidates participated are 85. These workshop/training programme were design to expose scientists, doctors, research scholars, technical assistants and students working in teaching and research institutions in the country with the operation of personal computers and scientific software that are being routinely used in the modern biological research. • In addition to the training programmes, the training on Database/Software Development, Phylogenetic Analysis, Primer Designing, Protein Modeling,

54 and Orthologous Clustering was provided to approximately 178 M.Sc. Bioinformatics / Biotechnology /B.Tech /MCA /M.Tech students. • Research work concerned with Molecular Modeling, Protein Structure Prediction and Analysis, Proteomics and Genomics such as modeling of pExp53 membrane bound protein of mycobacterium tuberculosis, Phylogenetic analysis of envelope Glycoprotein gp160 of HIV1 virus in Asian Countries, structure prediction of mannose binding lectine protein of Convovolus arvensis has been done. • The centre has established the video conferencing facility and the DBT sponsored training workshop held on 10-11 December, 2007 was inaugurated through video conferencing from CIMAP. • Infrastructure has been improved by the addition of 8 computer systems having TFT monitors. • Creating and maintaining websites for the other companies placed inside the park.

5. Infrastructure facilities in the Bioinformatics centre :- A. Computer & Communication Facility :- Bioinformatics centre has 1 Mbps radio link internet connectivity through Software Technology Park of India, Lucknow. • Server Campaq Proliant ML 370 - 1 No. • HP Campaq Proliant ML 370 - 1 No. • Computers (HP Compaq d330ut) - 5 Nos. • HP Computer (IV D 820 dual core 2.8 Ghz) - 8 Nos. • Computers (IBM. T.C.) - 3 Nos. • Computers (Compaq Deskpro ENL) - 5 Nos. • Network Lazer Printer(HP 2200 DN) - 1 No. • HP Network Color Laser Printer (3700 DN) - 1 No. • HP psc 2210 all-in-one - 2 Nos. • HP Officejet 4255 all-in-one - 2 Nos. • HP Scanner - 1 No. • UPS (5 KVA) online - 1 Nos. • UPS (3 KVA & 2 KVA) online - 1 Each • UPS (1 KVA) online - 2 Nos. • External CD Writer (HP 9600E) - 1 No. • Internal CD Writer (LG) - 2 Nos. • Canon 1600 Photo Copier - 1 No. • HP Digital Camera - 1 No. • HP Compaq Laptop - 1 No. • Projector (Toshiba) - 1 No. • Tablet PC - 1 No. • Video Conferencing System. - 1 No. • SGI machine - 1 No. Scientific Software packages - Macromedia Studio 8, Corel Draw x3, Microsoft Windows Server 2003 R2 Standard x64 Edition, Microsoft SQL Server 2005 Standard Edition, Microsoft Office Professional Plus 2007, McAfee Managed Virus Scan plus Anti Spyware. 55 B. Databases & other information resources- 1. Bio-diesel Database. 2. Database on Biofertilizers/Biopesticides. 3. Database on hemophelia. 4. Database on Educational Institutes in UP. 5. Database on Antidibetic plants based on clinical/experimental trial. 6. Details of Staff members working in the centre:- S. No Name of Designation Specialization Period of Absorption Staff working Status 1. Mr. Sunil System Bioinformatics 19th June, Non-Regular Kumar Network 2007 to till Gupta Administrator date 2. Ms. Shipra Senior Bioinformatics 31th Jan, Non-Regular Gupta Programmer 2007 to till date 3. Ms. Sarita Programmer Bioinformatics 19th June, Non-Regular Singh 2007 to till date 4. Mr. Gulam Data Entry Diploma in 18th Oct, Non-Regular Sabir Operator cum Computer 2006 to till Office Assistant Application date

7. Types of Services Provided: - Development of profile CD for Biotech Park, Development of Video CD showcasing the facilities available with Biotech Park and near by Research Labs, Educational Institutions, Development of application softwares and databases, Network management, Website management, Data retrieval and analysis, Email management, Development of human resources in Bioinformatics, Radio link internet connectivity, Video conferencing facility and Management of Web & Mail Server.

8. Educational activities with detail of placements: - Nil.

9. Initiative to validate the outcome of bioinformatics resources: - Nil.

10. Collaborative Works/Initiatives: - Jalaja Technologies Pvt. Ltd demonstrated Genocluster software which contains different modules for genome analysis and putative function of any predicted protein. Modalities for further collaborations are being worked out. 11. Databases/Software packages developed:- 1. Database on Biofertilizers/Biopesticides. 2. Database for hemophelia. 3. Database on Bio-Diesel. 4. Database on Fruits in UP. 5. Database on Educational Institutes in UP. 6. Database on Shizidata – surviving, schizophrenia – A database on Gene & Drug. 7. Database on Organic Farming. 8. Database on Pathways of Neurological disorder.

56 12. Paper published or presented in the conferences with references:- Presented in Conferences :- 1. Somvanshi P, Mishra B N., Seth P K(2006). Dengue virus 2 Envelope protein and its Phylogenetics Correlation by Bioinformatics Approach. Proceeding of National Seminar on Recent Advances in Biotechnology & Bioinformatics 24-25th July, Hyderabad, India. 2. Somvanshi P, Mishra B N, Seth P K(2006). Genome wide identification of vaccine candidates in consensus sequence of antigenically distinct variants of Dengue virus. Proceeding of GSM, Advanced Centre for Treatment Research and Education in Cancer, Tata Memoria Centre 23rd September, Navi Mumbai, India. 3. Somvanshi P, Mishra B N, Seth P K(2006). Genome wide identification of vaccine candidates in Antigenically Distinct Variants of Dengue Virus: A Bioinformatics Approach Proceeding of international Symposium on computational Biology & Bioinformatics ISBB,15-17th December, Bhubaneswar, India. 4. Rathi B, Somvanshi P, Seth PK (2006). Prediction of the promoter region in Unregulated genes of macrophagic stage in Mycobacterium tuberculosis Proceeding of International conference on Bioinformatics INCOB, 18-20th December, New Delhi, India. 5. Mehrotra M, Somvanshi P,Seth P K(2007). Development of Neuro Toxicology biomarkers Database Proceeding of International Conference on Biomarkers in Health and Environmental Management & XXXII Annual Meet of Environmental Mutagen Society of India 10-12th January, Coimbatore, India. 6. Somvanshi P, Rastogi O, Seth P K(2007). Phylogenetic Analysis of nif A gene in Nitrogenous Bacteria Proceeding of national Conference on Microbial Diversity: Avenues and Application 17-18th March, Dehradun, India. 7. Somvanshi P, Seth P K(2007).Insilico analysis of antigenic diversity of T cell epitopes in the prediction of Hepatitis virus polyprotein. Proceeding of BIOCONVENE international Conference on Bioinformatics and Drug Discovery: 16-22th December, Hyderabad, India. 8. Singh Sarita, Gupta Sunil Kr., Gupta Manish Kr., Dr. Seth P. K.(2007). Phylogenetic analysis of envelope Glycoprotein gp160 of HIV1 virus in Asian Countries. Presented in Proceeding of iCAB international Conference on Applied Bioengineering: 5-7 December, Chennai, India.

13. Initiation of R&D activities in Bioinformatics:- Research and development activities of the centre is focused in the area of Molecular Modeling, Protein Structure Prediction and Analysis, Proteomics and Genomics such as modeling of matrix protein of Chandipura virus, Mechanism of action of Anti diabetic herbs, clinical and experimental trails of anti-diabetic herbs, Database on Medicinal and Aromatic plants .

14. Detail of Training/Workshop organized and total number of user trained:-

57 The centre has organized four DBT sponsored training programmes /workshops and the total no. of candidates participated are 85.

S. No. Training No. of Duration Programmes/Workshops Participants Genomics: Databases & 24 18th – 20th May, 1. Web Technologies 2006 Proteomics & Drug 25 22nd – 24th August, 2. Development 2006 Tools & Languages for 24 9th – 10th November, 3. Database Development 2006 Bioinformatics Tools & Their 12 15th -17th February, 4. Applications in Biological 2007 Research

The centre provided training to 178 students in the year 2006-07 and overall persons trained by the centre are 263.

15. Impact shown by your centre on the growth of biotechnology and allied area: The Biotech Centre has made a significant impact about the Biotechnology as evident by increasing number of hits on website. It is also attracting the Entrepreneurs through its website and it helped in development of human resource through short and long term training programmes.

16. Future activities:- • To extend facility of SGI Work Station for Computational Biology and Drug Development applications to researchers of different institutions. • To organize long-term Training Programmes in the field of Bioinformatics. • Process scheduling of Biotech Park facilities and activities. • Updating and modifying facilities and website of the centre. • Developing of databases on Anti-Diabetic Plants and Medicinal & Aromatic Plants.

17. Additional details :- Name of the Coordinator: Dr. P. K. Seth Chief Excutive Officer Postal Address: Biotech Park , Lucknow Sector-G, Jankipuram, Kursi Road, Lucknow-226021 Phone Number: +91-522-2365050,4012076/77,4012091. Fax No: +91-522-4012081 Email: [email protected] [email protected] Website: www.biotechpark.org.in

58 Name of the contact person(s): Dr. P. K. Seth Email: [email protected] [email protected]

59 Birla Institute of Scientific Research, Jaipur Coordinator : Dr P Ghosh

1. Summary of the progress made by the centre from its inception: Birla Institute is a leading renowned center for Biotechnology research in Rajasthan. The institute undertakes goal-oriented applied research in the frontier areas of industrial biotechnology sponsored by government and industries as well as in-house research. Recognizing the importance of IT for pursuing advanced research in modern biology and biotechnology, DBT had started a Bioinformatics program envisaged as a distributed database and network organization. BISR has been identified as one such centre. This Centre was established in 1999. This is one of the core facilities in the field of Biotechnology providing access to the latest information of the world databases. Internet/E-mail facility at this centre is extensively used by the researchers of our institute and by other nearby academic institutes and universities. Recently, BISR has initiated research in Proteomics and Genomics area of Biotechnology. Besides, efforts are directed towards development of quality information resources in the form of databases and software for professionals in the area of biotechnology and Bioinformatics. In addition to research, training programs, workshops and scientific meetings are organized regularly. 2. Major research activities in Biotechnology and its related fields in your institution Birla Institute of Scientific Research (BISR) is involved in fostering and promoting various aspects of science and technology and has multi functional activities. The research programs of the BISR are concerned primarily with Biotechnology and Natural Resource Management.

Major Activities: • Conduct basic and applied research in established and emerging areas of science and technology. • Organize quality improvement and customer specific training programs in Biotechnology. • Establish and maintain effective linkages with industry, educational and research organizations.

3. Area of Specialization of the centre: • Industrial Biotechnology, • Microbial and Bioprocess Technology • Genomics and Proteomics • Applied Plant Biotechnology

4. Major activities of the centre during the year 2007- 08 a) National workshop on advance areas of Bioinformatics o Algorithms in Bioinformatics, 15-17 November 2007 o Biological Sequence Analysis, 17-21 December 2007 b) Research training to 5 students from different universities was imparted. c) Developed a database on Interaction-Specificity in Protein-Ligand Complex (DisProlic) d) Developed the interface of Virtual Proteomics Workbench. e) Developed an intranet mailing facility in the center. 60 f) Guest visit - Invited guest scientist from renowned bioinformatics centre like JNU, MASCON, University of Bergen, Norway. 5. Infrastructure facilities in the Bioinformatics Centre A. Computer & Communication facility • HP Proliant ML350 Server (double xeon ) • Windows NT Server HP Netserver E200 • IBM Intellistation (AIX 5) Graphics Workstation • One Laptop IBM PIV 2.4 GHz with 40 GB HDD, 256 MB RAM • Five numbers HP XE310 Celeron 1.1 GHz, Five number IBM Pentium III 500 MHz, Two numbers Acer Power 4100 Pentium II 333 MHz, Three numbers Acer power 4000 Intel Celeron 333 MHz, • One Iomega External Zip Drive, One HP External CD-WRITER • LCD Projector Infocus LP500 • One number HP 2100TN LAN Laser Printer, Two number HP LaserJet 6L Gold Printer, RICOH FT 3513 Photocopier • Three numbers TVS UPS 1.5 KVA Line Interactive, Eight numbers 500 VA UPS, two numbers APC UPS 1.5 KVA line interactive.

B. Scientific Software packages a) Exome Horizon, Vector NTI, Reference Manager, Library Management Software, Visual Studio, Discovery Studio Package

6. Details about staff members working in the centre

S. No. Name of Staff Designation Specialization Period of working 1 Dr M krishnamohan Scientist Microbial 9 years Biotechnology 2 P. S Solanki Information Bioinformatics 6 years Analyst 3 Shivani Chandra Research Genomics 2 years Associate 4 Radhakishan Technical Networking 4 years Assistant 5 Rakesh ojha Project Information 2 years Assistant Technology 6 Neha Sharma Project Web 1 year Assistant Technolgy 7 Sonia Gabhrani Project Maths & Stats 1 year Associate 8 Vanita Parashar Project IT 1 year Associate 9 Amit Nagal Project CADD 1 year Associate 7. Types of services provided The Institute works on Research projects in the frontier areas of Biotechnology with direct relevance to the Industry. It is important to be in contact with the latest happenings. A modern library with facilities for literature search, access to other

61 information centres, in-house development of databases etc. is essential. Towards this end an Integrated Information Centre has been setup.

The Bioinformatics Centre at BISR has created an infrastructure for providing facilities to the users working in the field of Biological Sciences. The users of Rajasthan, Jaipur in particular, are using facilities available at the Bioinformatics Centre extensively. Following is the brief description of the services offered by this centre:

E-mail and Internet facility: The Bioinformatics Centre has leased line Internet connection. The center has been providing E-mail facilities since 1997. The facilities have been used not only by the institute staff but also by personnel working in the area of life sciences from the neighboring institutions and organizations. Other functions of the centre include: b) Installing, implementing and maintaining software on computer. c) Preventive maintenance of computers. d) Updating the users with recent advances in computers/internet.

8. Databases/ Software packages developed A) Name of Database: DOMAP • Broad Subject Area: Plant Biotechnology • Broad Functional Area: Medicinal and Aromatic Plants of Rajasthan • Whether developed or acquired: Developed • Status of completion: Complete • Whether the database is accessible over the network: Yes B) Name of the software: Library management system • Function: Library automation • Acquired or developed: Developed • Status of completion: Completed • System requirement for running the package: Windows, Visual Basic Package C) Name of the Database: Database of Interaction-Specificity in Protein- Ligand Complex ( DISProLiC) • Broad Subject Area: Structural Biology • Broad Functional Area: Interaction Specificity in Complexes • Whether developed or acquired: Developed • Status of completion: About to Complete • Whether the database is accessible over the network: Yes

D) Name of the Software: Virtual Proteomics Workbench • Broad Subject Area: Proteomics • Broad Functional Area: Proteomics Data Analysis • Whether developed or acquired: Under development • Status of completion: About to Complete • Whether the database is accessible over the network: Yes

9. Initiation of R&D activities in Bioinformatics The Research activities at the center involve two areas related to evolutionary biology. The structural aspects as well as the comparative genomics are being 62 used for studying evolutionary Genomics of micro-organisms. Besides, the centre works in the area of database and software development specifically related to life sciences.

10. Details of Training/ Workshop organized In order to educate the users on latest advances in the field of computer and Information Technology the Bioinformatics Centre conducts workshops regularly. This year our center conducted two workshops of three days.

A) Algorithms in Bioinformatics (15 -17 November 2007) A three-day workshop was organized on the above topic and 40 participants were selected for the training from various institutes and universities in India. We invited guest speakers from leading Bioinformatics Institutes and Industries.

B) Biological Sequence Analysis ( 17 – 21 December 2007) A five-day workshop was organized on the above topic and 40 participants were selected for the training from various institutes and universities in India. We invited guest speakers from leading Bioinformatics Institutes and Industries.

C) Research Project and Summer Training: The center has imparted six-month research projects to 5 students from different universities in India. Some of the research topics include: • Virtual Proteomics Workbench Development using LAMP • Designed and developed improved algorithm of PCR primers • HMM based prediction for predicting post translation modifications

11. Impact shown by your centre on the growth of biotechnology and allied areas The institute is engaged in various research activities and centre provides the Bioinformatics support to the scientists. All scientists and researchers in the institute working in the different areas of Biotechnology and Natural Resource Management used the internet facility provided by the Bioinformatics centre. During 2006-07 institutes has published 14 research papers in peer reviewed journals. 119 nucleotide sequences were deposited in the Genbank during 2006-07.

12. Future activities Since our research work is mainly related with the biotechnology, Biochemical engineering, applied geology and Microbiology, the current work we can implement Bioinformatics in the following fronts: a) Sequence analysis software development related to molecular biology. It will involve the development of software for the quantitative analysis of the biological systems. b) Computer aided molecular designing and modeling of proteins to study the cause of their thermostability and adaptability in extremophiles. c) Whole genome sequence analysis of Rhizobium species to carry out comparative genomic studies. 63 d) Development of Virtual Proteomics Workbench. e) Construction of bioinformatics resource Meta server The goal of such server is to provide bioinformatics services to the international biology community by executing various bioinformatics tools, some of them locally, other remotely at other servers around the world, and to store, organize and present the results using a web oriented interface.

Additional Details: Coordinator’s Name: Dr P Ghosh Postal Address: Birla Institute of Scientific Research, Statue Circle, Jaipur 302001 Rajasthan Phone Number: 0141-2385283, 2385094; Fax No.: 0141-2385121 Website: www.bisr.res.in Email: [email protected] , [email protected]

Name of Contact Person(s):

1. Dr M Krishnamohan Mobile: +91-9314509942 [email protected],

2. Mr. P S Solanki Mobile : +91-9928365838 [email protected]

64 Birla Institute of Technology, Mesra, Ranchi Coordinator: Dr. A. S. Vidyarthi

1. Summary of the progress made by the center from its inception The Distributed Information Sub-Center (Sub-DIC) was established by the Department of Biotechnology, Government of India at Department of Biotechnology, Birla Institute of Technology, Mesra, Ranchi in the year of 2005. The center is involved in distributing information on various aspects of biology, providing access to different databases through internet, as well as some specialized databases, softwares and online bioinformatics journals used by the staff of our department. The center has a wireless Local-Area-Network with connectivity 512Kbps. All the major software packages (SYSTAT 11.0, SIGMAPLOT 9.0, GCG11.0, INSIGHT II, DS Gene scan etc.) were installed in the workstation successfully and working well. Organization of training programs, workshops and scientific meetings in order to create awareness of bioinformatics in the local community is among its regular activities. The database of medicinal and aromatic plants available at Jharkhand was developed and upgraded on regular basis. Efforts are directed towards development of quality databases and software for useful purpose in the area of medicinal and aromatic plants. The development of two software PROMET for structural mapping metal of ion binding’s proteins and PROANA for protein sequence analysis including all aspects are in progress. Study of HIV dynamics, Microbial (Flu virus and Mycobacterium tuberculosis) and plant Gene analysis (CVOMT, Ocimum sanctum) and annotations is going on.

2. Major research activities in Biotechnology and its related fields in your institution • Development of Database for medicinal and aromatic plants available in Jharkhand. • Study of HIV dynamics using Fuzzy Logic. • Phenetic and phylogenetic analysis of wild Commiphora wightii population. • Phylogenetic analysis of Chavicol-O-methyl transferase (CVOMT) gene in the family Labiatae. • Comparative modeling of CVOMT protein in the family Labiatae. • Chemo-informatics of Catharanthus roseus, Ocimum sanctum, Withania somnifera (Ashwagandha), Cassia angustifolia (Senna), Chlorophytum borivillianum (Safed Musli), brahmi Bacopa monnieri • Drug discovery by high through put screening against target molecules and known homologs from different medicinal plants. • Modification of Artemisinin (a compound extracted from the Artemisia annua, sweet wormwood artemisinin used as antimalarial drug) drug structure for better binding at target sitr of protein. • Analysis of differential gene expression in wheat plants induced by the leaf rust fungus: A Trancriptomic Approach • Analysis of differentially expressed proteins induced by the drought in rice plants: A Proteomics Approach • Analysis of Synonymous codon usage bias in Mycobacterium tuberculosis phages and its Implication in phage therapy. • Analysis of adaptive molecular evolution of Avian Influenza A Virus Subtype H5N1.

65 • A homology based approach for modification of ampicillin structure for its stability using Insight II. • Insilico prediction of 3-D structure of important metal binding’s proteins for findings of structure function relationship. • Genomic analysis of HIV viral gene. • Scanning of HIV viral genome and proteome for potential drug targeting. • Designing of small peptides for antigenic response in human and optimization of the same for human system. • Fruit & Vegetable Processing (Post Harvest Technology) • Species Identification and Strain Differentiation of Dermatophytes from tribal dominated regions of Jharkhand • Bio Fuels • Development & Evaluation of Herbal Medicines against Mycoses • Production of Industrial Enzymes • Production of Biopolymers from wastewater • Microbial community analysis of rhizosphere soil & Microbial Interaction • Protein structure function relationships and Effect of high pressure and temperature (Cereal and legume protein)

3. Area of specialization of the center Medicinal and Aromatic Plants, Molecular Modeling, drug designing and Computational Bioinformatics.

4. Major activities of the center during the year 2007- 08 • Upgradation of bioinformatics laboratory with new softwares (installation of server, installation of workstations and software packages installation) • Development of database of medicinal and aromatic plants available at Jharkhand is in progress. • Drug discovery by high through put screening against target molecules and known homologs from different medicinal plants • Phenetic and phylogenetic analysis of wild Commiphora wightii population, • Phylogenetic analysis of Chavicol-O-methyl transferase (CVOMT) gene in the family Labiatae, Comparative modeling of CVOMT protein in the family Labiatae, Chemo-informatics of Catharanthus roseus, Ocimum sanctum, Withania somnifera (Ashwagandha), Cassia angustifolia (Senna), Chlorophytum borivillianum (Safed Musli), brahmi Bacopa monnieri • Departmental projects for B. E. (Biotechnology) and M. Sc. Bioinformatics students (Phylogenetic analysis of a viral gene, in silico drug designing, 3D structure prediction of proteins etc.) were assigned in this lab. • A network (LAN) has setup within the bioinformatics lab as well as department with the server for fast transferring data among different lab within the biotechnology department. • The development of two softwares (PROMET and PROANA) for structural mapping metal ion binding’s proteins and protein sequence analysis was developed. • Genome analysis and annotations of Microbial (Flu virus and Mycobacterium tuberculosis) is going on. • 512 Kbps internet connectivity was established at the center.

66

5. Infrastructure facilities in the Bioinformatics Center

A. Computer and Communication facility Computer and peripherals: • SERVER: DELL PowerEdgeTM 1800(Processor Intel® Xeon™ processor at 3.2GHz/2MB Cache, 800MHz FSB, Operating System Windows® Server 2003, Standard Edition, Includes 5 CALs and LINUX) • 28 clients workstations: DELL Pentium IV workstations, 80GB HDD, 512 RAM, 3.8GHz, Operating System Windows® XP. • 2 clients workstations: DELL Pentium IV workstations, 380GB HDD, 1GB RAM, 3.8 GHz Operating System LINUX® WS. Networking Equipments: • Modem: 3 external (2 – 512 kbps, 1 – 512 kbps Lease Line), 30 nodes. • Internet connection: 512 kbps (dedicated) BSNL, Lease line 512 Kbps ISDN line. Power supply: UPS: 10KVA – 2. Printer: • Network Printer: HP Color LaserJet 4700dn (Print speed, color (best quality mode), Up to 31 ppm, Processor speed 533 MHz • HP LaserJet 3050 All-in-One, (Print, color scan, copy, and fax ), Automatic document feeder (30 pages), Incoming fax memory: 110 pages B. Scientific Software packages • GCG 11.0 (Sequence Analysis) • Insight II (Molecular Modeling) • SYSTAT 11.0, SIGMAPLOT 9.0 (Statistical Analysis) • HOMOLOGY (Comparative modeling and alignment) • DS GENE STATIC (Sequence search on Internet) • BIOPOLYMER (Protein and peptide designing) • BIOPERL (Programming Tools for bioinformatics) • Various molecular display programs (such as RASMOL, spdb Viewer, Qmol etc.) C. Databases & other information resources PDB database of proteins CDROM (from accelrys and rcsb).

6. Details about staff members working in the center Sr. Number Name of the Designation Specialization Period of Staff working 1. Dr. A. S. Professor & Bioprocess 4 years Vidyarthi HOD Engineering 2. Mr. Raju Lecturer Molecular 17 months Poddar modeling 3. Mr. Technical Computer 12months Shakaracharya Assistant networking

67 7. Types of services provided • Sequence analysis • Molecular modeling and drug designing • Homology modeling of protein structures • Internet facility for the study, research and reference searching purpose to students, research scholar and faculties • Computer education and training in bioinformatics

8. Educational activities with details of placement M. Sc. in Bioinformatics (2 years), PG Diploma in Bioinformatics (1 year) and B.E. in Biotechnology (4 years). Placement of the students in the institute is more than 70%.

9. Initiative to validate the outcome of bioinformatics resources • -NIL-

10. Collaborative works/initiatives • One collaborative research work is going on in host –pathogen interaction during leaf rust infection in wheat: a transcriptomics approach, with IARI, New Delhi and CCSU, Meerut. • Initiatives has taken to make a database of insects and plant diseases related to LAC plant in collaboration with INDIAN LAC RESEARCH INSTITUTE (Indian Council of Agricultural Research) Namkum, Ranchi - 834 010, INDIA • Another project is proteomics and genomics analysis of tasar with Central Tasar Research & Training Institute, Piska nagri, Ranchi - 835 303, India. • Another initiative was taken to upgrade medicinal and aromatic plant database with other BTIS center like CIMAP Lucknow.

11. Databases/ Softwares packages developed • Database for medicinal and aromatic plants available in Jharkhand, Software packages (developed by your centre with application). • ProMET (A platform for findings of metal binding’s site of a protein). • ProANA (A platform for analysis of new protein sequences including all aspects)

12. Papers published or presented in the conferences with references • Rocky Kumar, Partho Halder and Raju Poddar, Adaptive molecular evolution of virulence genes of avian influenza - A virus subtype H5N1: An analysis of host radiation, Bioinformation, 2006, 1(8): 321-326. • Ashutosh Ranjan, A. S. Vidyarthi and Raju Poddar, Codon bias perspectives in phage therapy of Mycobacterium tuberculosis, In silico Biology, 2007, 7 (30), 21- 30. • S. Srivastava, P. Shukla and Raju Poddar, In sillico study of sequence homology of Xylenase family 11.0 , Journal of Applied Sciences, 2007 (Accepted). • Ashutosh Ranjan, and Raju Poddar, Potential Therapeutic Targets of Salmonella typhi: A Subtractive Genomics Approach, JBMC, 2007 (Accepted). • Raju Poddar, Modification of ampicillin structure for better bindings and stability, Current Drug Targets, 2007 (commun.). • S. Sharma and Raju Poddar, Synonymous codon usage bias in Pseudomonas syringe phages: implication in Phage Therapy, Journal of Bioinformatics and computational Biology (JBCB), 2007 (commun.). 68 • S. Srivastava, P. Shukla and Raju Poddar, “Study of codonbais perspectives of fungal xylanase gene by multivariate analysis”, presented at 48th AMI annual conference, IIT Chennai, 18-21, December, 2007. 13. Initiation of R & D activities in Bioinformatics • Bioinformatics tool has been applied to analysis of differentially expressed proteins induced by the drought in rice plants, Phylogenetic and sequence homology studies of Microbial community of rhizosphere soil and dermatophytes etc.

14. Details of training/ Workshop organized and total no. of user trained

• “National Workshop on Functional Genomics of Prokaryotes” held on September 10-15, 2007 (number of participants 30). • “Potential and areas of growth in Biotechnology” to be held on March, 2008. 15. Impact shown by your center on the growth of biotechnology and allied fields. In this you may highlight the details number of paper published/number of paper published with the help of your center, How your center is promoting various activities of your organization and neighboring institution, Manpower trained tools developed patents & copyrights acquired and other services offered etc. a. Paper Published: 5 b. Center Activities regarding the promotion of Departmental Activities: Guiding the students, research scholars about the Application of Bioinformatics in the Field of Life Science, Helping them to find online Research papers, using different analytical tools, conducting the workshop. c. Patents & Copyrights: nil

16. Future activities : Research ¾ Microbial Genome analysis and annotations ¾ Medicinal plant database ¾ Molecular modeling ¾ Medicinal plant gene analysis Workshop: A workshop will be conducted on structural and knowledge based Bioinformatics. Training: Students will be allotted under the scheme traineeship and studentship to accomplish the tasks in Bioinformatics Infrastructure: Department plans to make centralized data storage system and make the data available to all the departments through Local Area Network.

Additional details

Name of the Coordinator: Dr. A. S. Vidyarthi Postal Address: Prof. & Head Dept. of Biotechnology Birla Institute of Technology, Mesra 835 215 Ranchi, Jharkhand Phone Number: + 91-651- 2276223, 2276590 Fax No.: + 91-651- 2275401 Email: [email protected] [email protected]

69 Website: www.bitmesra.ac.in Name of the contact person: Mr. Raju Poddar E-mail: rpoddar@bitmesra

70 Bose Institute, Kolkata Coordinator : Professor Pinak Chakrabarti

1. Summary of the progress made by the centre from its inception Since its inception in 1988 the Bioinformatics Centre at Bose Institute has fulfilled multiple tasks for the service of the scientific community in Eastern India. Its main activities have been: Information Distribution: Meeting the objective of the BTIS program, the Centre is involved in distributing information on various aspects of biology, providing access to different databases through internet, as well as purchasing some specialized databases, softwares and journals. Crossing the boundaries of the host institute, the service has been provided to the whole of the eastern region, reaching places like Tripura, Andaman Islands, Almora etc. Networking and Communications: In 1997 we have established a Local-Area- Network in both the campuses of Bose Institute and subsequently linked the two through Wide-Area-Network. A 1 mbps (that has been upgraded to 2mbps in 2006- 07) internet connectivity is used for the activities of the Centre and also serves as a backup resource to the ERNET connectivity used by the scientists in the Institute. Research Activities: The computational infrastructure developed at the Centre has provided the impetus for thriving research activities in bioinformatics and computational biology, as can be seen from a large number of publications made over the years and its recognition as the Centre of Excellence in Bioinformatics by DBT in 2004 and awards received by staff and students working at the Centre.

Awards/Recognition: Dr. T.C. Ghosh was awarded Biotechnology Overseas Associateships by DBT for the year 2000-01 and 2005-06 and was invited by UNESCO, European Office to give lectures in a course on Bioinformatics for East-European students during October 20-24, 2003. Based on their doctoral work in Bioinformatics Dr. D. Pal, was awarded INSA Medal for Young Scientist in the year 2000. Prof. B.B. Biswas outstanding Student Award of Bose Institute was awarded to Dr. D. Pal in 1999, Dr. U. Samanta in 2000, Dr. R. Bhattacharyya in 2002, Dr. R. P. Bahadur in 2003 and Mr. Mainak Guha Roy in 2007. The Nilratan Sarkar Award of the Institute was awarded to Dr. R. Saha 2006 and to Dr. S. Basak in 2007. Dr. R. Bhattacharyya has been awarded the JBS Haldane Memorial Prize 2006 by the Indian Statistical Institute, Kolkata. Prof. P. Chakrabarti has been awarded the JC Bose National Fellowship in 2007.

2. Major research activities in Biotechnology and its related fields at your institution In addition to carrying out independent lines of work, many of the activities in the Centre are directly related to and supplement the biotechnology programmes that are being carried out in the different departments of the institute. The following research activities are being actively carried out: ™ Genome analysis ™ Analysis and prediction of three-dimensional structures of proteins ™ Plant and mycobacterial genomics and proteomics

71 ™ Homology modeling of protein structures ™ Biomolecular structure determination using NMR and Xray crystallography ™ Protein-protein interaction, docking and molecular recognition ™ Protein folding and threading ™ Dynamics and protein networks

3. Area of Specialization of the centre Genome analysis; genetic engineering and molecular modeling.

4. Major activities of the centre during the year 2007 One Research Scientist, one Research Associate and eight JRFs/SRFs are working in the COE in Bioinformatics. For topics of research see item no. 2; list of publication in the year is provided in item no. 12 and the workshop arranged in item no. 14.

5. Infrastructure facilities in the Bioinformatics Centre Computer & Communication facility Computer Hardware (functional): Sun E420R Server, SGI O2 Desktop Workstation (three nos), SGI Octane Workstation, IBM PCs (thirty five nos), IBM X206(4 servers), IBM 226 (two servers), IBM X255 (two servers), IBM Color MFP, Pentium III PC (twenty nos), HP Scanner, HP Laser Printer, Cisco Router and Cisco Switch, Linksys Switches, HP photo printer, HP All-in-one printer, Xerox photocopier.

Communication Facilities: Since 1997 BIC has established LAN in both the campuses of the institute and subsequently linked them to the internet by a 1mbps leased line (ERNET). In December 2006, a 2 mbps internet connectivity has been made operational (through VSNL).

Scientific Software packages

A web-server, ProFace has been developed for dissecting protein-protein interfaces and deriving various physicochemical parameters. It is available at http://www.boseinst.ernet.in/resources/bioinfo/stag.html.

A web-server, IntGeom has been developed for calculating the geometry of interaction between planar side chains in protein structures. It is available at http://www.boseinst.ernet.in/resources/bioinfo/stag.html.

An online version of the standalone version of ConfPlot (reference: Pal D and Chakrabarti P (1999) Graphical representation of the salient conformational features of protein residues. Protein Engng. 12, 523-526) has been made and put on the web.

Most of the commercial softwares (such as Bio-suite, Accelyrs, etc.) and graphics and docking programs are available at the Centre.

72 Databases & other information resources Three different databases on interfaces in homodimers, protein-protein complexes and those in the crystal of monomeric proteins are available at the web-site, http://www.boseinst.ernet.in/resources/bioinfo/stag.html. These have been used in the analysis of protein-protein interaction.

A database on the conservation of some high priority medicinal plants of India, PlantCon, has been developed, and available at http://www.boseinst.ernet.in/resources/bioinfo/plantcon.html.

6. Details about staff members working in the centre (Name of the staff, Designation, Specialization and period of working. Please indicate their absorption status) Name of the Staff Designation Specialization Period of Working a) Dr. Tapash Chandra Ghosh Sr. Lecturer Genome analysis From 1993 b) Mr. Tushar Kanti Bhattacharya Technical officer Computer software From 1991 c) Mrs. Sujata Roy(Majumder) S.T.A. Bibliography From 1993 d) Mr. Sanjib Kumar Gupta S.T.A Networking From1994 e) Dr. Debjani Roy Research Scientist Molecular modeling From 2005 f) Mr. J.N. Mandal Sr. attendant From 1988

All, other than Dr. Debjani Roy, who was hired in the COE grant, are institute employees.

7. Types of services provided : Data retrieval, Sequence analysis, Molecular modelling and drug design, Ligand docking and virtual drug screening, Homology modeling of protein structures BIC personnel are involved in teaching and supervising projects in the Bioinformatics MSc/MTech courses being conducted by the Calcutta University, W B University of Technology.

8. Educational activities with details of placement BIC provides project work to students undergoing B.Tech/Mtech/MCA/DCA courses from a large number of institutes/universities. It offers a one- semester course in bioinformatics to the PhD students in the institute. Eight students have been selected under the studentship/traineeship programme for a period of 6 months. They are: Maitrayee Dasgupta, Baisakhi Halder, Sraani Chattopadhyay, Tina Begum, Priyanka Shah, Bipulesh Bhowmick, Manidipa Paul and Roopsha Brahma. Six students who finished their traineeship last year have all been well placed, joining an engineering college in Mumbai as a lecturer, PhD programmes at IIIT-Hyderabad and Bose Institute, MTech programme at IIIT-Allahabad, and IBM as a programmer. One of the earlier PhD students (Dr. Debnath Pal) is now a faculty of the Bioinformatics Centre, IISc. Two students (Mr. Anshuman Bagchi and Ms. Tania Banerjee), who finished their PhD theses, have been recruited as a faculty in the Biochemistry Department of Kalyani University and TCS, Kolkata, respectively.

73 9. Initiative to validate the outcome of bioinformatics resources The softwares developed at the Centre have been put on the net, so that these can be used worldwide, and people can use/validate the scientific output from the Centre. Besides, all the work are published (or under submission) in peer-reviewed international journals.

10. Collaborative works/ initiatives P. Chakrabarti and Prof. J. Janin of Universite Paris-Sud, Orsay, France have been collaborating for the past six years and a new project has been submitted to IFCPAR for funding. Collaborative work between T.C. Ghosh and G. D’Onofrio of Stazione Zoologica, Italy has been continuing.

11. Databases/ Software packages developed Details provided under item nos. 5B and 5C. 12. Papers published or presented in the conferences with reference (2007- 08) 9 D’Onofrio, G., and T.C. Ghosh and S. Saccone. 2007. Different functional classes of genes are characterized by different compositional properties. FEBS Letters (in press). 9 Basak, S., S. Roy, and T.C. Ghosh. 2007. On the origin of synonymous codon usage divergence between thermophilic and mesophilic prokaryotes. FEBS Letters (in press). 9 Bagchi, A., and T.C. Ghosh. 2007. Homology modeling and molecular dynamics study of the interactions of SoxY and SoxZ: The central player of biochemical oxidation of sulfur anions in Pseudaminobacter salicylatoxidans. Res. J.Microbiol. 2: 569-576. 9 Mukhopadhyay, P., S. Basak, and T. C. Ghosh. 2007. Synonymous codon usage in different protein secondary structural classes of human genes: Implication for increased non-randomness of GC3 rich genes towards protein stability. J Biosciences 32: 947-963. 9 Mukhopadhyay, P., S. Basak, and T. C. Ghosh. 2007. Nature of selective constraints on synonymous codon usage of rice differs in GC- poor and GC-rich genes. Gene 400: 71-81. 9 Kahali, B., S. Basak, and T. C. Ghosh. 2007. Reinvestigating the codon and amino acid usage of S. cerevisiae genome: A new insight from protein secondary structure analysis. Biochem. Biophys. Res. Commun. 354: 693-699. 9 Sau, K., S.K. Gupta, S. Sau, S.C. Mandal, and T.C. Ghosh. 2007. Studies on synonymous codon and amino acid usage biases in the broad- host range bacteriophage KVP40. J. Microbiol. 45: 58-63. 9 Banerjee, M., D.Roy, B. Bhattacharyya and G. Basu. 2007. Differential colchicine-binding across eukaryotic families: the role of highly conserved Pro268beta and Ala248beta residues in animal tubulin. FEBS Lett.581: 5019-5023. 9 Janin, J., F. Rodier, P. Chakrabarti and R. Bahadur. 2007. Macromolecular recognition in the Protein Data Bank. Acta Crystallogr. D63, 1-8.

74 9 Pal, A., P. Chakrabarti, R.P. Bahadur, F. Rodier, and J. Janin. 2007. Peptide segments in protein-protein interfaces. J. Biosci. 32, 101-111. 9 Saha, R.P., R. Bhattacharyya and P. Chakrabarti. 2007. Interaction geometry involving planar groups in protein-protein interfaces. Proteins. 67, 84-97. 9 Dasgupta, B. P., P. Chakrabarti and G. Basu. 2007. Enhanced stability of cis Pro-Pro peptide bond in Pro-Pro-Phe sequence motif. FEBS Lett. 581:4529-4532. 9 Guharoy, M and P. Chakrabarti. 2007. Secondary structure based analysis and classification of biological interfaces: identification of binding motifs in protein-protein interactions. Bioinformatics, 23: 1909-1918. 9 Chakrabarti, P. and R. Bhattacharyya. 2007. Geometry of nonbonded interactions involving planar groups in proteins. Prog. Biophys. Mol. Biol. 95: 83-137. 9 Vidyasagar et al. 2007. BioSuite: a comprehensive bioinformatics software package (A unique industry-academia collaboration). The NMITLI-BioSuite Team Curr. Sci. 92:29-38. 9 Kundu, S., and D. Roy. 2007. Computational study of glyceraldehyde-3- phosphate dehydrogenase of Entamoeba histolytica: implications for structure-based drug design. 25:25-33. 9 Pal, A., A. Chakrabarti and J. Basak 2007. New motifs within the NB- ARC domain of R proteins: probable mechanisms of integration of geminiviral signatures within the host species of Fabaceae family and implications in conferring disease resistance. J. Theo. Biol 246: 564-573. 9 Chattopadhyaya, R. and A. Pal. 2008. Three dimensional models of NB- ARC domains of disease resistance proteins in tomato, Arabidopsis and flax, J Biomol Struct and Dyna 25: 357-572. 9 Kundu, S. and D. Roy. 2007. Structural considerations for designing adenosine analogs as selective inhibitors of Trichomonas sp. glyceraldehyde-3-phosphate dehydrogenase. In Silico Biology 7: 0051.

13. Initiation of R&D activities in Bioinformatics The on-going research activities will be continued. 14. Details of Training/ Workshop organized and total no. of user trained A workshop on “Application of bioinformatics in molecular and structural biology” was organized during February 23-24, 2007. There were more than 100 participants.

15. Impact shown by your centre on the growth of biotechnology and allied areas. In this you may highlight the details like number of paper published/ number of papers published with the help of your centre, how your centre is promoting various activities of your organization and neighboring institutions, manpower trained, tools developed, patents & copyrights acquired and other services offered etc. In 2007, nineteen papers dealing with different aspects of bioinformatics have been published by people working at the Centre Many other publications have taken the services of the Centre.

75 16. Future activities Research activities given in item no. 2 will be continued. The staff strength and the number of students will be increased. Additional Details: Name of the Coordinator: Professor Pinak Chakrabarti Postal Address: Bioinformatics Centre, Bose Institute, P 1/12, C.I.T. Scheme VII M, Kolkata 700 054 Phone Number: +91 33 2355 6626 Fax No.: +91 33 2355 3886 Email: [email protected] Website:www.boseinst.ernet.in/bic Name of Contact Person(s): Prof. Pinak Chakrabarti Email: [email protected]

76 Central Agricultural Research Institute, Port Blair Coordinator: Dr. M. Balakrishnan

1. Summary of the progress made by the centre from its inception. The Distributed Information Sub Centre (Sub-DIC) was established at Central Agricultural Research Institute Port Blair, in the year 2005 with the support from DBT, Govt. of India. The Sub-DIC has been made well equipped with hardware including computers, proxy server, mail server, database server and VSAT (Institutional Facility). The mission of Bioinformatics Centre, CARI is to develop databases on Biodiversity of Andaman & Nicobar Islands, which would provide information to taxonomists, ecologists, biodiversity management specialists, policy makers, planners & related entrepreneurs to store, manage, and exchange electronically published scientific information in standard format. It also serves as an active site for bioinformatics research and development in the remote union territory of Andaman and Nicobar Islands.This centre has created both off-line and On-line database on biodiversity of Andaman and Nicobar Islands. 2. Major research activity in biotechnology ad its related fields at your institution A. Major Activities: Biotechnology Section of CARI, conceptualized, designed and developed during 1992, cell technology and molecular biology research including transgenic development and gene tagging for excess salt tolerance are undergoing currently. Cell and tissue culture, molecular analysis, transgenic development, transgenic rearing facility (DBT approved, Type II facility), dark room photography, microscopes (trinocular, florescence and inverted microscopes), electrophoresis and gel documentation, molecular marker, quantification facilities, radioisotope lab (Type II, BARC approved) are the major facilities available in this section. In addition, to screen saline/metal toxicity tolerant lines, a simulated screening facility and a mini repository of medicinal plants indigenous to Bay Islands have also been developed. Along with this various technology developed includes semi-dwarf salt tolerant Pokkali lines viz. BTS 24, BTS 28 and BTS-13 having productivity of ~3.5 tons/ha through exploitation of In vitro culture induced variations, AI & Fe toxicity tolerant lines in IR72 & C 14-8, transgenic lines carrying osmotine, cry IA(b), cry IA(b), cry IA(c), AmSOD & chitinase in indica rice through Agrobacterium – mediated genetic transformation, Production technology for tetraploid, gynogenetic & transgenic stocks (rtgh gene) in Indian major carps (IMC)- rohu, catla & mrigal and Efficient in vitro micropropagation protocols for mass production of planting materials in pineapple, banana. Cymbidium, Gerbera jamesonii & Bacopa monnieri (under grotek culture system) developed to undertake profitable agribusiness. Patent application for “Protocol for producing large number of viable plantlets of Bacopa monneri vitro gro-tek system system under liquid culture Mass Production System”. has been submitted to Indian Patent Office, New Delhi.

3. Area of specialization of the centre.

Development of database for the Biodiversity of A & N Islands.

77 4. Major activities of the centre during the year 2007-2008. The Centre during this year has been actively indulged in the creation of database for the biodiversity. IFS and mango along with training students of various universities in the field of molecular modeling and structure based drug designing from mainland. Apart from this databases such rice genome, PDB and Pfam are maintained. The centre has also successfully conducted a national conference on” Bioinformatics tools for gene and protein analysis” in collaboration with SIGC, Trichy. 5. Infrastructure facility at the Bioinformatics centre.

A. Computer and Communication Facility The hardware includes Pentium desktop computer (10 nos.). LAN, proxy server, mail server, database server and VSAT (Institutional Facility), digital photocopier, Network Printer, UPS 7.5 kw (2 nos)

B. Scientific & Software Packages Scientific software packages for Molecular modeling ( Modeller9v2, JACKAL, ICM Pro, CAChe, Discover studio), Sequence analysis (GeneDoc, Accelrys gene, CLC work bench 2, Bioedit.), In silico cloning tools (Gene Constriction kit 2, Vector NTI 9.1 and Plasmid draw 3.2) and phylogenetic analysis tools (PHYLIP, MEGA, Tree Viewer) are available.

6. Details about staff members working in the centre. Name of the Designation Specialization Period of Absorption Staff working Status Mr. Mayank RA M.Sc. August, nil Pokhriyal Microbiology 2007 Ms. Soma SRF M.Sc. Computer March, nil Mondal Science 2007 Ms. S. JRF M.Sc. October, nil Thenmozhi Microbiology 2007 Mr. Rajiv Studentship B.C.A August, nil Ranjan 2007 7. Types of service provided. Bioinformatics Centre at Central Agricultural Research Institute, Port Blair is focused on providing qualify consultancy services in the field of website development, database management and manpower training.Our team here at Bioinformatics centre can assist any progressive organization / institute in developing, integrating and maintaining valuable biological data so that it can be accessible in a safe and comfortable manner.

8. Educational activity with details of placement. 6 M.Sc. (Biotechnology) final year students along with 3 summer training students from mainland universities viz. Bangalore University, Bharathidasan University had successfully completed their dissertation work in field of molecular modeling, structure based drug designing and gene annotation. Currently a total of 11 students from Bharthidasan and Bharathiar University are undergoing their project work.

78 9. Initiative to validate the outcome of bioinformatics resources. N.A

10. Collaborative works/initiatives. A national level conference on “ Bioinformatics tools for gene and protein analysis was conducted in association with Shrimati Indira Gandhi College of Arts and Science (SIGC) , Trichy, T.N was successfully conducted . A total of 450 participants including research scholars, scientists and students from various institutions with in India attended the conference. Also initiative has been taken for further scope of collaboration with ICMR’s regional centre here in the islands and Anna university in the area of molecular modeling and database development.

11. Databases / Software package developed. Along with databases of medicinal plants, economically important pants, rice cultivars, orchids etc, recently Sub-DIC has also developed 4 more databases which include database for Integrated farming system models in A & N Islands, database of Biodiversity of A & N Islands, database for Mango and medicinal plant database.

12. Papers published or presented in the conference with references.

Balakrishnan, M and K.Meena (2006). A back-propagation algorithm applied to forecast coconut yield, AMSE international journal, 69160, tassin la demi-lune (France), Modeling D, Vol.27 n0 2 : pp.75-85.

Balakrishnan, M, 2007. Recent trends in Networking Concepts and communication technologies chapter in Bioinformatics and Statistics in Fisheries research Vol.III, CIFA, Bhubaneshwar, Orissa Vol(3): pp:124-132.

Balakrishnan, M., K.Meena, S.Sethi and A.N. Sarangi, 2007. Neural Network and its Application in Aquaculture chapter in Bioinformatics and Statistics in Fisheries research Vol.III, CIFA, Bhubaneshwar, Orissa Vol (3): pp: 145-151.

Balakrishnan, M., R.C Srivastava and Mayank Pokhriyal (2007). “Databases and Browsing Tools for Gene Prediction”, Bioinformatica Journal, National institute of Science & Technology, Orissa. Vol.1, Vol.4: pp.16-22.

Balakrishnan, M. Recent trends in networking concepts and communication technologies 2006, In Proc. of National workshop cum Training on Bioinformatics and statistics in Aquaculture Research organized by CIFA,(ICAR, Kausalyaganga, Bhubaneswar-751 002, on 7- 10 February 2006, pp.122-129.

Balakrishnan, M., R.Elanchezhian, R.C. Srivastava, Mayank Pokhriyal and Soma Mondal (2007), Database for Rice cultivars of Andaman and Nicobar Islands. In Proc. of International Symposium on Management of Coastal Ecosystem: Technological Advancement and Livelihood Security to organized by ISCAR at Science City, Kolkata, from 27-30 October, 2007, P.19

Balakrishnan, M., R.Elanchezhian, R.C. Srivastava, Mayank Pokhriyal and Soma Mondal (2007), Database for Indigenous Orchids in Andaman and Nicobar Islands. In Proc. of International Symposium on Management of Coastal Ecosystem: Technological Advancement and Livelihood Security to organized by ISCAR at Science City, Kolkata, from 27-30 October, 2007, P.41

79

Balakrishnan, M., N.Ravisankar, K.Meena, R.Elanchezhian, S.K Zamir Ahmed (2007).Yield Prediction through Feed Forward Neural Network Approach for Direct Seeded Rice (Oryza sativa) in Bay Islands. In Proc. of 3rd Indian International Conference on Artificial Intelligence (IICAI-07) NIA, Pune, India from 17-19, December, PP.1533-1541, 2007

13. Initiation of R & D activities in bioinformatics. Sub-DIC is actively indulged in research activities like application of bioinformatics in nucleotide and protein sequence alignment, gene prediction, protein structure prediction and homology modeling, fishing out gene responsible stress tolerance in crop plants and development of ANN model for gene prediction / classification

14. Details of training / workshop organized and total no. of user trained. Sl.No Topic Duration No. of From Participants To

1 One day workshop on 1 day 30 27th Mar bioinformatics and its 2008 application 2 Bioinformatics tools for 4 days 27 26th – 29th gene and protein Analysis July,2006 3 Database Development 5 days 27 19th – 23rd and its Application in February, Biodiversity 2007 4 National Conference on 2 days 450 “Bioinformatics Tools for 7th – 8th Gene and Protein Sept, Analysis” in collaboration 2007 with SIGC, Trichy

15. Impact shown by your centre on the growth of biotechnology and allied areas. The Sub-DIC is assisting research scholars and scientists from neighboring departments / institutes in updating their knowledge in bioinformatics through software’s available in the centre. The centre is also providing training on bioinformatics tools for gene and protein sequence analysis, gene annotation, database designing, web technology to M.Sc. students. Seven M. Sc. (Biotechnology) and 2 B.Tech students from mainland universities viz. Bangalore University, Bharthidasan University had undergone dissertation work and currently 11 M.Sc. (Bioinformatics) and two M.Sc students of Biotechnology and Microbiology are undergoing dissertation work in the Sub- DIC for partial fulfillment of M.Sc. degree.

16. Future activities. • Creation of database for stress responsive genes in agricultural crops • Gene expression studies related to agricultural crops of prime importance in A & N Islands • To design and develop database on plant genetic resources of Bay Islands • Development of Protein Prediction models (computer models) using the concept of Artificial Neural Network (ANN) and Data mining 80 • To establish an agriculture information system for villages in A & N Islands • Development of ANN model for disease prediction

Address Central Agricultural Research Institute Coordinator: Dr. M. Balakrishnan Bioinformatics Centre Biotechnology Section Port Blair E-mail: [email protected]

81 Central Drug Research Institute, Lucknow Coordinator : Dr. Prodyut K Roy

1. Summary of the progress made by the centre from its inception Right afer the creation of the Centre, The BTIS Centre at CDRI, Lucknow styartyed to create a state of the art infrastructure and environment to carry out R& D work in Bioinformatics in the area of drug development. Collection, retrieval and dissemination of Information on biomedical research has been among the missions of the BTIS Centre at the Central Drug Research Institute, Lucknow. BTIS centre has been catering to the information requirements of the users working in the area of Biotechnology. CDRI library which is the base of the BTIS user Centre has been functioning as the National Information Centre for Drugs And Pharmaceuticals (NICDAP) of the department of Science and Technology, Government of India for the last twenty eight years. As such this center has been serving the research community in the area of Drugs and Pharmaceuticals for quite some time. With the establishment of BTIS Center, the user profile of the center has widened to those working in the area of Biotechnology in Drug Research and Pharmaceutical Industry. User profile of the center include:

• Drugs & Pharmaceutical Industry • R&D Institution, CSIR, ICAR, DBT, DOD, State Science & Technology Councils, etc. • Universities/Departments of Biotechnology • Small Entrepreneurs • Students Pursuing Courses in Biotechnology And Bio- informatics • 2. Major research activities in Biotechnology and its related fields at your institution The institute has a major programme in the area of Biotechnology and in all the research projects; Biotechnology is one of the main components. The research Activities of the Institute include:

• Development of Drugs, Vaccines and Diagnostics • Cellular and Molecular Studies to understand Diseases • Cellular and Molecular Studies to understand Disease processes and reproductive physiology • Development of Contraceptive Devices and Agents • Systematic Evaluation of Medicinal properties of Natural products including terrestrial plants and marine flora and fauna • Development of Technology for drugs, intermediates and biologicals • Dissemination of information in the field of drug research, development and production • Consultancy and development of manpower. 2. To create and maintain infrastructure for R& work to be carried out in the Bioinformatic studies by the Centre as well as the scientists of the institute working in the area of drug design and development. Acquisition,

82 Compilation and Dissemination of information on Biotechnology to the people working in the area of Drugs and Pharmaceuticals.

3. Area of Specialization of the centre

4. Major Activities

Bioinformatics BTIS at CDRI initiated Bioinformatics work with the induction of traineesl research students in collaboration with the Molecular and Structural Biology research group of the institute. Two works carried out by the Centre during the year were : . StructuralBioinformatics Studies of Dihydrofolate Reductase Enzyme from Toxoplasma gondii . StructuralBioinformatics Studies of Putative Ubiquitin Conjugating Enzyme from Toxoplasma gondii

Information Services

Being a National Information on Drugs and Pharmaceuticals, our library caters to the information needs os the students, researchers of institutions/ universities involved in biomedical Research all over the country.

• More than five hundred queries from universities, Pharmaceutical industry, R & D organizations etc. are received annually and replied to with the help of available resources.

• Student pursuing postgraduate/ postdoctoral courses in Biotechnology, Pharmacy, Medicinal and Pharmaceutical Chemistry in various universities/ institutions visit the Centre regularly and utilize our resources. More than two hundred visitors from outside Lucknow visit the center every month. They are provided with required information and are helped to retrieve required information from available resources.

• A large number of local users including researchers in local universities and students of biotechnology, pharmacy, Chemical Engineering etc. visit the library on a daily basis to make use of the information resources and infrastructure available in the center.

• On an average two thousand online searches were made monthly by outside users to get information on drugs and pharmaceuticals and biotechnology.

Current Awareness services Current awareness service in the area of drugs and Pharmaceuticals research and pharmaceutical industry has been one of the main activities of the CDRI library, we have, from 2005 onwards, started publishing the two journals under the BTIS banner. The journals

83 are:

Drugs & Pharmaceuticals - Industry Highlights (Monthly) Drugs & Pharmaceuticals - Current R&D Highlights (Quarterly)

The biotechnology aspects of Pharmaceutical industry are given special emphasis in the two bulletins. From 2005 onwards, our emphasis is to cover biotechnology as much as possible in these bulletins. We have also decided to expand our clientele of information seekers among more and more academic institutions and smaller colleges where library and information facility is not very adequate and the bulletins could possibly fill the void. The small entrepreneurs in this field of biotechnology based pharmaceutical industry are also being targeted.

5. Infrastructure facilities in the Bioinformatics Centre (A) We have few computers attached to a server to cater to the users. However, with the grant made available by the BTIS in the year 2004- 2005 we are in process of acquiring more P4 computers and latest version of server. (B) Libsys for Library Networking • R&D Insight online & CD • Science direct (1800 journals) • Pharmacopoeias on CD • About 3400 online journals of all major publishers • More than 350 journals majority of which are foreign journals.

6. Staff Members associated with the center: Dr. P.K. Roy, Coordinator Dr. Sheela Tandon Mr. A.K. Srivastava Mr. S.K. Mallik Mrs. Seema Mehrotra Mr. Zafar A. Zaidi Mr. V.K. Vohra Mr. W. F. Rahman They are all working as regular employees of the institute for the last 15-20 years.

7. Types of services provided Current Awareness service in the Area of Biotechnology in Drug Development. Information Dissemination Query Service Full text Delivery Service

8. Educational activities with details of placement -

9. Initiative to validate the outcome of bioinformatics resources

84 Many Services were provided to the outside users on payment. The continuance at the users with the center and continuous inflow of information requests from existing users validate the resources.

10. Collaborative works/ initiatives Efforts are on to carry out more collaborative initiatives on the pattern of Lucknow Special Libraries Consortium. The Centre is a part of DELNET and would like to join hands with other BTIS Centres.

11. Databases/ Software packages developed Database already completed : • Natural Products And Medicinal Plants • Scientific serials available in Lucknow • Papers published by CDRI since 1951 Databases in progress: • Profile of Drugs under newly approved Drugs • Indian Patents

12. Papers published or presented in the conferences with reference • Ahmed, S Dul Qui, BX and Walworth, N Msc1 Acts through Histone H2A.Z to Promote chromosome stability in Schizosacchromyces pombe Genetics 177,1487-1497 • Akhtar, MS and Bhakuni, V Role of ionic interactions and linker in the domain interaction and modulation of functional activity of hyaluronate lyases Biochemical And Biophysical Research Communications 353,286-292 • Avasthi, Kamlakar Farooq, Sheikh M Bal, Chandralata, Kumar, Rishi Tewari, Ashish K and Maulik, Prakas, R Design and synthesis of pyrazolo[3,4-d]pyrimidine and triazolo[4,5- d]pyrimidine based dissymmetrical ‘Leonard linker’ compounds: 1H NMR and crystallographic evidence for folded conformation due to arene interactions Journal of Molecular Structure 842, 100-108 • Avasthi, Kamlakar Farooq, Sheikh M Aswal, Sangeeta Raghunandan, Resmi and Maulik, Prakas R 1H NMR and crystallographic evidence for tolerance of bulky electron withdrawing methanesulfonyl group on robustness of the U-motif in pyrazolo[3,4- d]pyrimidine core based ‘Leonard linker’ compounds and formation of plus (+) motif Journal of Molecular Structure 827, 88-94 • Bal, NC Agrawal, H Meher, AK and Arora, A Characterization of peptidyi-tRNA hydrolase encoded by open reading frame Rv1014c of Mycobacterium tuberculosis H37Rv Biological Chemistry 388, 467-479 • Bhadauria, S Singh, G Sinha, N and Srivastava, S Isoniazid Induces Oxidative Stress, Mitochondrial Dysfunction And Apoptosis In Hep G2 Cells Cellular and Molecular Biology 53, 102-114 • Guha, Mithu Choubey, Vinay Maity, Pallab Kumar, Sanjay Shrivastava Kumkum Puri, Sunil K and Bandyopadhyay, Uday Overexpression, purification and localization of apoptosis related protein from Plasmodium falciparum Protein Expression And Purification 52, 363-372 • Gupta, R Chakrabarti, P Dikshit, M and Dash, D Late signaling in the activated platelets up regulates tyrosine phosphatase SHP1 and impairs platelet adhesive functions: Regulation by calcium and Src kinase Biochimica Et Biophysica Acta (BBA) - Molecular Cell Research 1773131-140 • Gupta, SK Sisodia, BS Sinha, S Hajela, K Naik, S Shasany, AK and Dube, A Proteomic approach for identification and characterization of novel immunostimulatory proteins from soluble antigens of Leishmania donovani promastigotes Proteomics 7, 816-23 • Gupta, Subash Chandra Siddique, Rahman Hifzur, Mathur, Neeraj Vishwakarma, Lal Achchhe Mishra, Ranjit Kishore, Saxena, Krishna Daya and Chowdhuri, Debapratim Kar Induction of hsp70, alterations in oxidative stress markers and apoptosis against dichlorvos exposure in transgenic Drosophila melanogaster: Modulation by reactive oxygen species Biochimica et Biophysica Acta(BBA) - General Subjects 1382-1394 85 • Gupta, Swati Dube, Anuradha and Vyas, Suresh P Antileishmanial efficacy of amphotericin B bearing emulsomes against experimental visceral Journal of Drug Targeting 15, 437-44 • Jain, Akhlesh K Chalasani, KB Khar, RK Ahmed, FJ and Diwan, PVMuco-adhesive multivesicular liposomes as an effective carrier for transmucosal insulin delivery Journal of Drug Targeting 15, 417 427 • Laughton, CA Luisi, BF Pratap, JV and Calladine, CR potential molecular switch in an alpha helical coiled coil Proteins 70, 25-30 A • Lella, RK and Sharma, C EIS (enhanced intracellular survival) protein of mycobacterium tuberculosis disturbs the cross regulation of T-cells J Biol Chem 282, 18671-75 • Lundåsen, T Hunt, MC Nilsson, LM Sanyal, S Angelin, B Alexson, SE and Rudling, M PPARalpha is a key regulator of hepatic FGF21 Biochemical and Biophysical Research Communications 360, 437-440

• Meher, Akshaya K Lella, Ravi K Sharma, Charu and Arora, Ashish Analysis of complex formation and immune response of CFP-10 and ESAT-6 mutants Vaccine 25, 6098- 6106 • Misra, Gauri Aggarwal, Anita Mittal, Sonia Singh, Yogendra and Ramachandran, Ravishankar Purification, crystallization and preliminary structural analysis of nucleoside diphosphate kinase from Bacillus anthracis Acta. Cryst. Sect F 63, 1084-1086 • Naim, M Bhat, Sathesh Rakin, KN Dennis, S Choudhury, SF Siddiqi, M Imran Drabik, P Sulea, T Bayly, C Jakalian, A and Purisima, EO Solovated interaction energy (SIE) for scoring protein ligand binding affinities.1. Exploring the parameter space J Chemical Information & Modeling 47, 122-133 • Raghu Ram, EVS Kumar, Biswas, A Kumar, S Chaubey, AS Siddiqui, MI and Habib, S Nuclear gyr B encodes a functional subunit of the Plasmodium falciparum gyrase that is involved in apicoplast DNA replication Molecular & Biochemical Parasitology 154, 30- 39 • Rawal, Ravindra K Kumar, Ashutosh Siddiqi, Mohammad Imran and Katti, Setu B • Raza, S, Sahasrabuddhe, AA and Gupta, CM Nuclear localization of an actin-related protein (ORF LmjF21.0230) in Leishmania (+) Molecular & Biochemical Parasitology 153, 216-219 • Sanyal, S Båvner, A Haroniti, A Nilsson, LM, Lundåsen, T Rehnmark, S Witt, MR Einarsson, C Talianidis, I Gustafsson, JA and Treuter, E Involvement of corepressor complex subunit GPS2 in transcriptional pathways governing human bile acid biosynthesis Proceedings of the National Academy of Sciences USA104, 15665- 15670 • Shagufta, Kumar Ashutosh, Panda, Gautam and Siddiqi, Mohammad Imran CoMFA and CoMSIA 3D-QSAR analysis of diaryloxy-methano-phenanthrene derivatives as anti- tubercular agents Journal of Molecular Modeling (Online) 13, 99-109

• Sharma, Sarita and Bhakuni, Vinod Cloning and structural analysis of Mycobacterium leprae serine hydroxymethyltransferase Protein Expression and Purification 55, 189- 197

• Sharma, Sharad Kumar Gupta, Chittarmal, Dwivedi, Varun Misra-Bhattacharya, Shaija and Owais, Mohammad Prophylactic potential of liposomized integral membrane protein of Plasmodium yoelii nigeriensis against blood stage infection in BALB/c mice Vaccine 25, 2103-2111

• Singh, Ashok Chandra, Saurabh Gupta, Shrawan Kumar Chauhan, LKS and Rath, Srikanta Kumar Mutagenicity of leachates from industrial solid wastes using Salmonella reverse mutation assay Ecotoxicology And Environmental Safety 66, 210-216 • Singh, K and Bhakuni, V Cation induced differential effect on structural and functional properties of Mycobacterium tuberculosis alpha-isopropylmalate synthase BMC Struct Biol 9, 39 • Singh, R Shasany, AK Aggarwal, A Sinha, Sudhir Sisodia, BS Khanuja, SPS and Misra, R Low molecular weight proteins of outer membrane of Salmonella typhimurium are immunogenic in Salmonella induced reactive arthritis revealed by proteomics Clinical and Experimental Immunology 148, 486-493 86 • Song, GY Gibson, G Haq, W Huang, EC Srivastava, T Hollstein, M Daftarian, P Wang, Z Diamond, D and Ellenhorn, JD An MVA vaccine overcomes tolerance to human p53 in mice and humans Cancer Immunol Immunother 56, 1193-205 • Srivastava, Sandeep Kumar Dube, Divya Kukshal, Vandana Jha, Ashok Kumar Hajela, Kanchan and Ravishankar, Ramachandran NAD+ -dependent DNA ligase (Rv3014c) from Mycobacterium tuberculosis : Novel Structure-function relationship and identification of a specific inhibitor Proteins : Structure, Function And Bioinformatics 69, 97-111 • Srivastava, V Rouanet, C Srivastava, R Ramalingam, B Locht, C and Srivastava, BS • Tripathi, T Rahlfs, S Becker, K and Bhakuni, V Glutathione mediated regulation of oligomeric structure and functional activity of Plasmodium falciparum glutathione S- transferase BMC Struct Biol 17, 67 • Vatsyayan, Rit and Roy, Uma Molecular cloning and biochemical characterization of Leishmania donovani serine hydroxymethyl transferase Protein Expression And Purification 52, 433-440 Yadav, Sharada Prasad Ahmad, Aqeel and Ghosh, Jimut Kanti Addition of a small hydrophobic segment from the head region to an amphipathic leucine zipper like motif of E. coli toxin hemolysin E enhances the peptide-induced permeability of zwitterionic lipid vesicles Biochimica Et Biophysica Acta (BBA) – Biomembranes 6, 1574-1582

13. Initiation of R&D activities in Bioinformatics Structure–based anti–TB and anti–leishmania design Leishmania denovani serine hydroxyonethytransferase [SHMT] and chrosimate synathase [MTCS] have been identified for understanding mechanistic and structural information 14. Details of Training/ Workshop organized and total no. of user trained • Training provided to 13 students of students of information science giving them on-the-job training facility for a period of 6 months to 1 year. • One MSc. Biotechnology is undergoing studentship under the BTIS programme.

15. Impact shown by your centre on the growth of biotechnology and allied areas 16. Future activities With the acquisition of the hardware and other information resources made available with the fund of BTIS, the center plans to: • Modernize the information base of the center with introduction of state of the art hardware facilities. • To subscribe to the more user friendly and broader coverage databases to cater to the changing needs of users. • To develop in-house databases in the areas hitherto untouched by others. (Mostly information on work being carried out in Indian institutions and Indian Biotechnology based pharmaceutical companies.) • To have a network within the institute where Biotechnology information will be available on-line. • Procure state of the art information dissemination techniques and resources. • To bring out a monthly Newsletter (on-line) of the Biotechnology Information and activities of the BTIS Centre.

Additional Details:

Name of the coordinator: Dr. Prodyut K Roy Dy. Director & Scientist-in-Charge 87 Doc. & Library Services Division Central Drug Research Institute Lucknow-226001

Phone No.: 522-2613812 Fax. No. 522-623405 Email [email protected] Website: www.cdriindia.org Name of the Contact Person S K Mallik Email: [email protected]

88 Central Institute of Freshwater Aquaculture, Bhubaneswar Coordinator : A.K. Roy

1. Summary of the progress made by the centre from its inception The Central Institute of Freshwater Aquaculture (ICAR), Kausalyaganga, Bhubaneswar established during 1990-91 is a Distributed Information Sub- Centre (Sub-DIC) under Biotechnology Information System (BTIS) Network of the Department of Biotechnology, Ministry of Science & Technology, Government of India. The centre is specialized in the field of Aquaculture and serves as an information source in the country.

2. Major research activities in Biotechnology and its related fields in your Institution

¾ Statistical Analysis of Genomic sequence of Carps viz. Labeo and Cyprinus using SPSS package. ¾ Sustainable genetic improvement of Rohu (Lebeo rohita) for growth through selective breeding. ¾ DNA fingerprinting of fish microbial pathogens using RAPD-PCR. ¾ Development of DNA markers in Indian major carp, Labeo rohita for studying population genetic variation and identification of trait associated genes

3. Area of Specialization of the Centre: Aquaculture

4. Major activities of the Center during the year 2007-08

(A) Organisation of National Workshop:

¾ Workshop: On Bioinformatics and Statistics in Aquaculture Research during 22nd to 25th January, 2007 ¾ Inaguration: By Mr.Amiteshwar Dayal Seth, Manager, Infosys. ¾ Participants and resource persons: 51 participants comprising research scholars, scientists, associate lecturers, project Assistants and 30 Resource Persons ¾ Organisations/Institutes: IIT-Kharagpur, CDAC, Kolkata, ISI, Kolkata, CIFRI, Kolkata, BCKV, Kalyani, CRIDA, NAARM, Hyderabad, VIT, Vellore, CIBA, Chennai, IASRI, New Delhi, NCAP, New Delhi, RRL, Bhubaneswar, OUAT, Bhubaneswar, CIFRI, Berrackpore etc. ¾ Course content: Data Warehousing, Reverse Engineering of Gene Regulatory Network by Neural Network, Data mining and Databases, Modeling and Forecasting and Genetic Statistics, Econometric Analysis, Knowledge Discovery, etc.

(B) Genomic Sequence, Micro array Analysis and Modeling:

¾ Correspondence Analysis of relative synonymous codon usage values of nucleotide sequences of Labeo rohita and genes of Cyprinus carpio ¾ Statistical Analysis of Microarray data of Common carp. ¾ Modeling and Forecasting of Fish Production in India.

5. Infrastructure facilities in the Bioinformatics Centre

89 (A) Computer & Communication facility Hardware: PC's; Multimedia PC; Server; CD Mirror server; Macintosh SE; 1 KVA UPS; Dot Matri, HP DeskJet, HP LaserJet Printers; Cannon Bubble jet Printers; LCD; Color Scanner; Modem; CD Writer; 5.5 KVA Generator. Software: MS Office 97, 2000; Novel Netware 4.1; SPAR1; FoxPro; QPRO; Oracle; M.S. Project; Visual Studio. Operating System: DOS; Windows 95, 98, XP; UNIX; Linux. Communication and Network Linkage: The centre has acquired upgraded and maintenance the following communication facilities: BSNL Lease Line 512 kbps. Local Area Network (LAN): More than 100 Computers are distributed to different scientists, researchers and officers of the Institute and connected with the BTIS centre through LAN and IP based.

(B) Scientific Software Packages Statistical Analysis System (SAS); Statistical Package for Social Science (SPSS) version14.0; Quantity one (gel analysis); DNA Star; UVI – Software (gel analysis).

(C) Databases & Other Information Resources Renewed Aquatic Sciences and Fisheries Abstracts (ASFA) online of CSA; The FAO Fisheries Atlas; Diagnosis of Shrimp Disease –FAO; FAO - ICLARM (Stock assessment tool); FishstatPlus (V 2.3) – FAO, 2006; Archives of the Bay of Bengal Programme; Fish Base. FAO.

6. Details about staff members working in the centre (Name of the staff, Designation, Specialization and period of working) Sl. Name Designation Specialisation Period of working No. 1. Mr. A. K. Roy Pr. Scientist Ag. Statistics Sept. 96 to till date 2. Mrs. N. Panda T-6 Statistics Feb,2005 to till date 3. Mr. D. P. Rath T-4 Comp. 12.10.1990 to till date Application 4. Mr. S. N. Rath Studentship Bioinformatics Dec 2007 to 01.04.2007 5. Ms. S. R. Martha Studentship Bioinformatics 14.04.2007 to till date

7. Types of services provided

The services include, internet browsing, online and offline bibliographic databases search, statistical data analysis, creation of presentations, Photo scanning, printing, loading of software packages and trouble shooting.

8. Educational activities with details of placement ¾ Students (M.F.Sc) are regularly trained on application of Computers, software packages and Bioinformatics in Aquaculture Research. ¾ The training facilities are availed to research workers of various reputed organizations viz., Utkal University, ICMR, RRL, Regional College of Education. ¾ By the studentship and traineeship programmes students are regularly trained in Bioinformatics. 90

9. Initiative to validate the outcome of bioinformatics resources

Feed back through evaluation and impact of various workshops on ICT application indicated that Research workers from around the country are showing lots of enthusiasm in using on-line bibliographic search facilities of ASFA and use of statistical packages for multivariate data analysis. Lack of infrastructure facilities at various fisheries colleges/institutions in the country is retarded by the use of modern technologies by the trained researchers. Hands on training programme of longer duration are in demand.

10. Collaborative works/ initiatives

The Centre collaborates with various National and International Organizations like IASRI, NBFGR, CIBA, CMFRI, CIFRI, FAO/UNDP, NACA, World Fish Centre, etc. for exchange of information related to fisheries in the form of CD ROM database, software, etc.

11. Databases/ Software packages developed

Database system on socio-economic status of fish farmers is developed to provide in- depth details of socio-economic conditions of fish farmers of Kolleru Lake, which will support in boosting up the result oriented research and development of fish farmers.

12. Papers published or presented in the conferences with reference

¾ Roy, A. K, S. R. Martha and S. N. Rath. 2007. Correspondence Analysis of Codon Usage in Labeo rohita, International Symposium on Chromosome to Genomes (c2g), held during 3-5 July 2007 at CCMB, Hyderabad, India. 9 -10 (Abs.). ¾ Roy, A. K. and Martha. 2007. Correspondence Analysis in Study of Genomic Sequence of Labeo rohita, 8th Asian Fisheries Forum (8aff), Kochi held during 20 - 23 November 2007. 317 – 318 (Abs.GMO 008). ¾ Roy, A. K. and Martha. 2007. Multivariate Statistical Analysis of Codon Usage values of L. rohita. International Conference on Applied Bioengineering held at Chennai during 5th-7th December 2007(Abs.). ¾ Roy, A. K. and N. Panda, 2007. Study on Trend of Growth of Fish Production in North Eastern States in India. National seminar on Recent Advances and Rebuilding of Fish and Fisheries in North East India. Dept. of Pisci cult., St. Antony’s College, Shillong-793001. ¾ Roy, A.K., N. Sarangi and G. S. Saha, 2007. Estimation of Impact of Socio-economic and Farm specific variables on Technical Efficiency of Carp Culture Farms of Kolleru Lake, Andhra Pradesh, India. 8th Asian Fisheries Forum held at Cochi, India during 20-23 Nov., 2007. ¾ Roy, A. K. and N. Panda, 2007. Projection of Freshwater Aquaculture Fish Production in India. 8th Asian Fisheries Forum held at Cochi, India during 20-23 Nov., 2007. ¾ Roy, A. K., N. Panda and D.P. Rath, 2007. Forecasting of Culture Fishries Production in India. National symposium on Ecosystem health and fish for

91 tomorrow held at Bartackpore during 14-16 Dec., 2007 organised by IFSI, Barrackpore

13. Initiation of R&D activities in Bioinformatics

¾ Application of Statistics in Bio informatics related to Aquaculture. ¾ Genomic Sequence and Microarray Analysis of Carps.

14. Details of Training/ Workshop organized and total no. of users trained

Sl Name of the Training/Workshop Duration No. of No participants 1 National Workshop on Perspectives in Bioinformatics and February 11 Its Application to Aquaculture 22-26, 1994. 2 National Workshop on Networking and Biological Data February 23 Analysis 4-6, 1997 3 National Workshop on Information Technology in February 49 Aquaculture Research 10-13, 1998 4 National workshop cum Training Programme on February 28 Bioinformatics and Statistics in Aquaculture Research 2-5, 1999. 5 National workshop cum Training Programme on February 33 Bioinformatics and Statistics in Aquaculture Research 8-11, 2000 6 National workshop cum Training Programme on January 43 Bioinformatics and Statistics in Aquaculture Research 16-19, 2001 7 National workshop cum Training Programme on January 34 Bioinformatics and Statistics in Aquaculture Research 08-11, 2002. 8 National workshop cum Training Programme on February 51 Application of Bioinformatics and Statistics in Aquaculture 4 - 7, 2003

9 National Training Programme on Application of June 15 Bioinformatics and Statistics in Aquaculture 03 - 06,2003 10 National workshop cum Training Programme on Recent February 52 Development in Bioinformatics and Statistics in 10-13, 2004 Aquaculture, 11 National workshop cum Training Programme on February 39 Bioinformatics and Statistics in Aquaculture 7-10,2006 12 National workshop cum Training Programme on January 22- 51 Bioinformatics and Statistics in Aquaculture 25,2007 Total 429 15. Impact shown by your center on the growth of biotechnology and allied areas. In this you may highlight the details like number of papers published with the help of your center, how your center is promoting various activities of your organization and neighboring institutions, manpower trained, tools developed, patents & copyrights acquired and other services offered etc. ¾ Over five hundred researchers representing various organizations (State & Central) spread all over the country have been trained in application of Bioinformatics & Statistics in Aquaculture Research. ¾ Bibliographic literature search from ASFA are frequently provided to people. ¾ Analysis of Genomic and Microarray data using codon usage and SPSS package.

92 ¾ Web Publication: Web site of CIFA (http://www.cifa.in) has been hosted and updated from time to time with relevant resources on fisheries/aquaculture for sharing of knowledge. ¾ Books published: 1. Roy, A.K. and N. Sarangi. 2007. Bioinformatics and Statistics in Fisheries Research, Vol-III. Central Institute of Freshwater Aquaculture (CIFA), Kausalyaganga, Bhubaneswar. Pp. 558. 2. Roy, A.K. and N. Sarangi. 2007. Applied Bioinformatics, Statistics and Economics in Fisheries Research. NIPA, New Delhi. Pp. 550.(In Press).

16. Future activities

¾ Statistical Analysis of Microarray data in Fisheries ¾ Development of Biophysical and Econometric model through input-output analysis ¾ Modernisation of the present infrastructure ¾ Modelling and forecasting

Additional Details: Name of the Coordinator A.K. Roy Postal Address: Bioinformatics Centre, Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar - 751002 Phone Number: 0674-2465430 Fax No.: 0674-2465407 Email: [email protected]

93 Central Institute of Medicinal and Aromatic Plants, Lucknow Coordinator: Dr. Ashok Sharma

1. Summary of the progress made by the centre from its inception:

Bioinformatics Centre, since its inception in 1999 is the backbone of information need of all research activities in CIMAP, Lucknow. The centre started its R&D activities in the areas of Bioinformatics and research activities undertaken include database development, Software development and computational analysis in areas such as Genomics, Transcriptomics, Proteomics, Metabolomics, microsatellite markers identification, drug target identification, lead molecules identification and computer aided drug designing in Medicinal & Aromatic Plants. Apart from R&D activities, Bioinformatics Centre continues to provide facility and technical support for all IT and internet based services to scientific staff onto their desktop and to research scholars of CIMAP and nearby institutions. Centre continued to provide Human Resource Development through its summer and winter training programs.

2. Major research activities in Biotechnology and its related fields at your institution:

Characterization of biodiversity and conservation of genetic resources of medicinal and aromatic plants (MAPs) and other plants of interest; Defining of genes relating to the yield determining steps of metabolic pathways concerned with chemicals of interest and their modulation; Construction of transgenic plants; Detection and characterization of new anti-microibal, anti- cancer/ or pesticidal chemicals of herbal origin and their commercialization; Building up of MAP related databases; Development of human resources for R&D in the basic and applied areas of MAP science.

3. Area of specialization of the centre:

Bioinformatics of Medicinal & Aromatic Plants (MAPs).

4. Major activities of the centre during the year 2007-08:

In Silico analysis of SSR’s in ESTs corresponding to alkaloid, phenylpropenoid and terpenoid biosynthetic pathways in medicinal and aromatic plants; In Silico analysis of cytochrome P450 in medicinal plants; In Silico analysis of metal binding sites to study phytoremediation in medicinal plants; In Silico designing of oligonucleotides using ESTs of Mentha species; In Silico studies of alkaloid biosynthetic pathways in medicinal and aromatic plants; In Silico study of distribution and functional characterization of terpenes in plants; dbAlkaloid: A comprehensive database of alkaloid biosynthesizing genes; DbAlBioPath: A database on alkaloid biosynthesis pathways; DBMDR: A comprehensive database of MDR genes; dbTerpene: A comprehensive database of Terpenes; Database on menthol biosynthetic pathway

5. Infrastructure facilities in the Bioinformatics Centre: 94 A. Computer & Communication facility

Fiber optic based LAN with managed switches (>350 nodes) 2 MBPS radio link internet connectivity, Silicon Graphics Interface fuel station package, Sun Microsystems, IBM Pentium 4 with HT technology system, HP systems.

B. Scientific Software packages

GenoCluster package, SYSSTAT package, VMD 1.8.2 Viewer, Rasmol Viewer, Swiss PDB viewer, Pymol View, BioEdit, AutoSignal V.1.7, MGL Tools – Autodock tools, PMV, Sigmaplot, Cygwin, Modeller 7V7, DTMM, VeGA ZZ, Clustal X, Matlab V. 7.0, NAMD 2.4, Bioperl 0.7.2, Biojava 1.20, hmmer 2.1.1, Phylip, Python 2.5, Python 2.4, Emboss, Win pep 1.0, Threader, Octave, MDL Chime SP6, TurboC2, Tree View 32, Procheck_NT, blast-2.2.14-ia32-win32, modeller9v1, ActivePerl-5.8.8.822-MSWin32-x86- 280952, Cn3D-4.1, ACDLAB 8.0, Cluster, D2OL, MDL ISIS Draw 2.5 MS Visual Studio. Net, OCR Fine Reader, Macromedia MX, Oracle 9i, Application Server, Adobe Acrobat, MS Back Office Server 2000.

C. Database & other information resources:

a. Bibliographic Databases on CD-ROM Agris, Agricola, Medline, Biotechnology Abstract, Altmedex b. E-Journal Gateway Platform J-Gate (Agricultural & Biological Sciences) c. In Diskettes Current contents (Agriculture, Biology & Environmental Sciences), Abstract Edition from Vol.34 onwards. d. E-Journals (Through CSIR e-journals Consortium) Elsevier, Blackwell, Springer-Kluwer, Oxford University Press, Wiley, Royal Society of Chemistry, American Chemical Society, Cambridge University Press.

6. Details about Staff members working in the centre (Name of Staff, Designation, Specialization and period of working): Name of the Staff Designation Specialization Period of Absorption working status Dr. Ashok Sharma Scientist-F & Head Bioinformatics Permanent Permanent Feroz Khan Scientist-C Bioinformatics Permanent Permanent Kumar Parijat Project Assistant Bioinformatics 6-6-2006 Contractual Tripathi Sudeep Roy Project Assistant Bioinformatics 16-10-2006 Contractual Akansha Saxena Research Intern Bioinformatics 12-3-2007 Contractual Sanchita Project Assistant Bioinformatics 17-9-2007 Contractual Manoj Mishra Project Assistant IT 10-11-2006 Contractual Naresh Sen Project Assistant IT 20-9-2007 Contractual

95 7. Types of services provided:

E-mailing, Internet access, LAN management, System management, Web designing & hosting, Software development, Database development on MAPs, Digitization of MAPs information, Human Resource Development in Bioinformatics of MAPs, R&D and S&T Publications, Computational services, Information support.

8. Educational activities with details of placement:

• CIMAP-JNU Ph.D Programme in Life Sciences (Biotechnology and Bioinformatics) • Students placed as scientists in CSIR labs- ITRC, NBRI, as Faculty in University – Banasthali Vidyapeeth, Banasthali, as R&D staff – SGPGI, Lucknow and several others organizations like TCS, Mumbai

9. Initiatives to validate the outcome of Bioinformatics resources:

The activities of the centre has helped in popularizing the concept, utilities and tools of Bioinformatics among the user organizations and individuals. Centre has successfully met their information requirements. New databases in the areas of MAPs has been generated. The network and services created is playing instrumental role in communication, database research, patent searches and market search.

10. Collaborative work/initiatives:

Lucknow University, Lucknow, Bundelkhand University, Jhansi, Jawaharlal Nehru University, New Delhi, Allahabad Agricultural Institute, Allahabad, Veer Bahadur Singh Purvanchal University, Jaunpur, Mother Teresa Women’s University, Kodaikanal, Choudhary Charan Singh University, Meerut, Banasthali Vidyapeeth, Banasthali, Barktullah University, Bhopal.

11. Databases/Softwares packages developed: • DbAlBioPath: A database on alkaloid biosynthesis pathways • dbTerpene: A comprehensive database of Terpenes • MBiopath: A database on menthol biosynthesis pathway

12. Papers published or presented in the conferences with references • Ashok Sharma, Tanuja Rastogi, Menakshi Bhartiya, AK Shasany, SPS Khanuja. 2007. Type 2 diabetes mellitus: phylogenetic motifs for predicting protein functional sites. Journal of Biosciences 32(5): 999-1004. • Khanduri S, Roy S, Tripathi KP, Saxena A, Saxena A, Sharma A, Khanuja SPS. 2007. Putative metal binding motifs: An in silico analysis to study phytoremediation in medicinal plants. International Conference on Bioinformatics and Drug Designing (BIOCONVENE 2007), Hyderabad, 20- 22 December, 2007. • Tripathi KP, Khanduri S, Sudeep Roy, Saxena A, Sharma A, Khanuja SPS. 2007. Functional perspectives of SSR’s corresponding to alkaloid, terpenoid and phenylpropanoid biosynthesis. International Conference on

96 Bioinformatics and Drug Designing (BIOCONVENE 2007), Hyderabad, 20- 22 December, 2007. • A Saxena, Sudeep Roy, KP Tripathi, A Saxena, Sanchita, Manoj Mishra, J Singh and Ashok Sharma. 2007. Biopiracy of traditional knowledge: IPR protection. National Convention & Seminar on Business Enabling of Aromatic Plants Products (BEAP-2007), DehraDun, 21-22 November, 2007.

13. Initiation of R&D activities in Bioinformatics:

Genomics, Transcriptomics, Proteomics & Metabolomics (‘Omics’ sciences) studies in the area of MAPs.

14. Details of Training/Workshop organized and total no. of user trained: • One month CIMAP Summer Training on Techniques and Tools of Biotechnology and Bioinformatics (CST-2007) held during June-July, 2007. Trained 30 students. • One month CIMAP Winter Training on Techniques and Tools of Biotechnology and Bioinformatics (CWT-2007) from January – February, 2008. 24 students are likely to participate. • Dissertation/project work: Ten student’s trainees (B.Tech./M.Sc.) completed their six months training/dissertation at our centre.

15. Impact shown by the Centre:

Bioinformatics Centre of CIMAP, Lucknow is continuously progressing towards the centre of Excellence in the R&D of MAPs Bioinformatics. The extensive research is going on the secondary metabolism of MAPs, genomic sequence analysis (ESTs) for SSRs markers development on various MAPs plants e.g. Mentha, Catharanthus etc. Beside this, some of the impacts shown by the Centre are: Strengthen the ongoing research projects; Successfully organized the Bioinformatics training & teaching & contributed to manpower development.

16. Future activities:

Bioinformatics R&D in metabolic pathway modeling, computer-aided drug design, genomics, proteomics, protein structure prediction, phylogenetics, transcriptomics, metabolomics with particular reference to medicinal & aromatic plants; To organize short term training & workshop annually for the benefits of researchers involved in biotechnological/bioinformatics research; To develop teaching/training package in Bioinformatics with particular reference to the course work for Ph.D. research scholars; To cater the regional & national needs, the work on the specific databases development; Construction of Bioinformatics resource server.

Additional details: Name of the Coordinator : Dr. Ashok Sharma Postal Address : Central Institute of Medicinal & Aromatic Plants, P.O. CIMAP, Lucknow-226015 Phone Number : 0522-2357133 Mobile : 09839075970 97 Fax No. : 0522-2342666 Website : www.cimap.res.in Name of Contact Person : Dr. Ashok Sharma Email : [email protected] [email protected]

98 Central Plantation Crops Research Institute, Kasaragod, Kerala Coordinator : Dr. George V. Thomas

1. Summary of the progress made by the centre from its inception The center was initiated in 2001. During the last seven years the centre has concentrated on development of databases on plantation crops viz. cocoa, coconut and arecanut. The centre has developed eighteen databases covering different aspects of mandate crops dealt by the institute. The centre has also contributed for human resources development activities and conducted eleven training programs on various topics related to bioinformatics and information technology with specific reference to Plantation crops. Twelve students have completed their project work and four are doing their project work under studentship program. Seven were trained on different aspects of bioinformatics applications and at present three are getting training as part of traineeship program. A brainstorming session was conducted on Databases for the Management of Genetic Resource on Horticultural Crops. The Centre provides web- based services at http: www.bioinfcpcri.org. The centre has also developed and customized two softwares. 2. Major research activities in Biotechnology and its related fields at your institution ¾ Molecular markers based characterization of conserved coconut germplasm in national gene bank and selected farmer’s varieties in the IPGRI/COGENT poverty reduction site in India. ¾ Development of Molecular markers to fingerprint coconut accessions. ¾ Molecular studies for tagging root (wilt) resistance genes in coconut. ¾ Tissue culture for rapid multiplication of elite genotypes and basic studies in coconut ¾ Early sex determination and in vitro multiplication in palmyrah palm. ¾ In vitro Multiplication of Coconut and Arecanut ¾ Developing coconut molecular marker database.

3. Area of Specialization of the centre Bioinformatics applications in plantation crops (coconut, arecanut and cocoa) 4. Major activities of the centre during the year 2007- 08 During the reporting period the center has developed three databases Palm database, Copgene data base and Stress gene data base. Other databases were updated regularly. These databases are IP restricted and limited accessibility is provided at the website http:// www.bioinfcpcri.org. During this period the center has conducted a ten days training programme on “Applications of Bioinformatics and Biotechnology in Plantation Crops Research”. At present four bioinformatics students are doing their studentship project and three trainees are getting training under traineeship programme. 5. Infrastructure facilities in the Bioinformatics Centre a. Computer & Communication facility IBM web server, LAN server, Pentium 4 Computers, Nodes, UPS and other accessories with 512 Kbps leased line connectivity from BSNL. b. Scientific Software packages

99 Data mining and analysis tools 1. EMBOSS – Jemboss 2. GDE – Genetic Data Environment (Blast, Fasta, NCBI Tools, Read seq, Primer3, Fast PCR, SCPrimer, Phylip, Clustal W or X, Tree Tools etc.) 3. Staden Package 4. Forage 5. Protein docking software – Hex, Argus lab 6. Phred, Phrap, cap3 Phylogenetic & Map making Softwares 1.NTSYS 2.Phylip 3. Total Lab 4. Arelequin 5. Mapmaker 6. QTL 7. Popgene Bootable CDs with Bioinformatics software 1.Biolinux 2. Vigyann CD 3. DNA linux c. Databases & other information resources: 1. NISC Discover 2. Agris 3. Agricola 4. HortCD 5. Soil CD 6. CAB Pest CD 7. Tropag and Rural CD 8. Indian Science Abstracts on CD 9. AgEcon CD 6. Details about staff members working in the centre (Name of the staff, Designation, Specialization and period of working. Please indicate their absorption status) 1. Ramesh Kumar. 2.P.Saritha. 3. V.Sreesmitha 4. Anoop Raj P 5. Nishad.K.P Acting Information Officer Project Assistant Project Assistant Computer Data Entry Information Science M.C.A Bitechnology Operator Operator Six years (Permanent) 3 Months 1 month MCA DCE (Temporary) (Temporary ) 8months 3 months (Temporary ) (Temporary )

6. Types of services provided : Provides facilities to analyze the protein structure prediction and nucleotide / protein sequence homology search and molecular docking using bioinformatics softwares and tools. • Provides web based access to databases • This center provides internet services for data mining, literature survey etc. • Conducts training programmes and workshops in the field of Bioinformatics. 8. Educational activities with details of placement Under studentship program four students are doing their projects on following topics. a)Molecular marker database for coconut germplasm accessions. b) Molecular phylogenetic studies in palms. c) Database of coconut from root wilt endemic areas d)Validation of EST-SSRs in coconut and Cocoa e)Isolation and charecterisation of insect odorant binding proteins f)Detection of phytoplasma in palms using molecular technique 100 9. Initiative to validate the outcome of bioinformatics resources Researchers of the institute are using the software and databases developed by the centre. • The research community is utilizing all databases. • Software developed by the centre is being used for analyzing sequence data and protein structure. 10. Collaborative works/ initiatives Collaborative activities are taken up with the other Bioinformatics Centres working on similar crops. 11. Databases/ Software packages developed During this period 2006 –07 the centre has developed following databases. a. Palm database A database of Palm Resources. belonging to the family Arecaceae. The palms are monocots and have 202 described genera with about 2779 species. Evaluation of relationships among palms through molecular and morphological tools could provide some interesting insights to their phylogeny and its classification. This database provide genomical approaches and taxonomical details of Palms. b. Copgene database: Coconut and Oil palm putative gene annotated database provide the blast results and gene information of EST & Contigs of above crops. c.Stress gene database: Many genes and proteins are playing an important role in plantation crops. Dehydrin , DREB (Binding factors & transcription factor), Heat shock protein, LEA-Late Embryogenesis abundant, LTP- Lipid transfer protein, MAPKINASE - Mitogen activated protein kinase,SERK- Somatic Embryogenesis receptor kinase, SERK-Somatic Embryogenesis receptor kinase, WRKY- Transcription factor and14-3-3 protein are found an important proteins and genes in plants. These proteins & genes sequences can be retrieved with navigation menus of respective genes and proteins from this database. 12. Papers published or presented in the conferences with reference a)Anitha Karun, Rajesh, M.K., Sajini, K.K., Radha, E., Parthasarathy, V.A. (2007) Regeneration systems in plantation crops. Proceedings of National Seminar on Horticultural Biotechnology: Present Status and Future Action Plan. Held at IIHR, Bangalore on 8th December 2007, pp. 50-56. b)Jiji, G., Karun, A., Manimekalai, R., Rajesh, M.K. and Remya, P. (2007) Identification of RAPD markers linked to sex determination in palmyrah (Borassus flabellifer L.). Current Science, 93(8): 1075-1077. c)Rajesh, M.K. and Anitha Karun (2007) Isolation and characterization of stress responsive genes in coconut. Proceedings of National Seminar on Horticultural Biotechnology: Present Status and Future Action Plan. Held at IIHR, Bangalore on December 8th 2007, pp. 9-11. c)Rajesh, M.K., Anitha Karun, George V. Thomas, Parthasarathy, V.A. (2007) Databases for coconut and cocoa. Proceedings of National Seminar on Horticultural Biotechnology: Present Status and Future Action Plan. Held at IIHR, Bangalore on 8th December 2007, pp. 272-273. 101 d)Rajesh, M.K., Niral, V., Manimekalai, R., Devakumar, K., Anitha Karun and Parthasarathy, V.A. (2007) Molecular markers in coconut. Proceedings of National Seminar on Horticultural Biotechnology: Present Status and Future Action Plan. Held at IIHR, Bangalore on 8th December 2007, pp. 176-180. e)Riju et al., Bioinformation 2(4): 128-131 (2007)

13. Initiation of R&D activities in Bioinformatics 1. Gene expression studies and development of molecular databases on palms and cocoa. 2. Molecular Docking of chemical constituents of areca. 3. Creation of coconut genomic databases. 14. Details of Training/ Workshop organized and total no. of user trained 1. “Applications of Bioinformatics and biotechnology in plantation crops research” for the period of ten days with ten participants. 15. Impact shown by your centre on the growth of biotechnology and allied areas. In this you may highlight the details like number of paper published/ number of papers published with the help of your centre, how your centre is promoting various activities of your organization and neighboring institutions, manpower trained, tools developed, patents & copyrights acquired and other services offered etc. • The centre extends facilities for the researchers and students from Mangalore University, University of Kannur, University of Calicut, University affiliated colleges, IISR, NRC Cashew, NRC Oil Palm and all ICAR institutes • In the current year twenty-five research workers/ students were given training on various aspects of bioinformatics.

16. Future activities • Creation of database of stress – responsive genes • Gene expression studies and updating molecular markers databases on palms and cocoa. • Genomics and proteomics studies of coconut related genes. • Updating of existing databases. • Conducting training programmes.

17. Additional Details: Name of the Coordinator : Dr.George. V.Thomas Postal Address :Central Plantation Crops Research Institute, Kudlu P.O, Kasaragod –671124, Kerala, India. Phone Number : 04994-232974, 04994-232894, (5) Fax No. : 91-04994-232322 Email: [email protected] Website : http://www.bioinfcpcri.org Name of Contact Person(s) : Dr.George. V.Thomas, Coordinator Email : [email protected]

102 Central Sericultural Research and Training Institute, Mysore Coordinator : Dr. C. K. Kamble

1. Summary of the progress made by the center from its inception

The Bioinformatics Centre at CSRTI, Mysore was established in November, 1999 under the BTIS programme of the DBT, Govt. of India as a Sub-DIC. The center is well equipped with the infrastructure facilities comprising of 11 computers, one server, five printers, one digital video camera, one multimedia projector etc. The internet is being accessed through leased line of BSNL with 512 kbps speed. The website of the center is being hosted from the centre’s server with the URL www.btismysore.in. The main focus of the center is to support biotechnology research pertaining to Sericulture and so far seven databases related to the host plant, mulberry and silkworm have been developed. The center has conducted 14 workshops in which 451 personnel were trained.

2. Major research activities in Biotechnology and its related fields in your institution

Central Sericultural Research and Training Institute, Mysore is the premier Institute par excellence with all modern facilities and infrastructure, which has made a mark as leading R &D institution on Tropical Sericulture in country and is well recognized as a centre for higher learning and advanced training on International front. The research focus of the Institute is slowly but steadily shifting to the molecular biological aspects of sericulture and biotechnological investigations are likely to assume center-stage during the coming years. A total of 12 research projects mostly funded by DBT are being carried out on the areas like mulberry genome characterization, identification of QTLs for root traits and water use efficiency, cloning and characterization of epicuticular wax synthesizing genes, DNA markers associated with diseases and pest resistance in mulberry, transformation for draught tolerant mulberry, evaluation of transgenic mulberry for abiotic stress, cloning and characterisation of antiviral gene in silkworm, DNA markers associated with baculovirus resistance in silkworm, digital inventory of silkworm resources etc.

3. Area of Specialization of the center The main thrust area of this center is Seri-biotechnology and Seri-bioinformatics.

4. Major activities of the center during the year 2007-08

Seven Databases developed were updated and maintained. Infrastructure facilities and support through bioinformatics tools and techniques were provided for the scientists of the Institute for their projects and experiments. The center is hosting the 19th Annual All India Coordinators meeting of BTISnet during February 3-4 2008.

5. Infrastructure facilities in the Bioinformatics Centre

103 A. Computer & Communication Facility: The center has 7 Pentium III, 3 Pentium IV desktop computers, 1 Lap top computer, 1 HP Compaq ML 150 Server, 1 Epson Dot matrix, 2 HP inkjet and 2 HP laser printers, 3 CD and 2 DVD writers, 1 Sony digital Video camera, 1 5 KVA UPS and 1 Mitsubishi Multimedia DLP projector. The internet access is through 512 kpbs leased line from BSNL.

B. Scientific Software packages PHYLIP, SPSS, Cn3D, Clustal W, PDB – on five CDs, EMBOSS, Artimis – Genome analysis package, Pinnacle DV Studio.

6. Details about staff members working in the center Name of the staff Designation Specialization Period working Dr. S. K. Ashwath Scientist ‘C” M.Sc., P.hd April 2007 2. Mr. Anis Ahmed Shariff Technical B.Sc., PGDCA, PGDSM, November 1999 Assistant Computer Applications; Sericulture & Sericulture 8 years Management 3. Mrs. Gousia Kauser Technical B.Sc., STC in Sericulture, November 1999 Assistant Diploma in Computer Office Automation 8 years

4. Mr. K. Guruprasad Computer Master of Computer December 2004 Operator Application 3 year Computer Under Operator Recruitment Note : The recruitment of Information Officer is under progress 7. Type of Services provided The center is equipped with 512 kbps BSNL Leased Line Internet connectivity and internet facility is provided to all the research laboratories through LAN. The centre extends the infrastructure facilities and software support to the scientists working in the field of molecular biology and offers guidance to students for their dissertation or project work.

8. Educational activities with details of placement. The center does not offer any course in bioinformatics which can lead to placement.

9. Initiative to validate the outcome of bioinformatics resources The databases developed related to silkworm and mulberry biotechnology have been made accessible through the website of the center for the use by scientists working in seribiotechnology.

10. Collaborative works/initiatives The training in Bioinformatics has been incorporated in to the Adhoc Practical Training Course for M.Sc. Sericulture students from SPMVV Tirupati This centre is imparting need based training programmes in various topics in bioinformatics and also dissertation and projects works for students of both under graduate and Post graduate level from the engineering colleges and university of Mysore, Tamil Nadu, Andhra Pradesh and Kerala. 104

11. Databases/Software developed/maintained: The following Databases have been developed & maintained.

1. An Annotated Protein database for Silkworm and Mulberry : SILKPROT 2. Growth indices in popular breeds/hybrids of silkworm Bombyx mori L. in relation to nutritional conditions 3. Database of DNA sequences for important plant genes and mulberry. 4. Mulberry Genome database 5. The Silk e-Lab 6. Sample Web Application for Analysis of RAPD scores 7. Web Application for Mulberry varieties, diseases, products and byproducts utilization in sericulture 8. Wikipedia for the Bioinformatics Centre

The centre is planning to host the databases from its own server. The present databases are being updated and upgraded regularly.

12. Papers published or presented in the conferences with reference 1. Kaladishvarane K., Guruprasad K., Raveendra M., Dandin S. B., (2006). “Silkprot : a database of silkworm proteins”. Paper presented at International conference on Bioinformatics (InCoB) 2006. 2. Guruprasad K., Raveendra M., Girish Naik V., Dandin S. B., (2006). “Mulberry Genome database of silkworm proteins”. Paper presented at International conference on Bioinformatics (InCoB) 2006.

13. Initiation of R&D activities in Bioinformatics: The centre is involved in developing algorithm, designing database structure and modifying the same for the development of databases on silkworm proteins and ESTs.

105 14. Details of Training/Workshop organized and total no. of user trained: So far, this centre has trained 451 personnel through the following workshops and training programmes.

SL. Titles of Training Date No. of No. of Resource Persons NO Programme / Workshop From -To Partici pants External Internal Chair Faculty Faculty persons

1. Computer Basics and June 14-15,2002 14 7 - - Applications

2. Intensive Workshop on February 3 -7, 2003 78 16 4 8 Bioinformatics

3. Career Planning in June 20-21,2003 23 - 9 - Bioinformatics

4. Intellectual Property Rights August 25-28, 2003 30 13 2 -

5. Training Programme on August 29-30, 2003 26 3 4 4 Biotechnology And Bioinformatics in Sericulture

6. Workshop on Dec. 9-10, 2004 32 2 5 4 Biotechnology and Bioinformatics In Sericulture

7. Computer Basics & Mar.7-14 2005(BatchI) 30 - 3 - application in Modern Mar.28-Apr.7 2005 (Batch II) Audio Visual May 30-Jun.9 2005(Batch Presentations III)

8. Career Awareness April 5,2005 15 - 3 - Programme

9. Workshop on September14 –15, 2005 35 4 4 4 Bioinformatics

10. Workshop on October 17-18,2005 47 7 2 4 Bioinformatics

11. Workshop on Information February 23, 2006 30 ------Commu-nication Technology initiative

12. Workshop on August 38 9 3 4 Bioinformatics for BTech 28-29, 2006 Biotechnology students.

13. Workshop on December 32 04 3 4 Bioinformatics for B.Sc. & 28-29, 2006 M.Sc. Biotechnology and Life Science students.

14. Need Based training in 22.01.2007 to 01.02.2007 21 -- 3 -- Bioinformatics

Total 451

15. Impact shown by your centre on the growth of biotechnology and allied areas. 106 A total of 233 Research papers were published by the scientists of the Institute & Nested units (International - 31; National – 43; Books/Booklets – 6; Published in proceedings – 1; Presented in Conferences – 109; and Popular articles – 49). The institute is publishing the Indian Journal of Sericulture ( Biannual), Seridoc (Biannual) and Reshme Vahini ( Bimonthly). CSRTI, Mysore is has made a mark as a leading R & D institute on tropical sericulture in the country and is well recognized as centre for higher learning and advanced training on international front. With its well developed infrastructure and strong indigenously developed technological base, the institute Its role in generation of trained human resources has been always on high pedestals, both at domestic and international levels. As a major component of the institute mandate, training was provided to a total of 3757 persons under different programmes. Major Sericulture states were covered to impart training in different disciplines of sericulture. Students of biotechnology from colleges under Mysore University and engineering colleges in and around Mysore are being given training in bioinformatics and also projects/dissertation works are being supervised.. Applications for the patents were submitted for the technologies, like Chetak’ for controlling mulberry diseases and pests and Semi synthetic diet for rearing young instar tropical tasar silkworm. Further, products/machines, namely, Samrudhi (Juvenile Hormone Analogue), Spoorthi (Mulberry Health Drink), Plastic rotary montages and frames, Hydrodynamic incubator, Single cocoon pusher, Composite cocoon harvester, were licensed for commercial production.

16. Future Activities The existing databases will be enhanced to add further new feature. The same will be hosted from the present server. New databases on mulberry proteins, ESTs in silkworm will be developed and blast feature will be made available locally. This centre will conduct workshops and training programmes in Bioinformatics to suit to the needs of students and professionals.

Additional Details: Name of the Coordinator : Dr. C. K. Kamble Postal Address : Director and Coordinator, Central Sericultural Research & Training Institute, Manandavadi Road, Srirampura, Mysore 570008, Karnataka. Phone No.: (0821) 2362757, 2362406, 2363440 Fax No.: (0821) 2362845, 2362420 Email : [email protected], [email protected] [email protected] Website : www.csrtimys.res.in Name of Contact Person: Dr. S. K. Ashwath, Scientist ‘C’ Email : [email protected]

107 Centre for Cellular & Molecular Biology, Hyderabad Coordinator : Dr. K. Guruprasad

1. Summary of the progress made by the centre from its inception The centre has transformed itself from primarily hosting public databases to conducting research and development in bioinformatics. It has developed a number of useful databases & software applications in bioinformatics. Various research groups in the institute use & develop methods in bioinformatics for protein sequence- structure analysis, analysis of non-coding regions in human genome, SNP analysis, EST analysis, gene prediction, proteomics & micro-array data analysis, mathematical modeling of biological systems, plant host-pathogen interactions, protein pathways, comparative genomics, RNAi mechanism & structural biology. With state-of-the-art experimental infrastructure in place at the CCMB, such as, sequencing, micro-array, proteomics, confocal microscopy, AFM, crystallography & NMR, bioinformatics is central to integrating data generated from these resources.

2. Major research activities in Biotechnology and its related fields at your institution Identification of DNA markers associated with disease and pest resistance in Mulberry (Morus spp.). Development of microsatellite markers for mulberry, beetlevine, Red Panda/olive ridleys. Molecular & prenatal diagnosis for genetic disorders & chromosomal diagnostics. Molecular imaging. Cell and tissue engineering of animal and human cells. Stem cells from murine bone marrow and human fetal liver for use in hepatic regenerative medicine. Evaluation of new ceramic-based biomaterials for use as osteogenic implants. Nanomaterials and nanodevices in health and disease. Triglyceride sensor, lipid and peptide-based gene delivery strategies. Plasma proteomics in health and disease. Proteomics of mouse embryonic stem cells. Transgenics and aquaculture. Use of AI techniques for producing spotted deer. Gene- environment interaction to study drug response. Non-invasive detection of hormonal steroids in scat samples of lions. Antibacterial activity by peptides derived from human beta defensins. Gene silencing and RNA interference.

3. Area of Specialization of the centre Sequence/structure analysis of nucleic acids/proteins, micro-array & proteomics data analysis, comparative genome analysis, SNP analysis & mathematical modeling and protein networks, biodiversity analysis, wild-life identification, databases/software development.

4. Major activities of the centre during the year 2007-08 1. We are identifying triplet repeat associated genes in the human genome and studying their evolutionary conservation across different organisms. We are carrying out molecular analysis of the genes associated with sex determination/differentiation and using mitochondrial DNA analysis for studying human population diversity and the origin of deep rooting lineages of mitochondrial macrohaplogroup ‘M’ in India. We are analyzing non-coding regions in human genome. We have updated the following databases: beta-propellers (version 2.0) in protein tertiary structure, protein sequence-structure PSSARD (version 2.0), HETGRPANAL (version 2.0) database/software that can identify all the known hetero- groups in protein tertiary structure and their neighbouring atoms. We are 108 analyzing specific sequence patterns observed in protein tertiary structure and the binding preferences for some of the metal ions in protein structure. We have analyzed and generated database of disulphide bond connectivity patterns (DBCP) and intra-chain disulphide bridged peptides (ICDBP) in protein tertiary structure. A beta-version of the relational Database of Structural Motifs in Proteins (DSMP-O) is developed. We are analyzing the non-coding part of a genome in order to identify novel elements that function by programming the genomic packaging and to study genome organization and regulation of gene expression. We are identifying SNPs and SNP haplotypes, developing de novo gene finding methods and a database of signal transduction pathways. We used sequence analysis to show that the non-coding RNA controls the synthesis of cell division kinase protein in testis. We are modelling spatiotemporal organization in biological systems. We are carrying out genome–wide analysis of Bkm sequences (GATA repeats): Human, Mouse and Chimpanzee Genome. We are predicting the RDE-4 structure involved in RNA Interference pathway of C.elegans. We are analyzing the molecular dynamics simulation of alpha and beta-defensins.

5. Infrastructure facilities in the Bioinformatics Centre d. Computer & Communication facility Dell Poweredge 2850 Servers: Used for Web and Email Services. Compaq Alpha ES45 Server: Used for Scientific Software’s & Scientific Databases. Sun E420R Server: Used for Scientific Software’s. SUN UltraSparcII 60.0 workstation: Used for Sequence Analysis Server ONYX 2 Workstation: Molecular Modeling Server Dell Poweredge 2800 Servers: Used for Databases (like SPINE (Stores and Purchase Integrated Management Software, FBIS (Fine Biochemicals software) Dell Optiplex GX280 PC’s: These PC are used for Intranet Server, DHCP Server, Firewall (Check Point) Server, (Inter Web Scan and Internet Mail Scan) IWSS and IMSS Server Dell Optiplex GX280: It is configured for Scientific Software’s like sigma plot, SPSS, Reference Manager. Dell Optiplex GX280: PC is configured for Discovery Studio Modeling 1.1 Software Dell Optiplex GX270: Oracle Database Server. Number of PC’s in Bioinformatics Division: 40 PC’s. All the PC’s are connected to the Internet. Telephone Instruments in BIC: 4 External , 5 Internally connected Printers: 3 No’s (HP Laser Printers)

e. Scientific Software packages

1. Sigma Plot 9.0 : SigmaPlot 9.0 is specifically designed to aid in documenting and publishing research, specializing in the graphical presentation of results. It is used for data analysis.

109 2. Discovery Studio Modeling 1.5 from Accelry’s: It is used for basic functionality focused on protein characterization, X-ray analysis, proteomics functional annotation and homology Modeling. Discovery Studio Modeling 1.2 from Accelry’s: It is used for structure based drug design, including evaluation of ligand-protein interactions, de novo design and virtual screening. 3. SPSS 11.0: It is a package used for statistical analysis. 4. Reference Manager 11.0.1 for Windows: It is an online search tool. It provides a simple way to search online bibliographics databases and retrieve the references directly into Reference Manager 5. Local versions on HPC server model HCL of Blast, Clustal, T-Coffee, Phylip, EMBOSS, Repeat Masker, Phrap, SIFT, Polyphen, Mfold, MEME, Phred, Grail. 6. Smart Draw Suite ver.7 – a tool for creating flowcharts and technical diagrams. 7. Solar Winds Engineers ver.8 – Network Management 8. AVADIS for Affymetrix Gene Chip system

f. Databases & other information resources Nt, Nr, SP, PDB, EST, human genome (chromosome-wise), chimp genome, mouse genome, etc., for Blast.

Other Software’s and Databases installed at Bioinformatics are: Oracle 10g Database, MySql Database, Red Hat Linux Enterprise ES ver 3.0, Red Hat Linux Enterprise AS ver 3.0, MS Windows 2003 Advanced Server, MS Office 2003, Macromedia Web Design Studio, Adobe Acrobat 7.0, Adobe PageMaker ver 7.0, Adobe Photoshop 7.0, Macromedia Dreamweaver, Fireworks, Freehand, Homelite, Microsoft Windows XP, Microsoft Windows 98/2000, Microsoft Office 2000/XP

Local Area Network: CCMB has a Local Area Network (LAN) connecting all buildings in the campus at 1 Gbps core backbone speed and switched 10/100 Mbps to desktops, Spectroscopy, Proteomics and DNA sequencing facilities. Cisco 3825 series Router with 2 WIC’s, 2 NIC’s and 2 serial ports. One 48-port and two 24-port HP Procurve switches with 1 Gbps uplink fiber modules have been installed. The CCMB network is secured by Nortel Alteon Firewall with Checkpoint software and centralized gateway-level Antivirus (including Web and E-mail), SPAM prevention and Damage Cleanup Services (Trend Micro Neat Suite, Enterprise Edition). The last mile connectivity for the Internet leased line is connected with optical fibre cable from the nearest telephone exchange to the CCMB campus. The Internet leased bandwidth from VSNL is 2 Mbps. Internet kiosks, wireless access points provided during all major seminars and workshops. VPN connectivity between CCMB & IGIB, Delhi established for collaborative SNP project aimed at sharing details of populations as well as gene polymorphisms.

CCMB E-Mail Service: The Web Mail (Mithi Connect Server) including global access has been deployed on Red Hat Enterprise Linux AS3.0 with X86_64 bit architecture to enhance the processing speed with 2GB RAM and about 1TB RAID storage devices for storing mail users data. The primary mail server is supported with a redundant disaster recovery secondary server of 110 identical architecture mirroring the users data in real time along with an auto fail over.

6. Details about staff members working in the centre (Name of the staff, Designation, Specialization and period of working. Please indicate their absorption status): N/A (The staff employed against the sanctioned positions at the Bioinformatics centre have been absorbed).

7. Types of services provided :

The bioinformatics centre and infrastructure facilities are open round the clock for use by CCMB staff and research students/post-docs, summer students, project assistants/trainees, guest workers or collaborators. Periodic symposium/workshop are organized.

8. Educational activities with details of placement N/A

9. Initiative to validate the outcome of bioinformatics resources N/A

10. Collaborative works/ initiatives CCMB Bioinformatics staff participated in the NMITLI SNP network project, CSIR project with Proctor & Gamble, USA, and a number of internal collaborations with other CCMB staff and other external collaborations.

11. Databases/ Software packages developed 1. PSSARD: http://203.200.217.185:8000/rdpssa/index.htm 2. HetGrpAnal: http://203.200.217.185:8000/hetatm/index.htmDBCP: http://203.200.217.185:8000/dsbcp/index.htm 4. ICDBP: http://203.200.217.185:8000/dsl/index.htm 5. BETA PROPELLERS: http://203.200.217.185:8000/dsmpo/propellerversion2/home.htm The above databases/software were developed in-house and are freely accessible from our website. PSSARD is a database for the analysis of protein sequence-structure. HetGrpAnal is a database of heteratom groups in protein tertiary structure and an application to identify neighbours. DBCP is a database of intra-chain disulphide bond connectivity patterns in protein tertiary structure. ICDBP is a database of intra-chain disulphide bridged peptides in protein tertiary structure. Beta-propeller is a database of all known beta-propellers in the PDB. COMBITURNS is a database of combination of turns in proteins. Beta-propeller.pl is a software for the automatic detection of known beta-propellers in a given Protein Data Bank (PDB) file.

12. Papers published or presented in the conferences with reference 1. Settu Sridhar and Kunchur Guruprasad Conformational analysis corresponding to intra- chain disulfide bridged peptides in proteins of known three-dimensional structure. Protein and Peptide Letters (2007, in press). 2. Settu Sridhar, A. V. N. Babu and Kunchur Guruprasad PSSARD (2.0): A database server for making flexible queries relating amino acid sequences to main-chain secondary structure conformations for proteins of known three-dimensional structure and certain useful applications. Int J Biol Macromol. 2007 Jun 1;41(1):109-113.

111 3. V.Jai Kartik, T.Lavanya and Kunchur Guruprasad Analysis of disulphide bond connectivity patterns in protein tertiary structure. Int J Biol Macromol. 2006 May 30;38(3- 5):174-179. 4. Kunchur Guruprasad, V.Jai Kartik, T.Lavanya and Lalitha Guruprasad Juxtaposed half- cystines as disulphide bridged partners in protein tertiary structure. Protein and Peptide Letters 2006;13(6):577-579. 5. Aggarwal, R.K., Kivisild, T., Ramadevi, J., and Singh, L. Mitochondrial DNA coding region sequences support the phylogenetic distinction of two Indian wolf species. Journal of Zoological Systematics and Evolutionary Research 2007;45:163-172. 6. Bajpai, A. Settu, S., Reddy, H.M. and Rachel, A.J. BRM-Parser: A tool for comprehensive analysis of BLAST and RepeatMasker results. In Silico Biology 2007;7:27. 7. Rajesh, S., Sinha, S. and Somdatta Sinha. Synchronization in coupled cells with activator-inhibitor pathways. 2007, Physical Review E, 75:011906.

Poster presentations: 1. Bhardwaj, A. and Tiwari, S. Evaluating the association of mitochondrial SNP haplotypes with disease phenotypes using a novel in silico tool E- MIDAS. In: Proceedings of the 9th International Conference on Information Technology (ICIT 2006), IEE Computer Society, 17-20.

13. Initiation of R&D activities in Bioinformatics We have initiated R & D activities in protein sequence-structure analysis, comparative genome analysis, SNP analysis, drug-design, pathway modeling, systems biology and human genetic diversity analysis.

14. Details of Training/ Workshop organized and total number of users trained: ¾ 11th ADNAT Convention – A Three Day Symposium on ‘Advances in Structural Biology and Structure Prediction’, Feb 23, 24 & 25, 2007. ¾ 11th ADNAT Convention – Hands on Training Course on ‘Protein Structure Prediction and Structure Determination’, Feb 26 – March 8, 2007 [15 participants]. ¾ One-week DST sponsored Bioinformatics Training Programme for Senior Scientists & Technologists (working with Government of India) titled ‘Perspectives and Current Trends in Bioinformatics’, 12 – 18th September 2007 [42 participants]. There are a number of visiting scientists and guest workers apart from the regular staff and research scholars who use the facilities. We provide summer training (6-8 students) and also provide long-term training to 10-12 graduates/post-graduates under the DBT traineeship/studentship program every year. We also train our JRF batches.

15. Impact shown by your centre on the growth of biotechnology and allied areas. In this you may highlight the details like number of paper published/ number of papers published with the help of your centre, how your centre is promoting various activities of your organization and neighboring institutions, manpower trained, tools developed, patents & copyrights acquired and other services offered etc. Number of papers published: 7. The infrastructure facilities provided at the centre is helping users of these facilities both within the laboratory and from outside to add-value to their research. This is evident from some of the publications and patents listed at (http://www.ccmb.res.in). A number of project students and trainees have benefited by working at the centre. It has helped them procure jobs in industry or in further developing their career by

112 seeking Ph.D positions abroad. Some trainees have contributed to research publications and are therefore better qualified to seek Ph.D positions abroad.

16. Future activities We will develop databases/software tools relevant to bioinformatics. We will continue to accept post-graduate students for short-term training programs sponsored by the DBT and contribute to manpower development. We will organize symposium/workshops periodically. We will recruit project assistants & research associates funded by grant-in-aid programs to work on bioinformatics projects.

Additional Details: Name of the Coordinator: Dr. K. Guruprasad, Ph.D (Univ. of London, U.K.) Postal Address:CCMB, Uppal Road, Hyderabad – 500 007. Phone Number: +91 40 2719 2779 Fax No.: +91 40 2716 0591/0311 Email:[email protected] Website:www.ccmb.res.in Name of Contact Person(s): Dr. K. Guruprasad, Email:[email protected]

113 CSK Himachal Pradesh Krishi Vishvavidyalaya, Palampur Coordinator : Dr. S. R. Thakur

1. Summary of the progress made by the Centre from its inception Distributed Information Sub-Centre (DISC) at Advanced Centre of Hill Bioresources and Biotechnology, CSK HPKV, Palampur (HP) came into existence in October, 2002. The Centre has developed fairly good infrastructure that comprises 28 Computers, two servers (one is used as web server and other is internal server), Communication equipments and Printers, Photocopier, Fax machine etc. All the computers are linked through Local Area Network (LAN) and internet with 256 kbps lease line. The Centre has procured softwares like LINUX, ORACLE, WINDOWS NET SERVER WINDOWS SERVER 2003, BIO- SYSTEMATICA, SQL SERVER, ADOBE ACROBAT PROFESSIONAL, VStudio.Net, DNA Star and Gen CheckTM for day to day bioinformatics work and for software development, database creation and management. The Centre has also developed an e-Extension system for quick and efficient dissemination of agricultural technologies to farming community. The Centre is engaged in analysis of genome sequences of different crop species and plant pathogens. The rice genome is being analyzed for NBS-LRR (nucleotides binding site- leucine rich repeat) genes, which have been implicated in plant disease resistance. The lentil and red clover genomes are being analyzed for identifying genes associated with traits of agronomic importance and to identify markers linked to QTLs responsible for important plant traits. 2. Major research activities in Biotechnology and its related fields at your institution The Advanced Centre of Hill Bioresources and Biotechnology is engaged in research on following areas in Agricultural Biotechnology: i. Understanding molecular genetics of bacterial wilt resistance in pepper with implications in solanaceae genomes ii. Biofortification of maize for enhanced zinc and iron content in grains iii. Molecular marker-assisted pyramiding of blast resistance genes in rice iv. Development of DNA-based diagnostics for Fusarium species v. Development of SSR markers in Trifolium pratense and identification of QTLs associated with important plant traits vi. Mapping of rust resistance locus in Lens using genomic resources from related taxa vii. Probing the molecular mechanisms governing cold tolerance during reproductive growth in chickpea (Cicer aeritinum L.) viii. Molecular marker-assisted pyramiding of powdery mildew resistance genes in pea Development of sex-specific markers in sea buckthorn 3. Area of specialization of the Centre Bioinformatics & Agricultural Biotechnology 4. Major activities of the centre during the year 2007-08 Following databases have been upgraded by the Centre during 2007-08: 1. Database on Biological Wealth of Himalayas 2. e-Extension network system 3. Library Management System

5. Infrastructure facilities in the Bioinformatics Centre a. Computer & Communication facility 114 IBM servers (2), IBM Computers (13), HCL computer (Linux based), Thinkpad (3), eMac G4(1), LCD(1), Deskjet Colour HP printer 840(1), Laser jet HP Printer 2200D(1), Print server(1), UPS 6KVA(1), Fax machine(1), Scanner(1), Photocopier(1), Backup Device 250GB(1) b. Scientific Software packages Scientific Software: DNASTAR, Bio-Systematica , Bioedit, Mapmaker System Software: LINUX 9.0, Microsoft 2000 server, Microsoft server 2003 Standard Edition, Window XP Home edition (IBM recovery) Application Software: Adobe Acrobat Professional 7.0, Microsoft Vstudio.Net 2002, Open Office Org. 5.0, Win Zip 9.0, Win split c. Databases &other information resources ORACLE 9i and SQL Server 2000 Standard Edition 6. Details about staff members working in the Centre Name Designation Specialization Period of working Dr. T.R. Sharma Bioinformatics In Plant Genomics Since Aug., Charge & Bioinformatics 2006 Dr. Rajeev Bioinformatics Officer Plant Genomics Since April, Rathour & Bioinformatics 2004 Mr. Mukesh Technical Assistant* Computer Since Feb., Sharma 2004 Mr. Ajay Kumar Data Entry Operator* Computer Since April, Walia 2003 Mr. Pardeep Traineeship Computer Since April, Kumar 2007 Mr. Ashish Rana Studentship Computer Since April, 2007

*Not absorbed 7. Types of services provided 1. Internet and email facility to users 2. User access to Bioinformatics resources available in the Centre 3. Trainings in the field of bioinformatics 4. Bioinformatics course at Masters’ level 8. Educational activities with details of placement The infrastructure of the Bioinformatics Centre has been used in teaching a Bioinformatics course of 2 credit hours (1+1) to M.Sc. students of Agricultural Biotechnology. The students are given theory lectures as well as practical classes on various topics as prescribed by the Department of Biotechnology, Govt. of India in the course contents. The students are given hands on training on database development and the use of DNA sequence analysis software in sequence assembly and annotation for gene finding. The students are also taught about gene prediction, construction of restriction maps, drawing structures of various recombinant molecules and other bioinformatics tools of current and future importance. 9. Initiative to validate the outcome of bioinformatics resources The bioinformatics resources are being used by the students and scientists of the biotechnology Centre of the university. 10. Collaborative works/initiatives

115 The Bioinformatics Center is also catering to other scientists for bioinformatics analysis pertaining to R&D projects shown at S. No. 2 11. Databases/Software packages developed Following databases have been developed by the Centre: 1. Database on Biological Wealth of Himalayas 2. e-Extension network system 3. Library Management System (LMS) 4. DNA , RNA and Protein sequence alignment Tool The Bioinformatics Centre has developed its own website. Home page of website is www.hpbioinformatics.org 12. Papers published or presented 1. Chauhan RS. 2006. Bioinformatics approach toward identification of candidate genes for zinc and iron transporters in maize. Current Science 91: 510-515. 2. Hong CP, Plaha P, Koo DH, Yang TJ, Choi SR, Lee YK, Um T, Bang JW, Edward D, Bankroft I, Park BS, Lee JL and Lim YP. 2006. A survey of the Brassica rapa genome through BAC-End sequence analysis and comparison with Arabidopsis thaliana. Mol Cell 22: 300-307. 3. Kapila, RK, Yadav, RS, Plaha, P, Rai, KN, Yadav, OP, Hash, CT and Howarth, CJ. 2007. Genetic diversity among pearl millet maintainers using microsatellite markers.Plant Breeding: In press. 4. Lim YP, Plaha P, Choi SR, Uhm T, Hong CP, bang JW, Hur YK and Park BS 2006. Towards unraveling the structure of Brassica rapa genome. Physiol. Plantarum 126: 585- 591. 5. Sharma P, Sharma KD, Sharma Rajan and Plaha P. 2006. Genetic variability in pea wilt pathogen Fusarium oxysporum f. sp. pisi from north-western Himalayas. Indian Journal of Biotechnology 5: 298-302. 6. Sharma TR, Rana JC, Sharma Rajan, Rathour R, and Sharma PN 2006. Genetic diversity analysis of exotic and Indian accessions of common bean (Phaseolus vulgaris L.) using RAPD markers. Indian Journal of Genetics & Plant Breeding 66:275-278. 7. Sharma R, Singh S, Chahota K, Rathour R and Sharma SK 2005. Analysis of genetic diversity in white clover (Trifolium repens) breeding populations using agro-morphological and RAPD markers. Journal of Genetics & Breeding 59:297-302. 13. Initiation of R&D activities in Bioinformatics In Silico Development of simple sequence repeat (SSR) markers for genetic mapping: We have developed a set of 127 SSR markers by bioinformatics analysis of publicly available sequence of chromosome 12 of the japonica cv. Nipponbare (http://rgp.dna.affrc.go.jp). SSR motifs were identified among the BAC/PAC clones spanning 27.1 to 72.2 cM on the integrated genetic and physical map of chromosome 12 using simple sequence repeat identification tool (SSRIT) (http://gramene.org) and primers were designed from the sequences flanking the SSR loci using primer 3.0 software(http://frodo.wi.mit.edu/cgi- bin/primer3/primer3_www.cgi). The uniqueness of each primer was confirmed by BLAST analysis against the complete rice genome sequence database. SSRs were typed by amplifying the DNA of an indica rice genotype, HPU 741 and a japonica genotype, Fukunishiki with flanking primers. PCR conditions were optimized individually for each SSR using the gradient PCR. Majority of these markers amplified single locus polymorphic amplicons among the rice genotypes tested. These studies indicated that in silico analysis of rice genomic sequences available in public domain offers a speedy and cheap means to develop SSR markers for genetic mapping in rice, thus obviating the tedious procedure of constructing SSR enriched genomic libraries and their subsequent sequencing for developing SSR markers.

116 In addition, 100 SSR primers from BAC and EST databases of Medicago truncatula have been developed for genetic mapping in lentil and red clover. 14. Details of Training/Workshop organized and total no. of user trained Title Duration No. of participants Bioinformatics tools in genome 5th-7th July, 2006 20 analysis Role of computers in 17th-18th March, 2007 20 bioinformatics

15. Impact shown by your centre on the growth of biotechnology and allied areas. C. No. of registered /regular/online users : 100 D. Research Publications (including biotechnology) : 10 E. Technical/Project proposals (including biotechnology) : 5 IV) Abstracts/ Brochures/Training manuals : - for seminar/workshops/training (in bioinformatics) 16. Future activities During the coming year the Centre proposes to strengthen infrastructure in terms of software tools for biological data analysis for providing better services to the users. Besides this, the following activities will also be undertaken: 1. Using new bioinformatics tools for furthering biotechnology resaerch. 2. Developing software tools and writing algorithms for extracting information from model genomes and utilizing in biotechnology interventions in resource-poor crops.

Additional Details: Name of the Coordinator: Dr. S.R.Thakur Postal address: ACHBB, CSKHPKV, Palampur HP 176062 Phone No.: 01894-230314 Fax No.: 01894-230511 Email: [email protected], [email protected] Website: www.hillagric.ernet.in Name of the Contact Person(s): Dr. T.R.Sharma Email: [email protected]

117 Devi Ahilya University, Indore Coordinator : Dr. Anil Kumar

1. Summary of the progress made by the Centre from its inception: The Distributed Information Sub-Centre was established in the School of Biotechnology of Devi Ahilya University, Indore in 1993 under the BTIS-Net program of DBT. Since inception, we are engaged in Bioinformatics research and education. Our center has got BSNL 512 Kbps internet lease line connection and a user lab comprising of 40 desktop PCs and 24 hours internet connectivity. This facility is being used in Bioinformatics research and by the students and faculty of the department. We have also setup a web server (http://www.davvbiotech.res.in) having all the software and database developed/procured by the centre. The development of FTP server has been initiated. The development of a server for the identification and characterization of Genomic and Pathogenicity Islands has been completed and a research paper has been communicated in In-Silico Biology. PredictBias is available at http://www.davvbiotech.res.in/PredictBias. We have designed primers for endo-1,4-β Xylanase gene. We have also designed primers for DREB2A gene. We have published full length papers in primer designing of Xylanase as well as DREB2A genes. We have also presented papers for the above works in various conferences specified in the papers published section.

Since 1997, we are regularly organizing workshops on bioinformatics. As per records, till now 17 workshops have been organized and nearly 880 registered participants have been trained in these workshops. Many students do their research projects in the field of bioinformatics at our Centre (towards partial fulfillment of their M. Sc. Biotechnology/ life science/ biochemistry or BE/MCA or M. Pharma degree). During 2007-08, two students from Banashthali University have taken two months summer training at our Centre. Two students from BIT Jaipur will take six months training. We also offer studentship and traineeship to eligible candidates. During 2007-08, one studentship and traineeship is offered to a M. Sc. Biotechnology student and a research scholar, respectively.

2. Major Research activities in Biotechnology & related fields at our Institution: Our lab is mainly Enzyme technology lab, we also do research in the field of Plant Tissue Culture and Molecular Biology etc. We have developed following lab scale technologies: 1. Lab scale technology for production of glucose-1-phosphate using immobilized enzyme bio-reactors. 2. Lab scale technology for production of low molecular weight polygalacturonic acid and low methoxyl pectin. 3. Technology developed for fruit juice clarification using immobilized enzymes. Many papers have been presented in various national and international conferences. Our faculty members of biotechnology also authored books/Chapters in edited books/Encyclopedia. Twenty students have been awarded Ph.D. in Biotechnology.

3. Area of specialization of the Centre:

118 Sequence analysis, Biological software & database development related to medical bioinformatics and human resource development.

4. Major activities of the Centre in the year 2007-08: Database & Software Development: S. No. Name of the Functions Availability Software/Database 1 PredictBias Web application for detection of http://www.davvbiot Pathogenicity Islands in pathogenic ech.res.in/PredictBi bacteria. as/ 2 QGenBank A comprehensive parser of The development is GenBank file format in Java. currently in progress. 3 PredictSecSys A prediction server for the Data analysis has identification of Secretion systems in been completed. bacteria based on SVM.

Human Resource Development: During 2007-08, We successfully organized workshop (lecture cum hands on training) on “Genome Data Analysis” and trained nearly thirty five participants. Centre offered one-studentship to a student, Mr. Rustam Ali for doing his M.Sc. Biotechnology project in the field of Bioinformatics.

Provision of Information resources: Database & abstract search and scientific software are being provided to the staff & students of the University. Good Internet facility has been provided to the staff & students of the Department.

5. Infrastructure facilities in the Bioinformatics Sub-Centre: A. Computer & Communication facility: (i) Servers Web Server: HP Prolient ML 570 (Quad Processor with 4 GB RAM) Proxy Server: HP Prolient ML 150 with 1 GB RAM (ii) Desktops Pc’s, Printers & Scanners 1GB (RAM) 512MB 256 MB Others Desktop 15 6 13 11 Firewall System 1 Printer 4 Scanner 2 Photocopier 2 (iii) Communication Facility Leased Line Router Fax Switch/Hub Projector 512 Kbps Cisco 1751 2 5 3 B. Scientific software packages: MATLAB, DNASIS, PROSIS, AMOS, SPSS, MOE, Reference Manager 11.

C. Databases & other information resources: Derwent Biotechnology Abstracts from 1982 -2004, Journals like Nature & Journal of Bioscience & Bioengineering & Journals of Cell and Tissue Research.

6. Details about staff members working in the Centre: S. Name of the staff Designation Specializatio Period of 119 No. member n working. 1. Mr. Sachin Pundhir Information Bioinformatics. Two year & Officer. Ten months. 2. Mrs. Rachana Technical Biotechnology Seven Months Tiwari Assistant 3. Mr. Dhiraj Singh Computer Computer Three years & Panwar Operator. Engineering. four months. 5. Mrs. Kavita Yadav Computer Computer Seven months Operator Science 6. Mr. Amey Kekre Data Entry Computer Seven years & Operator. Applications. eight months. Absorption Status: University has approved the absorption of Bioinformatics Posts (as regular employees) in the meeting of Executive Council held on Dec. 01, 2007, subject to approval of State Govt.

7. Types of services provided: We provide Internet services to the teaching & non-teaching staff, postgraduate & research students of the School of Biotechnology. Database & abstract search is facilitated to the research community of not only our department, but also other departments of the University. We also provide our software for scientific work to researchers of other institutes. We also provide guidance & training to the students of Bioinformatics/ biological sciences of other Institutes / Universities.

8. Educational activities with details of placement: We impart bioinformatics training to the researchers, students & teachers through workshops. At present, we do not offer any course. Our University plans to start M. Sc. Bioinformatics program from 2008-09 Academic Session.

9. Initiative to validate the outcome of bioinformatics resources: Our Centre is actively engaged in Bioinformatics education. With the help of bioinformatics resources, we are training students who will fulfill the requirement of industries engaged in the field of bioinformatics.

10. Collaborative works / initiatives: We have Collaboration with NCCS, Pune and Jain Hi-Tech Industry, Jalgaon. 11. Databases / Software packages developed: Name of the Functions Availability Software/Database PredictBias Web application for detection of http://www.davvbiotech Pathogenicity Islands in .res.in/PredictBias/ pathogenic bacteria. MTGenomeDB A secondary database of http://www.davvbiotech Mycobacterium Tuberculosis. .res.in/MTGenomeDB/ OrchidDB A Taxonomical database of http://www.davvbiotech Orchid species of Indian origin .res.in/OrchidDB/ ResCut Program to find restriction enzyme’s cutting site nucleotide sequence. AnaSeq Program to analyze the effect of mutation on translation product 120 with BLAST facility

12. Papers published or presented in the conferences with reference: 1. Mishra, B.N., Singh S.P. and Kumar A. (1997) A biofilm model for fixed bed anaerobic reactors: Performance analysis considering diffusional resistances and axial dispersion. The Genetic Engineer and Biotechnologist 17 5-21. (MATLAB USED). 2. Singh, V.K. and Kumar A. (2000) PCR Recipe: Software for setting up PCR reactions, Biotechnology software and Internet Journal 1, 276-277. 3. Singh, V.K. and Kumar A. (2000) OLREA: A faster restriction enzyme analysis using JAVA. Biotechnology software and Internet Journal, 1, 278- 279. 4. Singh, V.K., Govindrajan, R., Naik, S. and Kumar, A. (2000) The effect of Hairpin structure on PCR amplification efficiency, Mol. Biol. Today 1 (3), 67- 69. 5. Samanta, J. and Kumar, A. (2001) TAXON: A software package for the Management of Plant Database using Visual Basic. Biotechnology software and Internet Journal, 2 (5), 201-203. 6. Singh, V.K., Mangalam, A.K., Kumar, A., Naik, S. (2001) Universal primers can amplify tumor necrosis factor gene across species. Mol. Biol. Today 2, 11-12. 7. Singh, V.K. and Kumar, A. (2001) PCR Primer Design. Mol. Biol. Today 2, 27- 32. 8. Khan, I., Desai, D. V. and Kumar, A. (2004) Carbochips – a New Energy for old Biobuilders. Journal Biosciences & Bioengineering 98, 331-337. 9. Garg, N. and Kumar, A. (2006) Primer designing of DREB2A, a drought resistant gene in soybean. 93rd Indian Science Congress Association meeting, Hyderabad, January 3-7, 2006. 10. Garg, N. and Kumar, A. (2006) Primer designing of DREB2A, a drought resistant gene in Glycine max. J. Cell Tissue Res. 6, 807-813. 11. Pundhir, S., Vijayvargiya, H. and Kumar, A. (2006) Poster presentation, Predict Bias: Detection of Pathogenicity Islands in Pathogenic bacteria, International Conference in Bioinformatics (InCoB2006), New Delhi, Dec. 18- 20, 2006. 12. Garg, S., Sohani, N., Pundhir, S. and Kumar, A. (2006) Primer Designing for Endo-1, 4-β-xylanase gene, Oral Presentation, National Conference on Biotechnology, Science & Environment, Indore, Dec. 28-29,2006. 13. Pundhir S. and Kumar, A. In Sillico Classification of Virulence factors, National Conference on Biotechnology, Science & Environment, Indore, Dec. 28-29, 2006. (Best paper award). 14. Garg, S., Sohani, N., Pundhir, S. and Kumar, A. (2007) Primer designing of for Endo-1, 4-b-18 Xylanase gene. J. Cell Tissue Res 7(3), 1147-1154.

13. Initiation of R&D activities in Bioinformatics: • Initiated the development of a parser for GenBank file format using Java. • Initiated the development of a comprehensive Database on Starch Phosphorylase. • Initiated the development of a prediction tool for the identification of secretion system in bacteria using support vector machine.

121 14. Details of Training/Workshop in 2007-08 organized and total numbers of user trained: S. Dates Theme of the Workshop / No. of No. Training Program Participants 1. Oct 29th - 02nd Nov. , Genome Data Analysis 35 2007 The workshop included lectures & demonstration sessions by speakers from our own Bioinformatics Sub-centre as well as eminent scientists from other institutions.

15. Impact shown by our Centre on the growth of biotechnology and allied areas: The Bioinformatics sub Centre is contributing in research field of biotechnology and enhancing the research activities. The research papers are published in national and international journals of high repute. We have also trained nearly 880 participants by successfully organizing 17 workshops since 1997. The Centre also provide information to the students and research scholars of biotechnology as well as to other neighboring departments/institute by the Internet facility, Scientific Software, Studentship, Abstract Database CDs and office automation software. 16. Future activities: Our University plans to start M.Sc. Bioinformatics program. We are also doing research & development work related to the primer designing for α- Glucan Phosphorylase. We also plan to design processes for enzymes.

Additional Details: Coordinator: Dr. Anil Kumar Postal Address: Professor & Head, School of Biotechnology Devi Ahilya University, Khandwa Road INDORE - 452001, M.P., INDIA. Phone Number: +91-731-2470372, 2470373; Fax No.: +91-731-2470372. Email: [email protected], [email protected] Website: http://www.davvbiotech.res.in

Name of Contact Person(s): (i) Dr. Anil Kumar, Email: [email protected]. (ii) Mr. Sachin Pundhir, Information Officer Bioinformatics Sub Centre. Email: [email protected].

122 Dr. Y S Parmar University of Horticulture and Forestry, H.P. Coordinator : Dr S V Bhardwaj

1. Summary of the progress made by the Centre from its inception The Distributed Information Sub Centre (Sub-DIC), at YSPUHF, funded by DBT, New Delhi became operational during June, 1999 The major achievements and progress made by the Centre since its inception are: • The Centre facilitates the research work of the department by providing bioinformatics softwares (PRISM and EXOME) and databases (Biotechnology Abstracts, Directory of Biotechnology Institutes) in addition to the online bioinformatics tools, email and online literature search facility. (i) The three genes of “Tomato leaf curl virus Himachal strain” ToLCHimV and a Bean yellow mosaic virus isolate Solan coat protein (CP) gene sequenced, were submitted to the NCBI and phylogeny of the genes was traced using bioinformatic tools. (ii) Sequencing of coat protein gene of Bean yellow mosaic virus (BYMV) from gladiolus (Gladiolus sp.) done.(iii) Phylogenetic analysis of Lily symptompless virus done. (iv) Primer designing against Lily symptompless carlavirus (LSV) infecting Lilium spp. using bioinformatics tools has been completed.(v) Studies on Molecular characterization of a potyvirus infecting radish (Raphanus sativus L.) in Himachal Pradesh have also been completed. • Research work being offered to Post graduate students in biotechnology using bioinformatics tools and applications like primer designing, phylogenetic/evolutionary studies, ligand receptor interactions and molecular characterization of viruses using CLUSTALX (1.8), CLUSTAL W, GeneDoc, EXOME, EXOME BLAST, EXOME HORIZON, AutoDock or DOCK or LUDI and other public domain softwares. • Four patents on plant biotechnology work and another one (PCT) with help of the Centre have been granted through the IPM Cell established in the Sub DIC. • Centre has organized 28 trainings/ workshops/ seminars till date and 741 persons have been trained/participated in them. • The Bioinformatics Centre has developed information systems viz, (i) Package of Practices of Fruit Crops in Himachal Pradesh ,(ii) Alternative Methods of Plant Disease Control (iii) Package of Practices of Vegetable Crops in Himachal Pradesh (Hindi version) • The Centre has developed a database on ‘Plant species ‘Germplasm’ available in the university. Further, the database on various crops i..e. HimCrop is under preparation. • The Centre has developed 5 video CDs on Temperate Horticulture in collaboration with the Directorate of Extension Education of the university. • The Bioinformatics Centre has also developed training manual on ‘Computer Basics’ for internal circulation. • The Centre has completed two adhoc research projects . • Website of the university was developed in Jan., 2000 and maintained till March 2004.

2. Major research activities in Biotechnology and its related fields at your institution The research mandate of the department of biotechnology of the university pertains to micro-propagation of plants, cell mutagenesis and cell selection for developing biotic and abiotic stress resistant plants, genetic transformation with marker genes and genes of interest, retrieval of virus free plant material from infected mother plants, development and production of bio-fertilizers,

123 molecular-characterization of plants by RAPD-PCR and application of bioinformatics in research.

3. Area of Specialization of the centre : Crop Biotechnology/Horticulture 4. Major activities of the centre during the year 2007-08 The Centre facilitates the research work of the department by providing bioinformatics softwares (PRISM and EXOME) and databases (Biotechnology Abstracts, Directory of Biotechnology Institutes) in addition to the online bioinformatics tools, email and online literature search facility and conducting workshops/trainings. i) Research • Studies on Molecular characterization of a potyvirus infecting radish (Raphanus sativus L.) in Himachal Pradesh were conducted while studies to know the effect of Asparagus adscendens Roxb. on molecular modelling of target-receptor interactions are continuing. • Comparative analysis of coat protein gene of Lily symptomless virus infecting Lilium species with other carla viruses was done. • Primer designing against Lily symptomless carlavirus (LSV) infecting Lilium species using bioinformatics tools. • Virus has been sequenced and primers for detection of the virus have been designed using bioinformatics tools besides evolutionary of the same virus.

ii) of Database Development The database on various horticultural crops of HP viz, HimCrop is under preparation. iv) Trainings/workshops • The Centre has organized 4 trainings on, ‘Computer Basics’ and 2 trainings on, “Creation and Management of Database” and a Regional Seminar on “Patenting in Biotechnology” during 2007. • The Centre proposes to organize a 3 days training on, “Bioinformatics Basics - Application in Biological Sciences” in Feb, 2008. 5. Infrastructure facilities in the Bioinformatics Centre ¾ Computer & Communication facility: 1 Xeon server, 21 PCs, 2 Modems, 2 Dot Matrix Printers, 2 Laser Printers (Black), a Colored Laser Printer, a 3KVA UPS, a 1KVA UPS, a 625VA UPS, a 8 Port Hub, a Scanner, a CD-Writer, a 8 Port Switch, a Thinkpad (laptop), Multimedia Projector and a Photocopier. ¾ Scientific Software packages: Prism, Exome, Exome ED , Exome BLAST, Hyperchem ¾ Databases & other information resources: Biotechnology Abstracts on CD ROM, Directory on Biotechnology Industries 6. Details about staff members working in the centre (Name of the staff, Designation, Specialization and period of working. Please indicate their absorption status) S.NO. NAME OF THE DESIGNATION WORKING SINCE ABSORPTION STAFF STATUS 1. Ms Anju Sharma Technical Assistant June, 1999 to May 2000 Not absorbed Information Officer May, 2000 2. Mr Kailash Sharma Technical Assistant June, 2000 Not absorbed 124 3. Ms Kamlesh Nagar Data Entry Operator June, 1999 Not absorbed 4. Ms Taruna Sharma Data Entry Operator September, 2006 Not absorbed 5. Mr Neel Thakur Data Entry Operator March 2005 Not absorbed 6. Ms Aarti Thakur Traineeship Holder March, 2007 For one year 7. Ms Taruna Sharma Studentship Holder July, 2007 For one year

7. Types of services provided • The Centre offers a high speed leased line internet connectivity to the host university and facilitates online and offline literature search in field of biotechnology, bioinformatics and other related areas that include bibliographic and patent search. The Derwent Biotechnology Abstracts (offline database) is being used for literature search. • The Intellectual Property Management Cell (IPM Cell) established in the Centre facilitates patent search and patent filing. • The data generated is being analysed statistically using Prism software and other public domain softwares. The Centre provides Nucleotide and Protein Sequence Analysis using online public domain databases and sequence analysis softwares viz Exome, Exome Blast, Exome Horizon etc. While the recently purchased Hyperchem software will facilitate chemical molecular modeling research. • The Centre offer trainings on basics as well as on advanced topics in computer application/bioinformatics/IPR to scientists, technical/ministerial staff and research scholars/students of the University. • The Centre has a collection of books (covering areas of biotechnology, bioinformatics, computers and horticulture) which are being kept in the University library for reference. • Besides above, some other services like creation of multimedia CDs, web page designing, scanning, CD writing, report writing, printing, preparation of presentations on powerpoint, conducting seminars and Xeroxing of documents etc are being provided to the students/scientists of Department of Biotechnology of the University. The Centre also provides complete technical support to various National or International workshops and seminars organized at the University. Minor hardware maintenance is also being provided by the Centre.

8. Educational activities with details of placement : The Centre proposes to start a one year diploma course in course in bioinformatics during the next academic session.

9. Initiative to validate the outcome of bioinformatics resources : NIL 10. Collaborative works/ initiatives: Gene sequencing work is being carried out in collaboration with the molecular biology laboratory of Central Potato Research Institute, Shimla, and CSIR Palampur, Himachal Pradesh. 11. Databases/ Software packages developed: The database on various horticultural crops of HP viz, HimCrop is under preparation. 12. Papers published or presented in the conferences with reference • Bhardwaj SV and Gupta R. 2007. Novel eco-friendly approaches for plant virus management. Paper presented in International Symposium on Viruses of Ornamental and Temperate Fruit Crops held at IHBT, Palampur (HP) on 17-18th December, 2007.

125 • Huddone S, Bhardwaj S V, Malhotra B, Thakur P D and Kanwar K. Comparative nucleotide sequence analysis of coat protein gene of lily symptomless virus isolate LSV Oh with other carlaviruses. Paper presented in Symposium on Eco-friendly Disease Management Approaches for Organic Farming in Horticultural Crops held at Dr Y S Parmar University of Horticulture and Forestry, Nauni-Solan, (HP) on 16-17th November, 2007. Abst. 61. • Bhardwaj S V, Sambyal P S, Thakur P D, Gupta R and Huddone S. Sequence analysis of tomato leaf curl virus Himachal strain (ToLCHimV). Paper presented in Symposium on Eco-friendly Disease Management Approaches for Organic Farming in Horticultural Crops. Dr Y S Parmar University of Horticulture and Forestry, Nauni-Solan, (HP) on 16-17th November, 2007. Abst. 57. • Malhotra B, Bhardwaj S V, Huddone S, Handa A and Kanwar K. Detection of lily symptomless carlavirus using specific primers. Paper presented in Symposium on Eco-friendly Disease Management Approaches for Organic Farming in Horticultural Crops. Dr Y S Parmar University of Horticulture and Forestry, Nauni-Solan, (HP) on 16-17th November, 2007. Abst. 60. • Huddone S, Bhardwaj S V, Malhotra B, Handa A and Kanwar K. Evolutionary pattern of lily symptomless virus isolate LSV-Oh using phylogenetic analysis. Paper presented in International Symposium on Viruses of Ornamental and Temperate Fruit Crops held at IHBT, Palampur (HP) on 17-18th December, 2007. Abst. No. 11. • Malhotra B, Bhardwaj S V, Huddone S, Thakur P D and Kanwar K. Designing specific primers for CP gene of lily symptomless carlavirus. Paper presented in International Symposium on Viruses of Ornamental and Temperate Fruit Crops held at IHBT, Palampur (HP) on 17-18th December, 2007. Abst. No. 14.

13. Initiation of R&D activities in Bioinformatics: Post graduate (MSc and PhD) students of the department are being given bioinformatics research problems.

14. Details of Training/ Workshop organized and total no. of user trained Topic Duration with Date (s) and year No. of From To participa nts Seminar on “ E-Commerce and latest 8th Feb, 2001 - 50 IT Trends” Training on “Windows 98 and MS 14th Feb,2001 28th Feb, 2001 22 Office 2000” Workshop on “Patent Awareness” 5th March,2001 40 Training on “Windows 98 and MS 9th July, 2001 21st July 2001 16 Office 2000” Workshop on “IPR Awareness 8th Nov, 2001 - 33 Programme with special reference to Plant Varieties and Farmers’ Rights Protection Act” Training on “Troubleshooting in 6th May, 2002 7th May, 2002 13 Computer Software and Hardware” Training on “Windows 98 and MS 15th Jan., 2003 28th Jan., 2003 11 Office 2000” 126 Training on “Windows 98 and MS 15th Jan., 2003 28th Jan., 2003 13 Office 2000” Training on “Introduction to Computer 29th Jan, 2003 3rd Feb, 2003 15 Networks and Internet” Training on “Introduction to Computer 29th Jan, 2003 3rd Feb, 2003 15 Networks and Internet” Training on “Windows 98 and MS 9th June,2003 21st June,2003 13 Office 2000” Workshop on “Patent Awareness” 18July, 2003 19 July,2003 58 National seminar on “IPR in 12 Oct, 2004 13 Oct., 2004 150 horticultural crops” Workshop on “IPR Awareness” 23rd Sep, 2005 24th Sep, 2005 20 Training on “Computer Basics” 9th Jan., 2006 17th Jan., 2006 20 Training on “Computer Basics” 7 Mar, 2006 14 Mar, 2006 17 Training on “Computer Basics” 17 April, 2006 22 April, 2006 19 Training on “Creation and 28 Aug, 2006 2 Sep, 2006 12 Management of Database” Training on “Computer Basics” 11 Sep, 2006 16 Sep, 2006 18 Training on “Computer Basics” 3 Oct, 2006 10 Oct, 2006 20 Training on “Computer Basics” 1 Nov, 2006 7 Nov, 2006 20 Training on “Computer Basics” 12 March, 2007 17 March, 2007 19 Training on “Creation and 19 March, 2007 24 March, 2007 12 Management of Database” Training on “Computer Basics” 9 April, 2007 16 April, 2007 19 Training on “Computer Basics” 21 May,2007 26 May, 2007 20 Training on “Computer Basics” 16 July, 2007 21 July, 2007 9 Regional Seminar on “Patenting in 17 July, 2007 - 56 Biotechnology” Training on “Creation and 16 July, 2007 20 July, 2007 11 Management of Database” TOTAL 741

15. Impact shown by your centre on the growth of biotechnology and allied areas. In this you may highlight the details like number of paper published/ number of papers published with the help of your centre, how your centre is promoting various activities of your organization and neighboring institutions, manpower trained, tools developed, patents & copyrights acquired and other services offered etc. Patents granted Patents filed Papers published

16. Future activities • Research work in different aspects of Bioinformatics including ligand receptor interaction to Ph.D/ M. Sc students in the department. • Development of information systems and databases on horticultural crops. • Atleast two short term trainings or workshops on Bioinformatics and / or IPR and one refresher course/training of 21 days on Bioinformatics • Procurement of databases, specialized scientific softwares, books and journals on computers/ Bioinformatics/ Biotechnology. • Establishment of database and web server. • Work on Crop databases, “HimCrop” will continue. 127 • A separate website of the centre shall be hosted.

Additional Details: Name of the Coordinator: Dr S V Bhardwaj Postal Address: Senior Virologist cum Coordinator, Sub DIC, Department of Biotechnology, Dr Y S Parmar University of Horticulture and Forestry, Nauni, Solan . HP. 173 230 Phone Number: 01792 252310, Mobile:094180 61835 Fax No.:01792 252242 Email: [email protected] Website: www.yspuniversity.ac.in Name of Contact Person(s): Dr SVBhardwaj Email: [email protected]

128 G. B. Pant University of Agriculture & Technology, Pantnagar. Dr. Soma S. Marla, MS (Comp., USA), Ph.D (Mol. Biol)

1. Summary of the progress made by the centre from its inception Bioinformatics sub-DIC was established in November 1998 in the College of Basic sciences & humanities, G.B.Pant University of agriculture & Technology, Pantnagar. This is one of the sub-DIC of Uttaranchal. Since inception the centre is actively involved in teaching and conducting research in Bioinformatics. The centre is also actively involved in disseminating information in biotechnology and assisting on-going research in the university aimed at improvement of crop & animal productivity. Two Bioinformatics courses- Elements of Bioinformatics (offered every semester) and “Use of computers in molecular modeling” are being offered by the centre to students at the Post graduate level. The centre has initiated electronic inventerization of plant biodiversity of Uttaranchal. A small green File database “Uttaranchal Plant Resource DB” of 50 plants, A “ Nutritional Plant Resource Database of Utttaranchal” , enumerating nutritional and other information about nearly 60 genotypes of small grains has been developed. Another Database “Cry gene Transgenic database” providing comprehensive information about transformed Cry genes in various crops has been developed. Similarly a Prokaryotic pathogen genome visualization tool have been developed and published in an international journal. The centre is also actively involved in hands on skill training of Bioinformatics skills by conducting workshops. So far ten training workshops were conducted with active funding support from DBT. A web site was launched on-line reflecting the various activities of the Bioinformatics centre, Pantnagar (http://www.gbpuat.ac.in/acads/cbsh/Bioinformatics/home.htm).

2. Major Research activities at G.B.Pant University G.B.Pant University of Agriculture & Technology is the first agricultural university in India. Since it’s inception, it has had very strong basic sciences disciplines like microbiology, biochemistry, Genetics, etc; helping the intensive efforts in plant breeding, plant pathology, horticulture, veterinary, process engineering and food technology. The University has been working on various projects in biotechnology in the areas of crop biotechnology, biological pest & disease control, biofertilizers, process engineering, funded by the Dept. of Biotechnology, besides its own efforts in the areas of vaccine development, immunodiagnostics, embryo transfer technology and plant tissue culture. Recently the University has been recognized by DBT as one of the centre of excellence and with a funding of nearly Rs 6 crores conducting active research in areas of plant abiotic stress, MAPKinase signaling networks in Brassica juncea, aromatic rice and metabalonomics of medicinal plants. Apart from disseminating and online accessing of relevant research information the centre is also providing support in experimental data analysis to the ongoing-research in the university. The bioinformatics centre is presently executing a project (BTPR7849/AGR/02/374/2006) on “Building MAP Kinase protein signaling networks in Arabidopsis and Brassica species” with DBT funding. The centre joined International initiative for sequencing of Brassica rapa genome and will be staring soon sequencing of part of Chr. 4 . Work on comparative metabolonomics for improvement of rice crop is 129 actively being conducted. Three hene sequences (LOX genes) from Octodecanoid pathway from Jasmonic acid biosynthesis ( regulating resistance to Blast disease) have been identified in silico and PCR amplified & sequenced gene sequences were submitted to GenBank. 3. Areas of specialization of the Centre ¾ development of Bioinformatics anlysis software tools & databases ¾ Metabolic pathway modeling & flux analysis. 4. Major activities of the centre during the year 2006-07.

1. Teaching: Every semester the introductory Bioinformatics course “Elements of Bioinformatics” is being offered to PG students of Biotechnology. 2. Research: The centre is also involved in conducting active research in development of databases for enumerating plant resources of Uttaranchal and two databases were developed. Also work on metabolic modeling and flux analysis of glycol sis in human cancer cells. Also a Prokaryotic genome visualization tool was developed . These research was findings were published in two international conferences and published in research journals. 3. Data analysis support: The centre has acquired state of the art bioinformatics packages such as DNA STAR, GCG Package, MOE, Hyperchem, and provides data analysis facility for the on-going research in area of Biotechnology. 4. Training Workshops: The centre has conducted has successfully conducted three DBT funded regional workshops - Fundamentals of Protein Docking (December, 18th-20th 2006) and Elements in Computer Assisted Analysis of Protein Structure and Function (12-14, Dec. 2005), Biological sequence analysis ( Nov, 16-18, 2007) and were attended by 87 participants respectively from all over the country. 5. Infrastructure facilities in the Bioinformatics Centre A. Broadband internet connectivity was started, B. Windows (25 computers) and Linux (2 computers), 2 servers, 2 printers. 6. Details about staff members: 1. Dr. Soma S. Marla, Coordinator, Since July 2006 to date , Two data wntry Operators on contractual basis hired, since 1999). 7. Educational activities with details of placement: Two bioinformatics courses- Elements of Bioinformatics and Use of computers in molecular modeling are being offered by the centre to students at the Post graduate level. Two Ph.D & two M.Sc students are being supervised in area of Bioinformatics. 8. Initiative to validate the outcome of bioinformatics resources Two plant databases documenting the plant resources of Uttaranchal. The database gave impetus to the currently executed project in GBPUAT on Bioprospecting of Uttaranchal plant resources. The centre is actively involved in knowledge mining from various online databases & disseminating knowledge available on the web. Various Bioinformatics packages available in the centre are very handy to the faculty in teaching & conducting, data analysis and knowledge discovery from experimental data. Bioinformatics approaches to metabolic pathway and flux analysis suggested by the centre are aiding the ongoing- research in departments of Biochemistry and Microbiology.Conducted metabolic modeling & flux analysis of Glycolasis in human cancer cells was presented at the Asia Pacific International Conference on 130 Bioinformatics held in N.Delhi, Dec. 2007. The outcome of the research is in Press for publication in a scientific journal. Bioinformatics centre, Pantnagar is also actively involved in training hands on experience in various Bioinformatics skills by conducting several workshops. These workshops became popular especially with student community attracting huge number of applicants, practically conducting the training programs hard due to limited funds and material resources available with the centre. Available Bioinformatics tools were placed in Centre’s web site: http://www.gbpuat.ac.in/acads/cbsh/Bioinformatics/home.htm. 9. Collaborative works/ initiatives: Bioinformatics centre from the very inception has been a good team player working with researchers from other disciplines such as Computer science, electronics, molecular biology and biochemistry. Bioinformatics centre is collaborating with Rothamstead research station as part of international initiative to sequence genome of Brassica rapa. For example the centre collaborated with the department of Electronics, Jaypee University of Information Technology, Shimla and successfully developed virtual electronic circuit that mimicked the Glycolasis occurring in human cancer cells. The centre is assisting the department of microbiology, GBPUAT in analysis the microbial pathways in Rhizobacterium species and building Phylogenic trees. The centre is also actively collaborating with Department of Environmental sciences in developing databases for managing crop environmental resources. 10. Databases and Software developed A Java based pathogen genome Visualization & annotation tool was developed at the centre. Development of Biological databases for documenting the rich diversity of Uttaranchal. Two databases were designed.A database of Cry genes present in Transgenic plants developed. 11. Papers Published Results of the work done at the centre was presented at two International Conferences and is being communicated for publication in Scientific journals as listed below: 1.Soma Marla and V. Singh (2007) Procaryotic Genome Visualization tool. In Silico Biol. 7, 0038 (2007) http://www.bioinfo.de/isb/2007/07/0038/ 1. Soma Marla et al, (2006), Comparative Structure and function analysis of chorismate synthase genes in Prevotella rumnicola, Online Journal of bioinformatics,Australia,7(1):35-45,2006 2. Harkewal Singh, Soma Marla and Manas Agarwal, (2006) Docking studies of Tau Protein, Engg. Letters, Hong Kong Protein, Engg. Letters, IMECS 2006: 154-159,http://www.informatik.uni-trier.de/~ley/db/indices/a- tree/a/Agarwal:Manas.html, Hong Kong. 3. Singh H, Marla SS, Verma D, 2007, Comparative Analysis of MMFF94x and AMBER99 force fields using Aspartic Proteases, Serine Proteases, Metallo-Proteases and Sugar- Binding Proteins asdifferent data sets. Online Journal of Bioinformatics, 8 (1) : 45-55, 200. 4. Rice DNA gene sequence submissions: LOX1, LOX2 & LOX3: GenBank Submission numbers: EU032587, EU032588 and EU146294. 12. Initiation of R&D activities in Bioinformatics Research in metabalonomics in humans and micro organisms is initiated in Initiation of R&D activities in Bioinformatics. Development of Biological databases for documenting the rich diversity of Uttaranchal and a databases was designedo of Cry genes present in Transgenic plants developed at the centre. Research in metabalonomics in humans and micro organisms is initiated in the centre. The bioinformatics centre is presently executing a project 131 (BTPR7849/AGR/02/374/2006) on “Building MAP Kinase protein signaling networks in Arabidopsis and Brassica species” with DBT funding. 13. Details of Training/ Workshop organized and total no. of user trained The center has conducted since its inception nine DBT sponsored training workshops and another two day workshop sponsored by Rural Bio complex for faculty of Plant Pathology was conducted. 14. Impact shown by the centre The database on Cry genes in transgenic plants was presented in the international conference on the Implications of the Cartogena Protocol on Biosafety, Held in N.Delhi in Nov., 2006. Conducted research on metabolic modeling & flux analysis of Glycolasis in human cancer cells was presented at the Asia Pacific International Conference on Bioinformatics held in N.Delhi, Dec. 2007. Soma Marla, Srivatsav.R, Patel G.(2007) PGV- Prokaryotic Genome visualization tool, Bioinformatics (In silico Biology, 2007).Various resources/ analysis tools available are available at Centre’s web site: http://www.gbpuat.ac.in/acads/cbsh/Bioinformatics/home.htm 15. Future Activities: Apart from continuing our initiated research efforts on development of databases and data analysis tools, research in metabalonomics we intend to strengthen this work in future. This we intend to do by employing comparative analysis of genomes of model species and there by discovery of agronomically useful orthologs in rice and Brassica. We are currently executing a DBT funded project (BTPR7849/AGR/02/374/2006) on “Building MAP Kinase protein signaling networks in Arabidopsis and Brassica species” with DBT funding. The execution of initiated research is severely hampered due to adequate infrastructure (hardware, furniture and equipment) and required software packages due to paucity of funds. To successfully conduct the current activities of teaching, training and research the Bioinformatics centre requires support in terms of manpower, infrastructure, acquisition of state of the art bioinformatics software packages.

Additional Information: Name of the Coordinator : Dr. Soma Marla ADDRESS : Coordinator, Bioinformatics sub-DIC MBGE, CBSH, G.B.Pant University of Agriculture & Technology, Pantnagar, USN.Dist.Uttaranchal. Tel:05944-233287, EMAIL: [email protected] , [email protected] WEBSITE: http://www.gbpuat.ac.in/acads/cbsh/Bioinformatics/home.htm Names of Contact persons: Dr. Soma Marla Coordinator, Bioinformatics centre EMAIL: [email protected]

132 Guru Nanak Dev University, Amritsar Coordinator : Prof. Gurcharan Kaur

1. Summary of the progress made by the centre from its inception : The Distributed Informatics Sub-Centre (DISC) at Department of Biotechnology, Guru Nanak Dev University, Amritsar was established in the 1995. Since its inception, the DISC has procured various scientific softwares like Microsoft Office 2000, SQL Server 2000, Borland Turbo c++ Suite, Visual Studio, Sigma Stat, Sigma Plot 2001, (V-7.1), Grafit version 4, Minitab 13.3, Lasergene-5 Sequence Analysis, Oracle 10g, Exome, Exome Blast and Exome Horizon software. In addition, different databases like Medline, Agricola, Agris, Life Science Collection, Food Science & Technology, Biotechnology Abstracts are also being subscribed for facilitating literature search by students and faculty members. So far about 22000 users comprising of students and teachers of Guru Nanak Dev University and neighbouring Institutes have availed the services of the Centre. The DISC is having 512 kbps leased line connectivity for Internet. At present the hardware installed includes Computers Systems (42) including three servers, two HP Coloured Laserjet Printer 5500 DTN and HP 3550, HP Laserjet Printers (six), Deskjet Printers (two), one Line Matrix Printer Wipro P500 LPM, one HP Scanner 6100C, one HP Coloured Scanner 7450C, Xerox Machine, Multimedia Projector and one laptop computer. In the last nine years the DISC has organized eight workshops benefiting more than 124 candidates.

2. Major research activities in Biotechnology and its related field at your institution : The biotechnology related research at Guru Nanak Dev University, Amritsar is being carried out in the Department of Biotechnology as well as in other Departments under the Faculty of Life Sciences. A number of research projects have been undertaken to study the molecular basis of stress adaptation in crops like sorghum and wheat which have resulted in cloning of many stress modulated gene fragments which are in the process of being characterized. Tissue culture techniques are being employed for micro propagation and production of secondary metabolites for different plants such as citrus, petunia, withania, delburgia, rose, cacti and datura. Lectins from different plant sources have been isolated and characterized for their possible biotechnological applications. Various enzymes of industrial importance have been purified from different microbial sources and characterised for biotechnological applications. Some of the enzymes included in the study are inulinases, xylanases, amylases, cellulases, glucose, isomerases, phytases, lipases, lignin, peroxiadases, etc. The potential of some of these enzymes is also being explored for biotransformation. Studies are also going on for determining the potential of selected microbial strains for bioremediation. Another potential area of research is in vivo and in vitro studies directing neuroaxogenesis and neurogenesis for rational therapy in neurodegenerative diseases and brain injuries.

3. Area of Specialization of the Centre : Biotechnology

133 4. Major activities of the centre during the year 2007-08 : A two day workshop on “Bioinformatics : Conceptualizing Biology in terms of Molecules” was organized on February 22rd & 23rd , 2007 by the Distributed Informatics Sub-Centre, Department of Biotechnology, Guru Nanak Dev University, Amritsar. Prof. S.I. Ahson, Head, Department of Computer Science, Jamia Millia Islamia, New Delhi, Mr. Vivek Mahale, Computational Biologist, Mascon Lifesciences, New Delhi and Mr. Y.M. Ragothaman, J.N.U., New Delhi were invited to deliver the lectures & to impart hands-on training to the participants The workshop was attended by sixteen participants from different Universities. The Centre has also started M.Sc. in Bioinformatics from the session 2006. Further, the Centre has purchased fifteen computers systems. DISC has also been updated by acquiring the latest version of Databases and Softwares. More than fifty research papers have been published in the last one year using the services of Centre.

5. Infrastructure facilities in the Bioinformatics Centre A. Computer & Communication facility : There are forty two Computer Systems (including three servers), one laptop computer, two coloured Laserjet Printer, one Line Matrix Printer, six Laserjet Printers, two Deskjet Printers, two Scanners, one Xerox machine. The center is also having one Multimedia Projector. Networking System : 512 kbps leased line connectivity Communication Facilities : Phone : 0183-2258431 Fax : 0183-2258272 ; Email : [email protected]

B. Scientific Software packages : Microsoft Office 2000, Microsoft Windows 2000, Windows 2000 Advanced Server (25 Client), SQL Server 2000, Borland Turbo c++ Suite, Visual Studio 6.0, Sigma plot 2001, Sigma stat, Grafit Version 4, Adobe Page Maker, Adobe Illustrator, Adobe Photoshop, Corel Draw, Minitab 13, Lasergene-5 Sequence Analysis software, Macromedia Studio MX-2004, Exome, Exome Blast, Oracle 10g and Exome Horizon.

C. Databases & other information resources Databases available are Medline, Agricola, Agris, Life Science Collection, Food Science & Technology, Biotechnology Abstracts.

6. Details about staff members working in the centre :

NAME OF THE DESIGNA PERIOD OF ABSORPTION STAFF TION WORKING STATUS Mr. Md. Sufian Badar Lecturer Since July, 2006 Sanctioned by the University in 2006 Mr. Manish Kumar Lecturer Since July, 2006 These three Mr. Harbhajan Singh Computer Since 3.10.2006 positions have Operator (Worked as DEO been taken over from 30.08.1995 - by the 2.10.2006) University w.e.f. DEO promoted to Computer Operator, Post advertised 01.04.1998 and will be filled shortly. Mr. Rajwinder Singh Computer Since 23.10.2007 Sanctioned by 134 Operator the DBT

7. Types of services provided : Every year about 3000-3500 students/research fellows/faculty members of Guru Nanak Dev University and from neighbouring Departments/Institutes are using CD-ROM based and online data, internet and computer facility of DISC. A 512 kbps leased line connectivity has been established in DISC Email, fax, Xerox, software analysis and data search facilities are also provided to other Life Science Departments.

8. Educational activities with details of placement : Department has introduced M.Sc Bioinformatics degree course from this session 2006-07 and DISC staff is imparting theoretical and practical training to the students of M.Sc Bioinformatics in Computational Methods for Sequence Analysis, Structural Biology and Bioinformatics, Genomics and Proteomics, Advanced Algorithms for Computational Biology, System Biology and Metabolic Pathway Engineering, Molecular Modeling and Computer aided Drug Design etc. Staff is also imparting theoretical as well as practical training to the students of M.Sc Biotechnology in Computer Applications & Bioinformatics.

9. Initiative to validate the outcome of bioinformatics resources : We are in the process to develop database which will be connected to NCBI server through the server of Indian Institute of Science, Bangalore. Then It will be easy for us to access online database of NCBI thru IISc Bangalore’s server.

10. Collaborative works/ initiatives : Biotechnology faculty collaborating with IHBT, Palampur, Delhi University, South Campus, Delhi, Jawahar Lal Nehru University, New Delhi, INSERM – France, AIST, Japan. Bioinformatics faculty from various DBT sponsored Bioinformatics Centres is regularly invited for delivering lectures to students of the department and training of research scholars & faculty during DISC workshops.

11. Databases/ Software packages developed : Database development : Global analysis of functional surfaces of core histones with comprehensive point mutants, Database of stress tolerant proteins of microbial, plant and animal system, Promoter prediction in E.coli.

12. Papers published or presented in the conferences with reference: More than fifty research papers have been published in the last one year using the services of Centre.

13. Initiation of R&D activities in Bioinformatics :

135 We are doing global analysis of functional surfaces of core histones with comprehensive point mutants.

14. Details of Training/ Workshop organized and total no. of user trained : In the last nine years DISC has organized eight workshops as per the details given below :

S.No. Title of Workshop /Year No. of Participants 1. Workshop on “Latest Trends in Bioinformatics” 16 March 4-6, 1998 2. Workshop on “ Use of Internet & Patenting in 14 Biosciences Research” March 23-24, 1999 3. Workshop on “ Role of Networking in Scientific 10 Information Processing” October 27- 28, 1999.

4. Workshop on “Internet and Web Designing” 15 October 5-6, 2000 5. Workshop on “Tools for Data Mining” 17 October 7- 8, 2003. 6. Workshop on “Tools of Bioinformatics” 21 March 3-4, 2005 7. Workshop on “Advances in Bioinformatics” 18 February 23rd & 24th , 2006 8. Workshop on “Bioinformatics: Conceptualizing 16 Biology in terms of Molecules” February 22nd & 23rd, 2007.

15. Impact shown by your centre on the growth of biotechnology and allied areas : The DISC is assisting students and faculty from neighbouring Departments and Colleges/Institutes to acquire scientific information through different databases/softwares available in the Centre. The Centre is also providing practical training in computer based application, software analysis, computational methods, etc. to M.Sc. Biotechnology & M.Sc. Bioinformatics and Doctoral students. Training workshops at regular intervals are also organized to apprise faculty and students of the latest developments in Bioinformatics. Sixteen thesis of M.Sc. students of the Department have been submitted last year taking assistance from DISC facilities. Introduced M.Sc. Bioinformatics programme from 2006 onwards with the help of facilities available in the Centre. Services of staff are being utilized for teaching of M.Sc Bioinformatics and M.Sc Biotechnology students.

16. Future activities : 1. Strengthening of M.Sc. Bioinformatics course. 2. To organize Workshop(s) for training of faculty and Ph.D. stdents. 3. Six months research project of M.Sc. Bioinformatics students. 4. Database development : Global analysis of functional surfaces of core histones with comprehensive point mutants, Database of stress tolerant proteins of microbial, plant and animal system, Promoter prediction in E.coli. 136

Additional Details : Name of the Coordinator : Prof. Gurcharan Kaur Postal Address : Distributed Informatics Sub-Centre (DISC) Department of Biotechnology Guru Nanak Dev University Amritsar – 143 005 Phone Number : 0183-2258431 Mobile : 09815450737 Email : [email protected] Website : http://department.gndu.ac.in/department/biotech.asp Name of Contact Person(s) : Prof. Gurcharan Kaur Email : [email protected]

137 Himachal Pradesh University, Summer Hill, Shimla Coordinator : Professor T. C. Bhalla

1. SUMMARY OF THE PROGRESS MADE BY THE CENTRE FROM ITS INCEPTION The Bioinformatics Centre of Himachal Pradesh University was established in 1999 with the approval and financial support of Government of India, Ministry of Science and Technology, Department of Biotechnology (DBT), New Delhi. The Centre is housed in the Netaji Subhash Chandra Bose Bhawan of Himachal Pradesh University This Centre has a DELL Make server (Xenon 2.8 GHz) running on Windows sever 2000/2003, 4 Intel Celeron 366 MHz and 3 HCL PIII 750 MHz machines running on Win 98 operating system and 10 Acer PIV 1.7 GHz machines running on WinXP operating systems. These entire machines are connected to server through LAN connectivity using CAT5 UTP cables. Internet connection is available through BSNL (ISP) and it can be accessed through all nodes. The Centre also has a Laser printer, Dot Matrix printer, 1200dpi Scanner, Inkjet printer, Xerox machine, Multifunctional printer, Laptop and a Multimedia projector, P-III 550 MHz server running on Windows 2000, ELNOVA; 1 KVA Off- Line UPS, Window XP Professional OEM Pack. The software’s available at the Bioinformatics Centre includes; Offline Derwent Biotechnology Abstracts CD- ROM database, Exome software for protein & gene sequence analysis and pDRAW32 Two databases were developed i.e. Traditional Fermented Foods and Beverages of Himachal Pradesh and Microbial and Mushroom Resources of Himachal Pradesh. The Centre has successfully organized thirteen training/workshops covering various aspects of the Bioinformatics and has trained around 202 participants during these trainings/workshops

2. MAJOR RESEARCH ACTIVITIES IN BIOTECHNOLOGY AND ITS RELATED FIELDS AT THE UNIVERSITY The research activities of the University in the area of biotechnology have major focus on following themes: i) Microbial enzymes: Purification, application in organic synthesis, medicine and food processing ii) Microbial diversity iii) Mycorrihzae iv) Traditional fermented food v) Nutraceutical aspects of mushroom

3. AREA OF SPECIALIZATION OF THE CENTRE i) Microbial diversity and resources ii) Enzymes: sequence, structure and functional relationship iii) Nucleotide and protein sequence analysis

4. MAJOR ACTIVITIES OF THE CENTRE DURING THE YEAR 2006-07 A Workshop training organized i) Two workshops were organized from May 4-6, 2006; Sep. 6-8, 2006 B Improvement expansion of databases 138 i) Traditional Fermented Foods and Beverages of Himachal Pradesh ii) Microbial and Mushroom resources of Himachal Pradesh C Research Project i) In silico study of cobalt binding proteins were initiated ii) Comparative genomics of fatty/lipid metabolism iii) Nucleotide and amino acid sequence analysis of Cholesterol Oxidase D Academic support activities i) Organized practical classes in ‘Computer Applications and Bioinformatics’ course for M.Sc. Biotechnology students. ii) Provided online/offline database access and internet facility to researchers and the faculty members of the various departments of the university E Following Infrastructure was added during the year 1. Ten Computer system Acer / HCL make (E-4300 processor, Intel Q965 chipset)/ 2. HP Color Laserjet-2605DTN Network Printer 3. HP Scanjet-4370/G3010 Photo Scanner

5. INFRASTRUCTURE FACILITIES IN THE BIOINFORMATICS CENTRE A. Computer and Communication i) Computer Hardware Server (Xenon 2.8 GHz, DELL Make) : One PC nodes (Acer 1.7 GH) : Ten Multi Media Projector (PLC-SU 30) : One Laser Printer (HP 2100 M, 1200dpi) : One Dot Matrix Printer (Wipro HQ 1040+) : One UPS (Pyramid, 3KVA, 30 min backup) : One Multifunctional printer (Modi XD-100) : One Xerox Machine (Modi 5821 IV) : One ELNOVA;UPS 1 KVA Off-Line UPS : One ii) Communication: Two Telephone lines: 0177-2832153 0177-2832154 Internet Facility, Email: [email protected] B. Scientific Software Packages i) Exome software for protein and gene sequence analysis ii) pDRAW32 for DNA cloning and sequencing C. Database and other Information Resources i) Offline Derwent Biotechnology Abstracts CD-ROM database

6. DETAILS ABOUT STAFF MEMBERS WORKING IN THE CENTRE

Name Designation Area of Period of working Absorption Specialization Status Prof. T.C. Enzyme and From the start of Bhalla Coordinator Fermentation Centre (1999) till date Technology Matter pending Mrs. Leena Data Entry Computer 9th July, 2001 till date with state Govt. Mishra Operator Applications for approval

139 7. TYPES OF SERVICES PROVIDED The Centre provided the following services to the students, research fellows, and faculty members of the University i) Derwent Biotechnology Abstracts Offline Database ii) Nucleotide and Protein Sequence Analysis iii) Bibliographic and Patents Search, E-Mail and Internet Access, Training in Bioinformatics iv) Bioinformatics library facility: Books 92, Journals 2

8. EDUCATIONAL ACTIVITIES WITH DETAILS OF PLACEMENT The Centre does not offer any Diploma/Degree course in bioinformatics

9. INITIATIVE TO VALIDATE THE OUTCOME OF BIOINFORMATICS RESOURCES: (N/A)

10. COLLABORATIVE WORKS/INITIATIVES i) The Centre has collaboration with the Department Biotechnology & Biosciences for development of databases. ii) Work related to structure, function relationship of enzyme has been undertaken in collaboration with Department of Biotechnology, Himachal Pradesh University, Shimla-5

11. DATABASES/SOFTWARE PACKAGES DEVELOPED Two databases were developed and validated i) Traditional Fermented Foods and Beverages of Himachal Pradesh ii) Microbial and Mushroom Resources of Himachal Pradesh

12. PAPERS PUBLISHED OR PRESENTED IN THE CONFERENCES WITH REFERENCES The Centre has not published papers in the area of bioinformatics However, the researchers from the Departments of Biotechnology and Biosciences have availed the facility of the Centre for publications

13. INITIATION OF R&D ACTIVITIES IN BIOINFORMATICS i) Structural, biophysical and biochemical aspects of various enzymatic proteins ii) Nucleotide and protein sequence studies of nitrile hydratase

14. DETAILS OF TRAINING/WORKSHOPS ORGANIZED AND TOTAL NUMBER OF USERS TRAINED This Centre has organized thirteen workshops/ training programs

1. Modern trends in retrieval of bioinformation (Oct 10-12, 2000) 2. Nucleic acid and protein sequence analysis (Sep 28-30, 2001) 3. Tools and techniques to access biological database (Jun 20-22,2005) 4. Recent trends in genomics and proteomics (Oct 24-26,2002) 5. Tools and techniques to access biological database-II (June22-23, 2005) 6. Trends in genomics and proteomics –II (Oct 20-22,2003) 7. Prelude to Bioinformatics (June14-16, 2004) 8. Internet Resources and Bioinformatics (Oct 11-13, 2004) 9. Tools and Techniques for Protein Structure & Drug Designing 140 10. (May16-18, 2005) 11. Application of Linux in Bioinformatics & Biocomputing (Sep.26-28.2005) 12. System Biology: A New Era in Bioinformatics (May 4-6, 2006) 13. Computational Biochemistry: Approaches and Applications(Sep.6-8,2006) 14. Tools and Techniques for Nucleic Acid & Protein Sequence (Sep.17-21, 2007) About 202 professionals from various institutions/ organizations have been trained through these training/workshops

15. IMPACT OF THE CENTRE ON THE GROWTH OF BIOTECHNOLOGY i) The facility of the on-line and offline database search related to literature in biotechnology has improved the quality of project reports, dissertations and publications ii) Exposure of M.Sc. Biotechnology students of the university to bioinformatics has helped students to join very good national R&D laboratories iii) The training of college teachers in bioinformatics at the Centre has proved beneficial in sensitizing undergraduate students to the domain of bioinformatics iv) 11 papers were published with the help our centre

16. FUTURE ACTIVITIES i) Sequence, structure and functional correlation of nitrile metabolizing enzymes ii) Development of simple software’s for enzymes and microbial growth kinetics iii) Development of a local database for some industrial enzymes

NAME OF THE COORDINATOR: Professor T. C. Bhalla POSTAL ADDRESS: Bioinformatics Centre (Sub-DIC), Himachal Pradesh University, Summer Hill, Shimla-171005. PHONE & FAX NUMBER: 0177 2832153, 0177 2832154 E-MAIL: [email protected], [email protected] NAME OF CONTACT PERSON: Professor T. C. Bhalla

141 Indian Agricultural Research Institute, New Delhi Coordinator : Dr. H. Chandrasekharan

1. Summary of the progress made by the centre from its inception Bioinformatics Centre at IARI, New Delhi was established in 1989 under Biotechnology Information System (BTIS) Network to function as a computerized information base in fields related to Agricultural Biotechnology in particular and fields allied to agriculture in general. Since its inception, the Centre has provided various services, such as on- line bibliographic search through network, off-line bibliographic search through CD- ROM server, electronic mail, internet, creation and update of database, Statistical analysis of research data, protein sequence analysis, training programmes, workshops on bioinformatics and current awareness services etc., to the researchers, students and farmers. Biotechnological Abstract Information retrieval System (BAIRS) was developed by the Centre and extensively used by students and researchers. The Centre became a part of Unit of Simulation and Informatics (USI) in November 2003. The USI is entrusted with the additional responsibility of maintaining the Institute’s campus network, the website and the web server administration. While initiating the work on e-agro-advisory in 2005, the Centre has developed the IARI Centenary Year documentary film on “‘IARI-A Catalyst of Change’ that was widely circulated to visiting dignitaries since 2006. During the year under report, apart from Bioinformatics Studies, a teleconference facility has been developed and made operational at IARI.

2. Major research activities in Biotechnology and its related fields at your institution • Structural and functional predictions of hypothetical proteins • Development of specific software in Bioinformatics, • Novel Gene Identification in Medicago trucatula using In silico approaches. • Analyses of database on pedigree management of wheat, maize, rice, chickpea and mung

3. Area of Specialization of the centre: Agri-Informatics (Comprising Computerized Information Systems in various branches of agricultural sciences with special reference to Agricultural biotechnology/Bioinformatics)

4. Major activities of the centre during the year 2007-08 (15 lines) • Insilco prediction of structure and function of hypothetical proteins: In our study we have tried to predict the structure and function of the protein (acc, no AAG 52239) of Arabidopsis thaliana which is hypothetical in nature. Arabidopsis thaliana is a mustard weed which contains 27,029 protein coding genes (TAIR7). Majority of proteins are still unannotated and have been termed as unknown or putative or hypothetical. The difficulty in the prediction of structure and function of hypothetical protein is due to its low similarity with other known proteins. Therefore, more emphasis was given on fold recognition and domain identification. In this study we used number of online as well as offline tools. We have found that our query sequence is quite similar to 2bw3A sequence and this template have the same domain i.e. hATC dimerisation domain.

• Novel gene identification in Medicago truncatual using in silico approaches: Present work was carried on completed sequences of Medicago truncatula which is a forage legume. Genes from M.truncatula share identity to legumes and established symbiotic relationships with nitrogen fixing Rhizobia and is colonized 142 by mycorrhizal fungi. In this study several gene finding programs were used to find genes in the sequences, which utilized one or the other gene-fining algorithmic strategies. For increasing gene prediction accuracy we included both instrinsic and extrinsic approaches by using ab-initio programs and blast search. We also used TWINSCAN which uses a combination of both approaches for prediction enhancement. The novel genes as predicted by most of the softwares was composed of single exons, hence there was no splice results when NNSplice and NetPlantGene were used on this gene which again validates our results. Some of the gene finding programs used were GENSCAN, GeneID, GrailEXP, GenMark.hmm and Augustus. BLAST analysis was performed on the genes predicted by these programs to infer homology. WU-BLAST was also executed against the EST sequences of M.Truncatula to enhance the validity of the gene. Further confirmation of the result was done through splice-site detection programs and gene prediction program well trained on dicotyledons databasets (Diogenes, TWIMSCAN). From the study, nineteen new genes were predicted from the seven sequences. Out of 19 sequences, 10 had a function, 8 were of unknown function and 1 sequence was novel gene.

5. Infrastructure facilities in the Bioinformatics Centre (25 lines)

A. Computer & Communication facility : Sun Enterprise 420R Server, SGI 02+ computer system, Alpha 200, 4/233 computer system, Axis online CD-net DVD Rom Server, Pentium –IV Multimedia Systems, ILL from both VSNL and ERNET are available for various web related activities.

B. Scientific Software packages: Centre is in possession of certain scientific software packages, which have been procured / developed over the years. These include Advanced Sequence Analysis Software “EXOME”; EASI/PACE image processing; SPANSGIS, simulation models such as WTGROWS, INFOCROP, ORYZA, CERES; user-friendly information system software for rice, maize, wheat pedigree, chickpea, rice IPM, Indian soils, pesticides; Biotechnological Abstract Information retrieval System (BAIRS).

C. Databases & other information resources: • Database of Crop Production & Productivity • Database of Area under High Yielding Varieties • Land Use Database

6. Details about staff members working in the centre (Name of the staff, Designation, Specialization and period of working. Please indicate their absorption status) • Dr.H.Chandrasekharan, Head & Principal Scientist (Agricultural Physics- hydroinformatics and DSS for Natural Resource Managent) - Permanent • Dr. S. K. Bandhyopadhyay, Sr.Scientist (Agronomy-Crop informatics and crop growth simulation modeling) – Permanent. • Mr. A. K. Mishra, Scientist (Computer Applications) – Permanent – now on study leave. • Mr. M. S. Pillai, Technical Officer – Permanent • Mr. Naresh Katoch, Technical Officer – Permanent • Mr. Rajender Sharma, Technical Officer – Permanent • Mr. Kamal Batra, Technical Assistant – Permanent • Mr. Sanjiv Kapur, Technical Assistant – Permanent

7. Types of services provided • Software and Simulation Models development 143 • Creation and update of databases (agri and bioinformatics) • Statistical analysis of research data (students and staff of the institute) • Human resources development

8. Educational activities with details of placement • Several M.Sc. and Ph.D students of IARI are being guided in their research by scientists of this Centre. A relatively new discipline of ‘Simulation and Informatics’ with four PG courses has been functioning at this Unit since the academic session 2005-06. This serves as a minor discipline for M.Sc. and Ph.D. students of IARI. Of these, the course titled, “Foundation Course on Informatics’ is one of the compulsory courses for all M.Sc. and Ph.D. students of IARI. • The Centre provides facilities for attachment training for a limited number of the final year students of M.Sc Bioinformatics for completing their short-term projects. Many students from outside universities and institutes avail this opportunity. More than five such trainee of the Centre got placement after completing their tenure at the Centre. 9. Initiative to validate the outcome of bioinformatics resources Work has been initiated for application and validation of various bioinformatics resources for nucleotide and protein sequence alignment, gene prediction, genetic markers establishment and protein structure prediction and modeling.

10. Collaborative works/ initiatives Our Centre has collaboration with Department of Science and Technology (DST), National Informatics Centre (NIC) and a score of other research and development organizations.

11. Databases/ Software packages developed Databases • Crop Production & Productivity • Area under High Yielding Varieties • Land Use • Fertilizer Consumption • Indian literature on Tissue Culture, Photosynthesis & Plant Molecular Biology

Crop growth simulation models • INFOCROP- a generic crop growth simulation model • INFOSOIL • INFOCANE • Simple models for tea and coconut

User-friendly information system software • Rice • Wheat Pedigree • Maize • Chickpea • Rice IPM • Indian Soils • Pesticides

12. Papers published or presented in the conferences with reference

144 1. Rajendra Sharma, Garima Khandelwal and Chandrasekharan H. 2007. Novel Gene Identification in Medicago truncatula using In silico approaches INCOB- 2007, Hong Kong 2. Rajendra Sharma, Abhiranjan Prasad and Chandrasekharan H. 2007. Micro Designer~a standalone tool for designing micro-RNA INCOB-2007, Hong Kong 3. Sharma, Sasmita Joshi and H. Chandrasedharan 2007. In-silco prediction Rajendra of Structure and Function of hypothetical protein of Arabidopsis thaliana. (Communicated).

13. Initiation of R&D activities in Bioinformatics Application of bioinformatics tools is being initiated for nucleotide and protein sequence alignment, gene prediction, genetic markers establishment and protein structure prediction and modeling. We aim to identify sequence genes and their products, which are responsible for quality traits, pest and disease resistance, drought resistance, salinity resistance in different crops and genes responsible for pesticide resistance in important pest species of crops. Besides, ICT tools are being used for designing user-friendly application software on agri-informatics which will ultimately be made online.

14. Details of Training/ Workshop organized and total no. of user trained • PG Education and Placement ¾ Scientists of this Centre are guiding M.Sc. and Ph.D. students of IARI as part of their research activities. Since last year (2005) the Unit is offering four PG Courses in the areas of ‘Simulation and Informatics’ at IARI. This discipline serves as a minor discipline for M.Sc. and Ph.D. students of IARI. Of these, the course titled, “Foundation Course on Informatics’ is compulsory for all PG students of IARI.

¾ The Centre provides facilities for attachment training for select final year students of M.Sc. Bioinformatics for completing their short-term projects. Many students from recognized universities and institutes avail this opportunity. During the year under report, two traineeship students of the Centre got placement after completing their tenure at the Centre.

o Details of Training organized

SNo. Name of the training Duration No. of From To Participants

1 Emerging trends in Agri- 13-2-07 05-3-07 20 informatics* (scheduled in February- March 2007)

2 Internet training 03-7-07 04-7-07 12 programme

15. Impact shown by your centre on the growth of biotechnology and allied areas. In this you may highlight the details like number of paper published/ number of papers published with the help of your centre, how your centre is promoting various activities of your organization and neighboring institutions, manpower trained, tools developed, patents & copyrights acquired and other services offered etc.

145 Centre is entrusted with developing the discipline of Bioinformatics as a component of Agri-informatics under the Unit of Simulation and Informatics at IARI. The Centre has taken active role in developing crop related databases, simulation models, user friendly information software in agriculture and imparting bioinformatics related training to the stake holders from time to time. Efforts are on to upgrade the present set up to a Division having M.Sc. / Ph.D. degree programme in the field of Agri- Informatics during the XI Plan period.

16. Future activities 14. Strengthening research on bio- and agri-informatics aspects as related to crops 15. To make IARI website as state of art for knowledge dissemination of Agri- Bioinformatics to various stakeholders.

Additional Details:

Name of the Co-ordinator Dr. H. Chandrasekharan, Head, Unit of Simulation & Informatics, Address A-0 Block, LBS Building, IARI, New Delhi-110012 Phone 011-25841255, 011-25842490, Fax: 011-25843719 Email [email protected], [email protected]

Name of Contact persons

Dr.H.Chandrasekhran, Mr.M.S.Pillai, Mr Rajendra Sharma < [email protected] > Indian Institute of Science, Bangalore Coordinator : Professor M. Vijayan

1. Summary of the Progress made by the Centre from its inception The Centre has been recognized as a Centre of Excellence in structural Biology and Biocomputing by the Department of Biotechnology, Government of India. The Centre created in 1985 was one of the earliest in the country to establish information dissemination and formal teaching in bioinformatics. In tune with the evolving nature of this discipline, there has been a paradigm shift in the focus of the Centre’s activities, which are now directed towards strengthening integrated research programmes in several areas of bioinformatics with a long-term goal of developing computational models of biological macromolecules, metabolic pathways and cellular processes at different levels of abstraction, to aid in new hypotheses generation, new ways of research in biology and in generating application opportunities in drug and vaccine discovery.

2. Major Research Activities Genome Analysis, De-novo Design of Bio-molecules, Protein Structure Prediction, Structural Biology and Structural Bioinformatics, Systems Biology, Pathway Modeling and Application in Drug Discovery, Computational Immunology, Biological Networks, Protein Function Prediction, Drug-DNA interactions, Creation of Value-added Knowledge-bases, Algorithm Development and Software Engineering

146 Significant leads & achievements Possible Applications Systems biology System design, Pathway modeling, Drug target M.tuberculosis system level models identification, Gene essentiality prediction

Pharmacodynamic modeling Predicting adverse effects of drugs- useful in every stage of drug discovery Integrated Databases- LectinDB Integrated knowledge-bases of lectins CancerlectinDB CADB-2.0 Analysis of backbone conformation angles

Genome Sequence Analysis Algorithm development PocketDepth A novel algorithm for cavity detection in proteins FAIR (Finding All Internal Repeats) Efficient data retrieval from massive databases, Protein classification and similarity estimation Data mining Non-canonical interactions in protein Drug-receptor interactions, Derivation of structures fundamental parameters for protein structural Determinants of ligand recognition analysis,

Software engineering PSAP Protein structure visualization and knowledge RPMS extraction RP-2.0

Structural bioinformatics Protein Interaction Finger Printing, Anion recognition modules and Structural and interactions modules Phospholipase-A2 complexes Building macromolecular assemblies Fast access to latest information that enables Mirror sites large scale data mining research PDB, SCOP, GDB Training several students in bioinformatics for Human Resource development academic institutions and industries

3. Areas of Specialization of the centre Structural Biology, Structural Bioinformatics, Genome Analysis, Structural and Functional Genomics, Systems Biology, Fundamental aspects of Drug and Vaccine Discovery (including Structural Pharmacology and Computational Immunology), Development of highly specialized and versatile Databases, Development of software tools and software engineering.

4. Major research activities during the year 2007-2008 The major research activities at the Bioinformatics Centre can be classified into the following areas: (a) Genome sequence and structural analysis, (b) Development of new algorithms in bioinformatics, (c) Internet computing, (d) Integrated Database development, (e) Structural analysis of biological macromolecules, (f) Structural pharmacology, including in-silico drug discovery, (g) computational immunology and (h) Systems biology. While the first four pertain to development of new concepts and resources that often goes back into the public domain resource bank in bioinformatics, the other areas pertain to application of the existing information to generate new kinds of knowledge that may ultimately lead to useful applications not only in the understanding of basic science but also as useful therapeutic pointers. Examples of specific projects are ‘de novo’ design of biologically active and conformationally important peptides,

147 structural biology and bioinformatics of phospholipase and thermophilic enzymes, deriving determinants of carbohydrate recognition, creation of an integrated plant lectin knowledge-base, metabolic- flux balance analysis and modeling of pathways relevant to Mycobacterium tuberculosis, development of a virtual mycobacterial cell, development of algorithms for predicting T-cell receptor antigens and analysis of protein-protein interaction networks.

5. Infrastructure facilities at the Bioinformatics Centre The Bioinformatics Centre, which is funded by the Department of Biotechnology (DBT), has been successful in providing continuous and up-to-date information and access to databases and software. Databases include nucleic acid and protein sequences and their 3-dimensional structures. Software available at the centre enables sophisticated analysis of sequences, manipulation, visualization and study of the three-dimensional structures of biomolecules as well as a wide range of genome analysis. The centre has SYBYL and INSIGHT modelling packages. In addition, the centre has several computing machines, graphics workstations and several Intel based Linux and Solaris workstations.

6. Details of faculty members working in the centre Dr. S. Ramakumar Professor Structural Bioinformatics, Machine learning methods in life sciences, Sequence Analysis, Genome Analysis

Dr. K. Sekar Principal Research Structural Biology, Internet Scientist computing, Datamining, Algorithm Development and Creation of Integrated knowledgebases

Dr. Nagasuma Chandra Principal Research Systems biology and its Scientist application in drug and vaccine discovery Sequence and Structural bioinformatics

Dr. Debnath Pal Asst. Professor Structural bioinformatics Comparative genomics, Systems Biology

7. Types of services provided The centre plays an active role in disseminating various types of information in biological sciences. Some examples are, the three-dimensional Protein Structures, and the gene sequences of all the genomes available in the Genome database. In addition, the centre hosts a major mirror server for Structural Classification of Protein structures. The recently available genome databases as well as derived specialized knowledge bases are also made available at the centre. Further, the centre also has Cambridge Structural Database (CSD), which contains more than 4233,752 small molecule structures. The faculty at the centre also provide advice to various research groups about bioinformatics methods relevant to their research problems as well as in their interpretation.

8. Educational activities with details of placement Hundreds of research associates and other personnel have been trained at our institution under several DBT programmes. 64 project assistants, 22 project trainees and 80 summer trainees have been trained at the Bioinformatics centre 148 and the Interactive Graphics Facility. The faculty members of the centre have participated in the training of scores of Ph.D. students at the institute. Most of them are well placed in IT and Biotech companies and in reputed academic institutions in India and abroad. In addition, the faculty members of the centre are offering the following three courses to the Ph.D. students of the institute.

SE 301: Bioinformatics SE 302: Computational approaches to Drug Discovery SE 303: Chemoinformatics Further, training programmes and workshops are a regular feature of the activity of the centre to introduce the available facilities and their application to users.

9. Initiative to validate the outcome of bioinformatics resources The faculty at the Centre has been publishing scientific papers and articles in well recognized international journals. This is a pointer to describe the outcome of the usage of the bioinformatics resources available at the Centre. In addition several other research groups, both within and outside IISc have also acknowledged the usage of the facilities in their publications and research thesis. Another major outcome of the usage of the resources is the large number of databases and software tools that are made available through the world-wide- web, accessible from anywhere in the world.

10. Collaborative works/initiatives The faculty members of this centre are actively engaged in several collaborative projects such as (a) the International structural genomics program on Mycobacterium Tuberculosis funded by National Institutes of Health, USA, (b) Institute wide Computational Genomics project funded by Department of Biotechnology, Govt. of India (c) The faculty members of the centre are involved in the Institute wide Structural Genomics funded by Department of Biotechnology, Govt. of India, (d) a collaborative project with Satyam computers for profiling in drug discovery, (e) joint project using genetics aided systems biology for identifying interactions between genes involved in E.Coli protein biosynthesis funded by DBT and (f) participant in centre of excellence on molecular strains of mycobacteria funded by DBT.

11. Database/software packages developed The centre is actively involved in creating softwares and databases for those who are working in the area of structural Bioinformatics. Some of the softwares developed at the centre are PSAP, RPMS and RP-2.0. The faculty members of the centre are involved in creating web-based databases like CADB-2.0 etc.

12. Papers published or presented in the conferences with reference The faculty members of the centre have published several papers (about 30 in the year 2007) in the international journals, which have a high impact factor. In addition, the members of the centre are involved in guiding/co-guiding several Ph.D. and M.Sc (Engg) students.

13. Initiation of R & D activities in Bioinformatics In the last few years, the faculty members of the centre have provided consultancy, advice or training to the biotechnology institutions/ industries 149

14. Details of Training/workshop organised Every year, the centre conducts workshops and training programmes in areas related to Bioinformatics. The workshop and hands-on experience sessions were well appreciated by participants from all over the country. This provided an opportunity for useful interactions among people from various fields, which is particularly important in the area of bioinformatics, a purely multidisciplinary subject. The following seminars were conducted.

Course Sponsoring agency Duration Target group Drug Design Workshop DBT & IISc 5 days, Biology , Pharmacology & July 2007 Medicinal chemistry Faculty, Post-docs, graduate students, Pharma R & D Structure and Ligand Open Eye Software 1 day, Dec Bioinformatics & biophysics based drug design 2007 Students & Faculty

15. Future activities The range of projects being carried out, reflect the long-term goals of the centre towards genomic-scale studies of hypotheses generation, new ways of research and in generating application opportunities. The following are the main thrust areas: Systems Biology, Structural Biology and Bioinformatics, Molecular Design, Molecular Modelling, Structural Pharmacology and Computational Immunology and Human Resource development. The centre will continue to emphasize the activities of structural bioinformatics. In the future, newer databases and software will be developed. The centre will continue to contribute significantly in the field of Systems biology, computational approaches to inhibitor design, drug and vaccine discovery.

Name of the Coordinators: Professor M. Vijayan, Coordinator, Interactive Graphics Based Molecular Modelling, Professor, Molecular Biophysics Unit and Distinguished Biotechnologist, Indian Institute of Science, Bangalore 560 012, India (Phone: 080-23600765; Fax No. 080-23600683; E-mail: [email protected]) Professor S. Ramakumar, Coordinator, Bioinformatics Centre, Indian Institute of Science, Bangalore 560 012, India. (Phone: 080-23601409; Fax No. 080-23600683; E-mail: [email protected])

Name of Contact person for both facilities Dr. K. Sekar, Bioinformatics Centre, Indian Institute of Science, Bangalore 560 012, India. (Phone: 080-23601409 and 080-22933059; Fax No. 080-23600683; E-mail: [email protected] and [email protected]).

150 Indian Institute of Spices Research, Calicut, Kerala Coordinator : Dr. Santhosh J. Eapen

1. Summary of the progress made by the centre from its inception The Bioinformatics Centre was established at the Institute as a sub-centre under the BTIS network during 2000. It has a mandate to provide computational support and training to students and scientists. The centre, since its inception, has organized over a dozen training programmes, some of them of 21 days duration. The Centre has a dedicated Internet connectivity (1 mbps), necessary hardware and software resources to initiate and support the Spice Bioinformatics/Biotechnology programmes. A Bioinformatics Library with more than 100 reference books, journals, databases etc. was also set up. A round the clock browsing facility, SpicE-Lab, is also made available for the benefit of students and research fellows. Development of integrated databases on various aspects of spices viz. genetic resources, their chemical constituents, pathogens of spices etc. was one of the key activities of this centre. As on today, there are 14 databases to its credit and many of them are available online. Biodiversity informatics: Information management has central place in the conservation of plant and microbial genetic resources. Realizing this, the Centre has launched several databases under the series ‘Spice Genes’. a. Spice Genes – Part 1: Black Pepper: A database of black pepper germplasm resources available at IISR. Available online as well as CDs (http://www.iisr.org /germplasm/index.htm). b. Spices Genes-Part 2: Curcuma Species: An offline database on various Curcuma species. c. Spices Genes-Part 3: Myristica Species: A database of different Myristica species and nutmeg germplasm. d. ‘Piperbase’ – a database of Piper species of India that includes botany, taxonomy, agronomy, biochemistry and medicinal properties of various Piper species. e. PLASBID: A database on plant associated bacteria integrated with several tools like sequence editing, primer analysis etc. f. PhyDisH: A database on Phytophthora diseases also includes searchable information on Phytophthora cultures maintained in the Institute repository. Chemoinformatics: Integrated databases pertaining to chemical compounds available in various spices are also developed. A library of chemical compounds of spices is under preparation. a. Chitinase database: An online database (http://www.iisr.org/bioinformatics /project/index.htm) on plant chitinases. b. PAL database: An enzyme database of Phenylalanine Ammonia Lyases (http:// http://www.iisr.org/bioinformatics/project/index.htm) c. CardCC&Mpbase: A cheminformatics database on chemical compounds in cardamom. Other databases: Several other databases dealing with patents, tissue culture protocols, spice literature are also developed by the Centre.

2. Major research activities in Biotechnology and its related fields at your institution The major areas of Biotechnology work at IISR are: • Molecular characterization of spice germplasm accessions, pathogens and biocontrol agents. • Diagnostics for major pests and pathogens in spices.

151 • Gene expression and genetic transformation in spices for desirable agronomic traits. • Marker assisted selection in major spices and efficient biocontrol agents. • Cloning and sequence analysis of genes of economic importance from spices and related genera, OUT in plant viruses, bacteria, fungi and nematodes etc. • Biosynthesis of secondary metabolites and characterization of bioactive principles in spices. 3. Area of Specialization of the centre Biodiversity and Biotechnology of Spices 4. Major activities of the centre during the year 2007- 08 The Centre has developed two databases viz. PLASBID - a bioinformatics based bacterial identification database and PASSCOM, on predicted activity spectra of spice compounds. During the reporting period only one bioinformatics training programme of one month duration was conducted for the M.Sc. students. The centre has provided traineeship to two candidates and three students were selected for doing their M.Sc. project work. The Centre has sustained the Bioinformatics lab with a dedicated leased line connectivity, hardware and software tools which is an excellent asset to the research community of the region. The centre also maintained the Institute website (www.spices.res.in) and continued to provide intranet (SpiceNet) and web mail (Spicemail) services to the institute. Support on website development was extended to other organizations under ICAR too.

5. Infrastructure facilities in the Bioinformatics Centre iv. Computer & Communication facility Item No. Remarks Internet connectivity - Reliance Leased line – 1 mbps Servers 3 HP & HCL Work station 1 - PCs 16 - Laser printers 2 - Scanners 2 - Dot matrix printer 1 - UPS 2 5 KVA & 4 KVA LCD projector 1 - Photocopier 1 - Router, switches & - For leased line connectivity modem Scientific Software packages Discovery Studio of GENE- DS GENE, JEMBOSS, EMBOSS, Modeller, Autodock, BLAST and FASTA, ClustalW,X, Phylip, Chime, Rasmol, Cn3D viewer and Swiss PDB viewer, Fast PCR. CAP3, PHRAP and SEAN. Databases & other information resources Crop Pest CD, Derwent Biotechnology Abstracts, Ekaswa Patent Database, Dspice – Literature database on spices, Functional Plant Biology, Mycological research 6. Details about staff members working in the centre (Name of the staff, Designation, Specialization and period of working. Please indicate their absorption status) Name Designation Specialization Period of Absorption working status K. Jayarajan Technical Computer Permanent staff Permanent staff Officer Science 152 A. Chandrasekar Research Msc.Biotech. 17-10-2007 NIL Associate onwards V. Sathyanath JRF MCA 20-03-2006 NIL onwards A. Riju JRF Msc. 22-10-2007 NIL Bioinformatics onwards 7. Types of services provided a. Computational and Information support to various R&D projects of the institute. b. Maintenance and updating of the institute website (www.iisr.org), intranet (‘SPICENET’) and the email facility (‘Spicemail’). c. Designing and developing customized databases, web portals and software for scientists, administration etc. d. Providing round the clock access to Internet and Bioinformatics tools through the facility called E-Lab. e. Organizing in-house training for institute staff in computers and other IT areas. 8. Educational activities with details of placement Bioinformatics Centre collaborates with NIT, Calicut and offers Bionformatics as an informatics subject for M.Tech (Computer Science) students. The Centre provides opportunity to MSc Bioinformatics students from other institutes and universities to carry out their project work. 9. Initiative to validate the outcome of bioinformatics resources The above mentioned databases developed by the Centre are utilized by the other departments and nearby institutes. Software programmes like SpicePat and Sign–O-Bacteria are also validated in wet lab studies. In silico designed primers are routinely used in wet lab studies. 10. Collaborative works/ initiatives Active collaboration with nearby BTISNet centres, especially with the centres at CPCRI, Kasaragod and Calicut University in organizing Bioinformatics trainings and sharing of resources. The Centre also collaborates with NIT, Calicut for conducting a Bioinformatics course for M.Tech students. 11. Databases/ Software packages developed • PLASBID: A database on plant associated bacteria integrated with several tools like sequence editing, primer analysis etc. • PASSCOM: A database on predicted activities of spice compounds is being developed. The module on black pepper has been completed. • Integrated database on Phytophthora spp.: The databases PIR and PHYDISH are integrated to serve as a National Repository of Phytophthora. 12. Papers published or presented in the conferences with reference • Eapen, S.J and Chandrasekar, A, 2007. Primer designing and molecular visualization. Paper Presented at Workshop on Applications of Bioinformatics and Biotechnology at Bioinformatics Centre, Calicut University.

13. Initiation of R&D activities in Bioinformatics R&D activities have been initiated on EST analysis of various spices. The outcome of this study will be used for developing an exclusive database on Spice Genomics. Work on an integrated database on spices with different modules has also been initiated. 14. Details of Training/ Workshop organized and total no. of user trained • Summer training 2007 in Biotechnology and Bioinformatics, 05th May to 05th June 2007, 20 trainees.

153 15. Impact shown by your centre on the growth of biotechnology and allied areas. In this you may highlight the details like number of paper published/ number of papers published with the help of your centre, how your centre is promoting various activities of your organization and neighboring institutions, manpower trained, tools developed, patents & copyrights acquired and other services offered etc. Several students are availing the facilities of the Centre for carrying out their M.Sc. and Ph.D. research projects. Currently out of the 22 M.Sc. students, 12 are from the Biotechnology stream while three are Bioinformatics students. The Centre has submitted two research papers for publishing in reputed scientific journals. Two molecular biology papers published from the Institute had significant support of the Centre. As in the previous years, the Centre played a crucial role in the HRD activities of the Institute. The Summer School in Bioinformatics organized at the Institute during May-June 2007 was well attended. The faculty has extended support to the Bioinformatics training programmes organized at CPCRI, Kasaragod and Calicut University. 16. Future activities R&D activities in comparative genomics, chemoinformatics, EST analysis and QSAR studies on bioactive compounds in spices will be strengthened. Bioinformatics support will be extended for gene/QTL mapping, expression studies etc. The existing databases and institutional repositories will be updated and maintained. Development of a holistic database on spices is also envisaged. HRD and educational activities will be continued in collaboration with nearby institutions like NIT, Calicut and DOEACC, Calicut.

17. Additional Details: Name of the Coordinator : Dr. Santhosh J. Eapen Postal Address : Bioinformatics Centre Indian Institute of Spices Research, P.B. No. 1701, Calicut – 673012, Kerala Phone Number : 0495-2731410, 0495-2731566 FAX : 0495 2731187 E.Mail : [email protected] Website : www.spices.res.in Name of Contact Person(s) : Dr. Santhosh J. Eapen E.Mail : [email protected], [email protected]

154 Indian Institute of Technology, New Delhi Coordinator : Dr. A. K. Srivastava

1. SUMMARY OF THE PROGRESS MADE BY THE CENTRE FROM ITS INCEPTION. The Biochemical Engineering & Biotechnology department was established in 1969 at IIT Delhi to generate quality human resource & undertake research work particularly in the area of Biochemical Engineering & Industrial Bio- technology. The department is presently offering a unique five-year dual degree (B.Tech and M.Tech) program in Biochemical Engineering and Biotechnology. The department also has a two-year M.S. (By research) and very interdisciplinary Ph.D. program in the area of Biochemical Engineering and Biotechnology.

The BTIS sub-centre at IIT Delhi was established in 1989 (equipped in 1991) by the support of the DBT, GOI, New Delhi, as a part of the nation wide networking of Biotechnology Institutions of National importance. 2. MAJOR RESEARCH ACTIVITIES IN BIOTECHNOLOGY AND ITS RELATED FIELD AT YOUR INSTITUTION. The department is very actively engaged in almost all emerging areas of Biotechnological research e.g., Bioprocess Engineering, Down Stream Processing, Bioprocess control, Modeling and Simulation of Bioprocesses, Plant Cell technology, Animal cell Technology, Genetic Engineering, Environmental Engineering, Bioinformatics, Molecular Machines and Nanotechnology etc.

The BTIS-sub centre acts as an integrated information resource centre in the teaching and research in all the above areas of Biochemical Engineering and Biotechnology. The centre provides total computer support for extensive computations, information retrieval and dissemination for all the departmental courses and to the ongoing research projects (M.Tech., Ph.D. and sponsored projects) of the department and also to the neighboring educational centers. Recently the sub-centre has graduated from an Information Resource Centre to an “Instruction facility” for quality teaching and research particularly in Mathematical Modeling of bioprocesses, Artificial Neural Network based bioprocess control and Bioinformatics. 3. AREA OF SPECIALIZATION OF THE CENTRE. The main research areas of the department are Biochemical Engineering / Industrial Microbiology / Fermentation / Bio-informatics 4. MAJOR ACTIVITIES OF THE CENTRE DURING THE YEAR 2007 - 08 • The Department organized an International Symposium “Biohorizon 2007”, “A Joint Indo-Korean Symposium on Biotechnology” during 22-24 Feb - 2007. • Fifth Practical Summer Training in Biochemical Engineering & Biotechnology during June 20 – July 21 2007. • Proposed workshop on “Bioinformatics Fundamentals and Whole Genome Analysis” during February 2008 5. INFRASTRUCTURE FACILITIES IN THE BIOINFORMATICS CENTRE A. COMPUTER & COMMUNICATION FACILITIES

155 IBM Netfinity 5000 Server : 1, Dell Server with dual Processor : 1, Intel Xeon Server : 1,Desktops (Pentium IV/III/II) : 4/2/1, Workstations (Intel Core 2 duo/ Dual core): 5/10, Silicon Graphics Workstation : 1(From Institute grant), Color LaserJet Printer: 1(From Institute grant)LaserJet Printer: 3, DeskJet Printer : 2, Scanner : 2, Fax Machine: 1, Xerox Machine: 1, Networking speed through IIT, Delhi network : 2X5 Mbps. B. MAJOR DATABASES /SOFTWARE PACKAGES: DNA Star, Chem Draw, Design Expert (Statistical Optimization Software), Matlab 2007 with Bioinformatics Tool Box (Access through Institute LAN), Windows Operating Systems (Windows XP, Windows Server), Microsoft Office, Derwent Biotechnology Abstract (1982-Till date) (on CD), Medline(1982-1998) (on CD), Science Direct by Elsevier Science (On-line Access), Institute is the member of INDEST consortium initiated by MHRD, Institute has the provision for procurement of printed as well as electronics version of selected journals.(Details on www.iitd.ac.in). C. DATABASES & OTHER INFORMATION RESOURCES: Bibliographic Database of research publications of the Department, Catalogue of Departmental Library, Bibliographic Database of Departmental Theses, Full Text Database of Departmental Theses 6. DETAILS OF STAFF MEMBERS WORKING IN THE CENTRE:

S.NO. NAME OF THE DESIGNATION WORKING ABSORPTION STAFF SINCE STATUS 1. Nibedita Mishra Project Assistant May 2007 contractual 2. S. K Patra* Project Assistant Jan 2007 contractual *Resigned w.e.f September 2007, Two posts advertised, One full fledged faculty member with Ph.D. in Bioinformatics short-listed, interview 18.1.08 7. TYPES OF SERVICES PROVIDED: Literature Search: Information retrieval and storage facility from its rich In- house / On-line database(s) & Journals to the faculty, student and researchers of IIT Delhi/ Neighboring Institutions. Bioinformatics Courses & Project work: Students taking elective course on Bioinformatics, Genomics & Proteomics for the dual degree (B.Tech & M.Tech) students heavily use the infrastructure facilities of the center. Beside final year M.Tech students of the department / students form the other universities also do their dedicated 6-12 months Major Project work using the center’s facility. 8. EDUCATIONAL ACTIVITIES WITH DETAILS OF PLACEMENT Elective course on Bioinformatics (2-0-2, 3credits) for M.Tech students of the department, Elective course on Genomics and Proteomics (3-0-0, 3credits) for M.Tech students of the department, Elective course on “Data Analysis for DNA Microarrays” (3-0-2, 4 cedits) for the M.Tech students of the Department. All the students get excellent placement from the Institute. Ongoing projects in Bioinformatics >To study phylogeny of eukaryotic single cell organisms whose shole genome is sequenced and annotated. (Vikas Balhara Supervisors G.P.Agarwal, DBEB & Jayashree Santosh, Computer Service Center), 2007-2008. Completed Projects in Bioinformatics >To formulate “Intelligent” methodology to remove redundancy of genes from a large set of microbial genomes. (Abhishek Dubey Supervisors G.P.Agarwal, DBEB & Jayashree Santosh, Computer Service Center), 2007.

156 >Chromosomal grouping of Saccharomyces cerevisiae and Ashbya gossypii and its implications on their evolution. (Vamshi Krishna, T Supervisor G.P. Agarwal), 2007. >Development of an ab-initio Eukaryotic gene predictor. (Sahil Sethi Supervisors B. Jayaram. Chemistry Department & J.K.Deb, DBEB), 2007. >Identifying Early Nuclei in folding Kinetics: novel methods in Protein structure prediction. (Deepak Suri, Supervisors Nalin Pant, Chemistry Department & Saroj Mishra DBEB), 2007. >Development of new tools for comparing large segment of nucleotide sequences (Nitin Chanduka Supervisors G.P.Agarwal, DBEB & Jayashree Santosh, Computer Service Center), IIT Delhi, 2007. >Studies on protein based Nano drug delivery system (Shipra Jain, Supervisor Prashant Mishra DBEB), 2007 >Expression of recombinant chaperones in Escherichia coli and studying their role in the folding of recombinant proteins like maltodextrin glucosidase / malate synthase G or single chain antibody (Vatsala Dutta Supervisor Tapan K. Chaudhury, DBEB), 2007. >Designing of circular ribozyme targeted to Gemini Virus (Punita Mittal Supervisor J.K.Deb, DBEB) 2007. 9. IINITIATIVE TO VALIDATE THE OUTCOME OF BIOINFORMATICS RESOURCES The Sub-centre is publishing the papers in the area of Bioinformatics. 10. COLLABORATIVE WORKS / INITIATIVES: The center has active collaboration with various departments within the Institute e.g Mathematics, Chemistry and Computer Science & Engineering (CSE) of IIT Delhi. The department has also strong collaboration with Institute of Genomics and Integrated Biology (IGIB) New Delhi, All India Institute of Medical Sciences, (AIIMS), New Delhi and Jawaharlal Nehru University (JNU), New Delhi. 11. DATABASES/SOFTWARE PACKAGES DEVELOPED: Catalogue of “Departmental Library” about 2,000 records, searchable by author, title and keywords, Bibliographic database of Ph. D and M.Tech theses of the department about 522 records, About 150 Full-Text versions of the Ph.D. and M. Tech. Thesis of the department using “Greenstone Digital Library Software”, Institutional Repositories of thesis, Dissertation and other biological information, Other In-house developed specialized databases like Plant Cell Culture (PCC) Animal Cell Culture (ACC) etc., Different custom made soft wares for Bioprocess Modeling & Simulation. 12. PAPERS PUBLISHED OR PRESENTED IN THE CONFERECE WITH REFERENCE: PLEASE SEE www.iitd.ac.in 13. INITIATION OF R & D ACTIVITIES IN BIOINFORMATICS The department is involved in Teaching & Research (one semester research projects) in the area of Bio-informatics for dual degree students. 14.DETAILS OF THE TRAINING/WORKSHOP ORGANIZED AND TOTAL NO. OF USER TRAINED. Following Short-Term Courses & Workshops were organized 1. An International Symposium “Biohorizon 2007”, “A Joint Indo-Korean Symposium on Biotechnology” during 22-24 Feb- 2007. 2. Fifth Practical Summer Training in Biochemical Engineering & Biotechnology during June 20 – July 21 2007.

157 3. Proposed workshop on “Bioinformatics Fundamentals and Whole Genome Analysis” during February 2008 15.IMPACT SHOWN BY YOUR CENTRE ON THE GROWTH OF BIOECHNOLOGY. Patents & Technology Transfer Bisaria V.S., Srivastava A.K., Baldi A, Jain A., Gupta N. (2007) A process for enhanced production of bio-active compounds, Indian Institute of Technology Delhi , India. Patent Application No. 1266/Del/2007. i. Research Papers published in peer reviewed journals by using BTIS Sub – Centre’s Support. The Department has published more than 425 journal papers, 30 Books / Book Chapters, More than 100 conference publications since 1990 in different peer reviewed journals with the help of BTIS facilities of the centre. Details of the publication are available Faculty / Area wise on our website www.iitd.ac.in. ii. Bioinformatics Research Papers Published, in peer Reviewed journal by the centre. 1. Alok Malviya, James Gomes “In-Silico methods for rapid screening and isolation of industrially important Micro organisms (2007), Bioinformatics (Submitted). 2. Gupta, Shwetank; Bansal, Saurabh; Deb, Jahar K; Kundu, Biswajit (2007) Interplay between DtxR and nitric oxide reductase activities: a functional genomics approach indicating involvement of homologous protein domains in bacterial pathogenesis. Int.J. Exptl..Pathol., 88,377-85.88 377-385. 3. Salony, N. Garg, R.Baranwal, M. Chhabra, S.Mishra, T.K.Chaudhuri and V.S.Bisaria. Laccase of cyathus bulleri; structural, catalytic characterization and expression in Escherichia coli. Biochem. Biophys. Acta – Proteins and Proteomics (2007), doi:10.10.1016/j.bbapap,2007.11.006 4. Patra, S.K. “HIV/AIDS Research in India: A bibliometric study” Library and Information Science Research 29, 2007, 124-134. 5. B. Chandra, S. Shankar, Saroj Mishra, “A new Approach: Interrelated two way clustering of gene expression data Statistical Methodology 2006, 3 (1) 93-102. 6. Chaudhuri T.K and Paul S. “Protein misfolding diseases and chaperone based therapeutic approaches”. FEBS Journal (2006) Vol 273, pp 1331-1349. 7. Eli Chapman, George W. Farr, Renata Usaite, Krystyna Furtak,Wayne A. Fenton, Tapan K. Chaudhuri, Elise R. Hondorp,Rowena G. Matthews,Sharon G. Wolf, John R. Yates, Marc Pypaert, and Arthur L. Horwich. “Global Aggregation of Newly-Translated Proteins in an E.Coli Strain Deficient of the Chaperonin GroEL”. Proceedings of National Academy of Science (PNAS, USA) Vol.103, No.43, pp15800-15805 (2006). 8. Jana S, Chaudhuri TK and Deb JK. “The effects of guanidine hydrochloride on the conformation and enzyme activity of streptomycin adenyltransferase monitored by circular dichroism and fluorescence spectroscopy”. Biochemistry (Moscow), 71 (11) 2006. 9. Parul Gupta, Nishtha Aggarwal, Pragya Batra, Saroj Mishra and Tapan K. Chaudhuri*. “Co-expression of chaperonin GroEL/GroES enhances in vivo folding of yeast mitochondrial aconitase and alters the growth characteristics of Escherichia coli”. The International Journal of Biochemistry and cell Biology, Vol. 38 (11), 2006, 1975-1985. 10.Patra, S.K. and Mishra, S., “Bibliometric study of Bioinformatics Literature. Scientometrics Vol 67 No-3, 2006, 477-489.

158 11. Tapan K. Chaudhury and Subhankar Paul, “Protein Misfolding diseases and chaperone-based therapeutic approaches FEBS Journal 273, 2006, 1331-1349. 16. FUTURE ACTIVITIES 1. An interdisciplinary 4 Semester M.Tech (Bioinformatics) program in collaboration with Biochemical Engineering & Biotechnology, Mathematics, Chemistry and Computer Science & Engineering Departments is being proposed at IIT Delhi 2. Attempts will be made to train more students for Bioinformatics related projects. The centre will focus on the development of user-friendly interactive software tools for Modelling & Simulation of Bioprocessing, Bioprocess control etc. 3. Attempts will be made to develop Multimedia Course Materials for different key areas of Biochemical Engineering & Biotechnology and these can be eventually put on the BTIS centre Web Server for access by other BTIS centers and sub centers of the country.

ADDITIONAL DETAILS: NIL

NAME OF THE COORDINATOR: PROF. A. K. SRIVASTAVA POSTAL ADDRESS: DEPARTMENT OF BIOCHEMICAL ENGINEERING AND BIOTECHNOLOGY, IIT DELHI, HAUZ KHAS, NEW DELHI 110016 PHONE NUMBER: 26596109 M OBILE: 9868551429 EMAIL: [email protected] WEBSITE: www.iitd.ac.in

Name of Contact Person(s): Prof. A. K. Srivastava

159 Indian Institute of Technology, Kharagpur Coordinator : Professor S. C. Kundu

1. Summary of the progress made by the centre from its inception Bioinformatics activities have been initiated in January 1999 with the aim to provide Bioinformatics facilities to students as well as the research community not only to the Institute but also to the surrounding region. The Centre is having its own space in the Department of Biotechnology. The centre provides facilities to the B.Tech and M. Tech and Ph. D students to carryout their project work and summer trainings in the field of Bioinformatics. A number of research students in and around the region have been using the centre for the bibliographic searches using the Bioinformatics tools available in the centre and Internet searches for their research work. The Institute has introduced two separate 3- credit courses in Bioinformatics and Algorithms for Bioinformatics for the students. A number of thesis, publications in journals, oral and posters presentations are being made in national and international conferences.

2. Major research activities in Biotechnology and its related fields in the Institution • Scale up of recombinant proteins, molecular farming of therapeutic and diagnostic proteins, Immunodiagnostics studies and bio-hydrogen production in different bioreactors • Evolution genomics, Indian non-mulberry silkworm and its medical applications as biomaterials. • Cloning, expression and purification of response regulator domains from Mycobacterium tuberculosis and Cloning and expression chitinases of Entamoeba invadens

3. Area of specialization of the centre Comparative genomics, protein modeling and Database development

4. Major activities of the centre during the year 2007 - 08 A two-day (Sep 21st and 22nd) workshop on “Bioinformatics in Genomics and Proteomics” was conducted to train the participants (M. Sc. / Ph. D students / teachers) to get them acquainted with the frontier areas of Biological Data Banks, Molecular Modeling, Genomics and Proteomics, Analysis of Nucleic acid and Proteins.

5. Infrastructure facilities a. Computer & Communication facility Computer hardware: Several Pentium Core2 Duo PCs, Silicon Graphics O2, Workstation, Sun Server with 10 numbers Thin Client. HP Color Laser Printer, HP Scanner, Fax, Digital Xerox machine. Operating systems: MS Windows Vista, Redhat Linux 9.0, Mandrake Linux 10.2, and Sun Solaris 9. Internet facility: 10 mbps direct satellite link from ThaiNET. b. Scientific software packages

160 Sequence analysis: OMIGA 2.0, Sequencer 4.1.4, EMBOSS. Molecular modeling: GCG Wisconsin Package, MSI Insight II (Perpetual licensed), Modeler, DS Modeling, Swiss PDB viewer

c. Databases & other information resources SciFinder, ISI Web of Knowledge, Springer Verlag, Elsevier Science Direct, Biomednet and PNAS etc. (Access through the INDEST Consortium. Central Library receives hard copies of several journals like Bioinformatics, EMBO J, Nature Biotechnology, Nature genetics, Cell, Nature Medicine and other CD-ROMs and Current Protocols related to Biological Sciences; Derwent Biotechnology Abstracts; Dialog on Disc Biotechnology and Bioengineering; CAB Abstracts (Commonwealth Agricultural Bureau Abstracts); CURRENT CONTENTS (CC) Agriculture, Biology, Environmental Sciences and Life Sciences.

6. Details about staff members working in the centre Name Designation Specialization Period of Absorption work status Mr. Baghirathi Technical Assistant System 8 years Not absorbed Nayak administration IO, SPA & Re advertised Data Entry Operator

7. Types of services provided The centre offers a, good collection of the electronic resources of large number of journals full text and several abstracts through INDEST consortium. High-speed broadband Internet facility (10 mbps leased line) and access to GCG Wisconsin Package, INSIGHT II software on SGI machine and other computational facilities.

8. Educational activities with the placement details Institute offers two separate 3-credit courses to the students (UG/PG and research scholars). The Bioinformatics related companies through campus interview select B. Tech and M. Tech students and others opt for pursuing further studies in the areas of Bioinformatics abroad.

9. Initiative to validate the outcome of Bioinformatics resources Publications were made in peer reviewed journals; every year and average of 75 students are being trained in the Centre; creation of database Wild silkworms; a committee headed by the Director to monitor the progress and assets maintained as per the Institute rules.

10. Collaborative work/ initiatives Linkages have been established with some Institutes/ organizations like Indo - Norwegian Institutional Cooperation Programme on structural and functional studies of the major pathogenic proteins of Tuberculosis, Clean Energy Research Institute, College of Engineering, University of Miami, and University of Ruhr-Bochum, Germany for improvement of hydrogen production, Institute of zoology, Dresden University, Germany on Biotransformation, biomaterials and Tissue Engineering at NSW University, Sydney and UCSD, San Diego and Institutions like IICB, Bose Institute and Jadavpur University, Kolkata.

161 11. Databases/ software packages developed Development of integrated search tools to decipher sequence alignments, gene mapping/manipulation and enhancing polymerase chain reaction and Development of versatile portable software for bioinformatics) are being initiated by this Institute. A database called WildSilkBase is being developed using MySQL and PHP. 12. Papers published or presented in the conferences with reference (2007- 2008) • Functional insights from the molecular modeling of a novel two- component system, Biochem.Biophys.Res. Commun. 344, 1327 – 1333, (2006) • Molecular phylogeny of silk producing insects (Saturniidae family, Genus, Antheraea) based on 16S ribosomal RNA and cytochrome oxidase genes, Journal of Genetics, 85, 31-38. (2006) • Molecular identification of tropical tasar silkworm (Antheraea mylitta) ecoraces with RAPD and SCAR markers. Biochemical Genetics.44, 72- 85. (2006) • Repetitive DNA in topical tasar silk worm Antheraea mylitta.Gene.370, 51-57. (2006) • Genetic variation in ecoraces of tropical tasar silkworm, Antheraea mylitta using RFLP technique. Curr. Sci, 90, 100-103. (2006) • Exploration of the secondary structure specific differential solvation dynamics between the native and molten globule states of the protein HP-36. J. Phys. Chem. B 110, 20629-20634. (2006) • Entamoeba histolytica: Computational identification of putative microRNA candidates, Experimental Parasitology, 113, 239-243. (2006) • Simulation and modeling of continuous H2 production process by Enterobacter cloacae IIT-BT 08 using different bioreactor configuration, Enzyme. Microb. Technol. 31, 867-875. (2006) • Crystallization and preliminary X-Ray diffraction analysis of protease inhibitor from the hemolymph of the Indian Tasar silk worm Antheraea mylitta, Acat Cryst. F, F62, 669-671. (2006) • Molecular phylogeny of silk producing insects based on internal transcribed spacer DNA1. Journal of Biochemistry and Molecular Biology 39, 522-529, (2006) • Cyclosporin Abinding to Mycobacterium tuberculosis peptidyl-prolyl cis- trans isomerase A Investigation by CD, FTIR and fluorescence spectroscopy. FEBS Letters, 580, 6846-6860. (2006) • Crystallization and preliminary X-ray diffraction analysis of a protease inhibitor from the haemolymph of the Indian tasar silkworm Antheraea mylitta. Acta Cryst, F62, 669-671. (2006) • Copper complexes of (-)-Epicatechin gallate and (-)-Epigallocatechin gallate act as inhibitors of Ribonuclease A. FEBS Lett. 580, 4703-4708. (2006) • The binding of 3´-N-piperidine-4-carboxyl-3´-deoxyara- uridine to Ribonuclease A in the crystal. Bioorg. Med. Chem. 14, 6055-6064. (2006) • Interaction of (-)-Epigallocatechin-3-Gallate With Human Serum Albumin: Fluorescence, Fourier Transform Infrared, Circular Dichroism, 162 and Docking Studies. Proteins 64, 355-362. (2006) • 3′-N-Alkylamino-3′-deoxy-ara-uridines: A new class of potential inhibitors of ribonuclease A and angiogenin. Bioorg. Med. Chem. 14, 1221– 1228. (2006) • Comparison of metal–amino acid interaction in Phe–Ag and Tyr–Ag complexes by spectroscopic measurements. Biophysical Chemistry 120, 215 – 224. (2006) • Correlation between the dynamics of hydrogen bonds and the local density reorganization in the protein hydration layer.J. Phys. Chem. B 111, 7626-7630 (2007). • Influence of experimental parameters on identification of whole cell Rhizobium by matrix-assisted laser desorption / ionization time of fight mass spectrometry. Eur. J. Mass Spectrom., 13(2), 165-171. (2007) • Probing the nucleotide binding and phosphorylation by the histidine kinase of a novel three-protein two-component system from Mycobacterium tuberculosis. FEBS Letters, 581, 1903-1909. (2007) • Temperature and urea induced conformational changes of the histidine kinase from Mycobacterium tuberculosis. Int. J. Biol. Macromol, 41, 154-161, (2007) • Molecular Cloning, expression and Analysis of Antheraea mylitta Cypovirus Genome Segments 8 and 11. International Journal of Virology, 3(2): 60-72. (2007) • Molecular cloning, sequence analysis and expression of genome segment 7 (S7) of Antheraea mylitta cypovirus (AmCPV) that encodes a viral structural protein. Virus Genes. 35(2):433-41, (2007) • Transient expression, purification and characterization of bioactive Human fibroblast growth factor 8b in tobacco plants, Transgenic Research 17(1) 19-32 2008.

13. Initiation of R&D activities in Bioinformatics Bioinformatics research activities are being carried out at the UG/PG / research student level by providing different Bioinformatics projects for their academic / project work. Database and software developments - Developing a few specialized databases. • Molecular modeling - Structure solving, dynamics and interaction study of the some virulence protein of Mycobacterium tuberculosis • Specific gene analysis – Analysis of virulence genes of Entamoeba histolytica and Mycobacterium tuberculosis, hydrogenase gene of Enterobacter cloacae and fibroin, sericin and seroin genes of economically important tasar silkworm, Antheraea mylitta. • Comparative Genomics – Molecular phylogeny and molecular clock analysis based on the mitochondrial genes, RAPD-PCR, ISSR profiling and retrotransposons of different ecoraces of Antheraea mylitta and inter-species

14. Details of training/ workshop organized and total number of user trained The Center conducts workshop on Bioinformatics and its applications, and Bioinformatics in Genomics and Proteomics in the fourth week 163 of September every year for research students, scientists, doctors, university and college faculties to cater them hands-on training on different aspects of Bioinformatics (trained 75 persons every year)

15. Future activities Molecular genetics of silkworm species; characterization of DNA markers; cloning of silk protein genes fibroin and sericin; identification and analysis of retrotransposons. Genome analysis of Entamoeba histolytica production analysis and creation of database for Antheraea mylitta ESTs. Molecular modeling of proteins and structure-function relationships of tuberculosis organism; Database on Biomaterials and Tissue Engineering.

Coordinator : Professor S. C. Kundu, Department of Biotechnology, IIT- Kharagpur, 72 13 02. Phone: 03222 283764, Mobile: 09434012848, iitkgp.ernet.in Co-coordinator : Professor S. Dey Contact person:Professor S. C. Kundu (email. [email protected])

Indian Veterinary Research Institute, Izatnagar Coordinator: Dr. Rajendra Singh

1. Summary of the progress made by the centre from its inception The Bioinformatics Centre, actually started functioning in 1992, is ready to get online /offline information from DICs, sub-DICs and other centers to meet users specific requirements and also to provide online/offline information to DIC, DISC, etc. The Centre has following credentials at his credit a) Centre developed nine bibliographic, one livestock related database and one wild life disease database. b) Seven softwares using FoxPro/Clipper/Visual Basic with Microsoft and Perl were developed. c) More than sixteen softwares were downloaded. d) Sites of many databases were listed for utilization in research work. e) More than sixteen sites of bibliographical databases were listed in the year. f) Centre in collaboration with NLVS produces more than eight Databases.

2. Major research activities in Biotechnology and its related fields in the institution i) Number of divisions/Centers doing research in the area of Biotechnology are involved in developing improved diagnostics/vaccines for differential diagnosis and recombinant vaccines using RFLP, SSCP and synthetic peptides etc with the help of bioinformatics data bases and softwares. ii) Molecular modelling, gene analysis, sequencing, genetic identity index and genetic distances were used to analyse information obtained from different research projects persude in different divisions of the intiitute and

164 these data were also used for developing and updating related databases. iii) A large number of new sequence information was submitted to EMBL GenBank.

3. Area of Specialization of the centre : Veterinary Bioinformatics.

4. Major activities of the centre during the year 2007-08 i. Wild life disease database software was completed and database was updated. ii. Different databases and softwares were updated and improved respectively. iii. Online/Off-line information was collected and disseminated. iv. Different primers and probes were developed to improve upon diagnostic techniques, vaccines, etc. v. Efficiency of different softwares were examined for analysis of nucleotide and protein data. vi. Different techniques were evaluated for removing the noise in microarray data. vii. Students and Scientists of IVRI and other research workers in the field of Biotechnology and Bioinformatics from other organizations are trained in handling Bioinformatics databases for sequence analysis, primer designing, Probe searching and microarray analysis. viii. We are in the process of offering 3 credit course in the fields of Bioinformatics, Biostatistics and Information technology to Ph. D. and M. V. Sc. Students of the Institute. ix. Scientists and students of this institute used different databases for sequence analysis, probe search, etc.

5. Infrastructure facilities in the Bioinformatics Centre: A. Computer & Communication Facility : The following are the new development/augmentation of Bioinformatics: 512 kbps VSAT from EARNET. Up-gradation of V-SAT. Addition of 2 server. Faster E-mail and Internet facilities. A Bioinformatics Lab containing almost all the facilities available at any center of bioinformatics in the country. The Centre is connected with all divisions/sections of the Institute by LAN and EPABX. B. Scientific Software Packages : i) DNA Star ii) Genocluster Software. In-house developed Softwares: 1. PhDTHESPACK 2. WILDLIFEPACK. C. Databases and other information Resources IVRI Ph.D. Thesis Abstract Database, Wildlife Disease Database and Livestock Database. 6. Details about staff members working in the Centre SL. NAME OF THE DESIGNATIO SPECIALIZATION WORKIN NO STAFF N G 1. Dr.Rajendra Project Data Management & 2001 Singh Coordinator Sampling 2. Sh. K.N. Tech. Officer Information & Com. 1992

165 Kandpal programming 3. Sh.J.P.Yadav T-3 (Rep.) Reprography 2007 7. Types of services provided i. Online/Off-line collection and dissemination of information. ii. Search and alignment of sequences and microarray analyses. iii. Training, Workshop, etc. iv. Internet, E-mail facilities, use of Libsys and other database.

8. Educational activities with details of placement : Not applicable

9. Initiative to validate the outcome of bioinformatics resources A number of diagnostics, differential diagnostics, identifications of marker genes for improving productive and reproductive efficiency, characterization of species and breeds, estimation of genetic diversity, vaccines, etc. were achieved due to efficient use of facilities available at Bioinformatics Information Sub-center, IVRI, Izatnagar. These technologies are in the process of patenting.

10. Collaborative works/initiative Institute has more than ten National/International projects and Bioinformatics centre is providing all possible support in these research projects.

11. Databases/Software packages developed 1. Wildlife Disease, 2. Livestock Databases 3. Bibliographic Databases 4. Softwares: i. THESPACK, ii. PUBPACK, iii. RUMPACK, iv. LIGPACK, v. FMDPACK.

12. Papers published or presented in the conferences with reference One Manual and Nine research papers have been published in National and Inter-National Journals.

13. Initiation of R&D activities in Bioinformatics A number of divisions/centres like Bacteriology and Mycology, Veterinary Public Health, Avian Disease, Pathology, Parasitology, Biochemistry, Animal Genetics, National Biotechnology Centre, and Centre for Advance Disease Research and diagnosis are involved in developing improved diagnostics/vaccines and genome analysis work. In order to get inside into the structural genomics, genome analysis of different species were carried.

14. Details of Training Workshop organized and total no. of user trained During the year about 230 scientists, students and other research workers have been trained in Bioinformatics and Information Technology. National Workshop : National Workshop cum Training Programme on “Bio- computing” was organised from March 24 to 27, 2007 at Bioinformatics Centre, IVRI, Izatnagar. We declare only 10 seats for participants but pressure from different corners compelled us to admit more then 52 students in this workshop.

166 Students Trained: One student of M.Sc. (Bioinformatics) from Bioinformatics Centre, Jamia Millia University, New Delhi was trained under Summer Training from 5.6.2007 to 4.7.2007 in “Evaluation of Bioinformatics Tools for Sequence Alignments” at Bioinformatics Centre,IVRI, Izatnagar. Students Trainees: i) Two student trainees from J.N.U. were trained in Bioinformatics on Cancer patients database and Sequence Alignment Analysis. ii) Two trainees who have already completed their degrees have been trained in Bioinformatics on Microarrays and development of information databases.

15. Impact shown by the centre on the growth of biotechnology and allied areas: The information provided by Bioinformatics Centre helped in developing diagnosis of diseases, development of vaccines and epidemiological studies in different disciplines of veterinary and animal science. Polymerase chain reaction amplified nucleic acids for epidemiological studies of diseases like Infectious Bursal Disease, New castle disease, Orthopox viral diseases etc. Full-length genes are also amplified by self-designed primers based on sequence information available in various sequence databanks. The Bioinformatics Centre extended all possible support on its command for all round development, education and training in Biotechnology and related subjects.

16. Future Activities: The future plan can be delineated into following three major activities: a) Scientific Support: The centre will cater the support to different National, International and Post Graduate Research Projects of the Institute where use of Biostatistics is required. The exchange of information in the field of Bioinformatics will be continued. b) Training and P.G. Education: The centre will organize short term and long term training programmes for the students and research workers in the fields of Biotechnology and Bioinformatics. Workshops will also be organized for hands on training and better interaction among the people working in the field of Bioinformatics. The Bioinformatics is in the process to be introduced into course curricula of Ph.D. and Masters’ degree programmes of Deemed University, IVRI, Izatnagar. During the present five year plan our endeavor will be to open Master’s Degree Programme in Bioinformatics. c) Research and Development: a. Major tools used in Bioinformatics will be assessed for sequence alignment, using nucleotide and protein sequences of different organisms, breeds, species, with varying origin, time and space. b. Statistical and computational tools will be adapted and developed to reach the conclusion with efficiency. c. Univariate and multivariate statistical and computation tools will be adapted and developed for better comparison of different tools for sequence alignment. d. To develop tools for Correction of noise in microarray data under finite population. e. To estimate effect of different factors causing variability in microarray data. f. To adopt and develop statistical techniques for arresting the outliers in finite population. 167 g. To adopt and develop statistical tools and softwares for efficient analysis of microarray data . h. To develop databases of different zoonotic diseases to safe guard human and livestock population from hazard . i. To develop databases of livestock diseases to make livestock sector economically viable. j. To develop softwares for experimentation to assess efficacy of different diagnostic and profilectics at the place of livestock .

Additional Details:

Name of the Coordinator: Dr. RAJENDRA SINGH, Principal Scientist

Postal Address: Distributed Information sub-centre, NLVS, Indian Veterinary Research Institute,Izatnagar (U.P.) - 243 122 Phone No. 0091-581-2300207/ 2300305 FAX No. : 0091-581-2303284 E-Mail : [email protected] Website : www.ivri.nic.in

Name of Contact Person: K.N.KANDPAL, Technical Officer E- Mail: [email protected]

168 Indian Institute of Advanced Research, Gandhinagar, Gujarat Coordinator : Dr. Desh Deepak Singh

1. Summary of the progress made by the centre from its inception: Indian Institute of Advanced Research at Gandhinagar, Gujarat is engaged in research in the areas of biotechnology and biosciences. The bioinformatics centre sanctioned by DBT is engaged in the training of scientists in the field of bioinformatics, database and software tool creation, etc. The centre has organized a training program for fifty five participants (Faculty, students, scientists) from all over Gujarat, developed a database on adhesins and extracellular matrix proteins, a database on plant pathogens and their virulence factors, software tools like auto-PSIBLAST, motif search and annotation of adhesin-like proteins. Two students from neighboring institutes have completed their Masters projects of six months duration.

2. Major research activities in Biotechnology and its related fields: (a) To compile the information on plants and their pathogens in a user friendly database in conjunction with useful tools. This will help to forecast a plant diseases in advance based on weather conditions. (b) Identification of pathogens based on their characteristics and information on support measures available for the control of diseases. (c) To collect and compile data which will help us understand the tropical pathogens more comprehensively.

3. Area of Specialization of the centre: (a) Database and software tool development. (b) Identification and analysis of virulence factors from tropical pathogens. (c) Extension of bioinformatics work to cloning and 3-D structure solution.

4. Major activities of the centre during the year 2006-07: (a) Training Program: A three days bioinformatics training program was held at IIAR from May 16-18, 2007 and fifty five participants (Faculty, students, scientists) from all over Gujarat participated in it. The participants were imparted lectures by eminent faculty Like Dr. AS Kolaskar, Dr. T Madhan Mohan. Dr. GPS Raghava, and practical hands on training was also given. (b) Development of software tools: Various software tools are developed, being developed in the centre for data analysis. A motif search tool for detection of particular motifs in sequence database has been developed and is available online at our website. Auto PSI-BLAST tool for automatic analysis of multi sequence, multi iteration queries against various databases has been developed and is also available online. A tool for gene annotation utilizing BLAST, HMMER, Threader is at advanced stage of development and will also be made available online for free use by the community. (c) Development of Adhesin database: A database on Adhesins has been developed using MySql and is currently being updated to make it dynamic. Adhesins are an important category of proteins in host-pathogen interactions and this database will help us understand this process more efficiently. Also it will be made available to user community freely for use. (d) Database on plant-pathogen interaction: A database on Plant Pathogen interactions on Oracle 10g is being developed currently and it will 169 be made available with useful analysis and predictive tools and at a later stage it will become a useful tool for the farmers for disease forecast and preventive measures. (e) Students training: Two students: one from SP University, Vallabh Vidyanagar and one form DAIICT, Gandhinagar have done their six months project work as part of their Masters curriculum with us and benefited from the centre. Two other students are currently working as trainees in the centre.

5. Infrastructure facilities in the Bioinformatics Centre: A. Computer & Communications facility: SGI Fuel One number IBM Z pro Xeon 3.0GHz Six number Dell Precision Quad core Four Number Dell Desktops core 2 duo Ten number HP Desktops PIV Five number IBM e servers 2X Xeon 3.0GHz Three number HP laserjet printers Two number B. Scientific Software packages: MOE, Rasmol Pymol, BLAST standalone, Autodock, Oracle 10g, FUGUE, etc. C. Databases & other information resources: Refsequence, genome sequences of pathogen

6. Details about staff members working in the centre:

Sl. NAME OF THE DESIGNATION WORKING ABSORPTION No. STAFF SINCE STATUS (YES/NO) 1. Mr. Vijay Singh Project March, 2006 With IIAR Assistant 2. Ms Divya Nair Project March, 2006 With IIAR Assistant 3. Mr. Bhavesh Programmer July, 2007 With IIAR Kataria 4. Mr. Ved Prakash Trainee May, 2007 In DISC Tiwari project 5. Ms. Shivani Trainee July, 2007 In DISC Viradia project

7. Types of services provided: (a) Training (b) Genome analysis (c) In-silico anlaysis of protein-ligand interactions.

8. Educational activities with details of placement: We are shortly starting PhD program and shall be enrolling students.

9. Initiative to validate the outcome of bioinformatics resources: Since we are relatively newly established the databases and softwares developed by us are being extensively validated right now.

170

10. Collaborative works/ initiatives: We are developing linkages with Labs. having relevant expertise to extend the bioinformatics analysis work to actual wet Lab. experiments.

11. Databases/ Software packages developed: Same as 4(b), (c), (d) above.

12. Papers published or presented in the conferences with reference: Singh, V., Singh D. D., (2008). Leishmania major: Genome analysis for identification of putative adhesin-like and other surface proteins. Exp Parastol 188, 139-145 (available online August 3, 2007).

13. Initiation of R&D activities in Bioinformatics: (a) Genome analysis of tropical pathogens like tritryps etc. is in progress to find out virulence factors in these pathogenic organisms. (b) Work is in progress to identify the virulence factors in M. grisea which causes rice blast disease. (c) In-silico analysis and docking studies are being conducted to identify pharmacophores modulating virulence factor expression in pathogens.

14. Details of Training/ Workshop organized and total no. of users trained: A three days bioinformatics training program was held at IIAR from May 16- 18, 2007 and fifty five participants (Faculty, students, and scientists) from all over Gujarat participated in it. The participants were imparted lectures by eminent faculty Like Dr. AS Kolaskar, Dr. T Madhan Mohan. Dr. GPS Raghava, and practical hands on training was also given.

15. Impact shown by your centre on the growth of biotechnology and allied areas: (a) Research work undertaken in the centre published in peer review journal. (b) Training of students, faculty, staff and scientists from all over Gujarat. (c) Bioinformatics resource centre for the Institute. (d) Maintaining institutional computational activities.

16. Future activites: The current activities undertaken at the centre will be further augmented in the coming time. More training programs will be organized, databases and software tools will be developed and we hope to publish a lot more of the work we do. We ultimately hope to be a nodal centre for Bioinformatics in western India. Name of the coordinator: Dr. Desh Deepak Singh

Postal Address: Indian Institute of Advanced Research, Puri Foundation, Block-2, First Floor, Udyog Bhawan, Sector-11, Gandhinagar-3820017, Gujarat

Phone number: 079-30514150

Email: [email protected] 171

Website: www.iiar.res.in

172 Indian Institute of Integrative Medicine, Canal Road, Jammu Coordinator : Dr. G.N.Qazi

1. Summary of the progress made by the centre from its inception ¾ Establishment of Molecular Modeling factility The centre is now equipped with complete molecular modeling facility with relevant software and hardware and qualified manpower to process the same. ¾ R&D activities started Based on the above said facilities, a lot of Research & Development activities have been started by the centre, with a focus on molecular docking and QSAR studies. ¾ Official website of RRL (now IIIM) Jammu Launched Official website of Regional Research Laboratory Jammu (now Indian Institute of Integrative Medicine) is completely designed and hosted which is available at http://www.iiim.res.in and http://www.rrljammu.org. ¾ Complete Networking of RRL-J and also branch lab Srinagar Complete networking of RRL was done with Fiber Optics back bone and managed switches for better interconnectivity within the lab. ¾ Up gradation of Infrastructure & Internet connectivity 2 Mbps Leased line connection is now functional for faster access to Internet in addition to the Microwave Radio Frequency link with a maximum speed of 128 Kbps and CSIR-Net through the VSAT.

2. Major research activities in Biotechnology and its related fields in your institution In the Division of Biotechnology there are a number of projects being actively pursued. The highlights of some of these:

Exploration and exploitation of microbial wealth of India for novel compounds and biotransformation process. Bioprospective of microbial wealth of North Western Himalayas Development of Technologies for Pathway Engineering of Withania somnifera – an important plant component of Ayurvedic drugs. Exploration and exploitation of microorganisms from North-Western Himalayas for the present of Industrially important enzymes.

3. Area of Specialization of the centre Medical, Drug discovery by Molecular Modeling & QSAR.

4. Major activities of the centre during the year 2007-08

9 QSAR analysis of aryl, alkyl, imine/amide based efflux pump inhibitors QSAR studies of several amide molecules (from IIIMJ repository) have been done for their inhibitory activity against NorA and a final QSAR model with r2 = 0.866 has been arrived at. For further refinement and validation of the QSAR 173 model developed, two external validation tests were performed and the results obtained were in accordance with the validation criteria known for QSAR studies. In order to further validate the statistical quality of the model developed, Leave- 25%-out experiment was also carried out, which further validated the derived model. The results are incorporated in the manuscript, which is submitted to the European Journal of Medicinal Chemistry. 9 Molecular Docking of Ovalbumin 3-D structure of the protein ovalbumin (1OVA) was downloaded and ligands (chiral) prepared at RRLJ were docked on to the protein to arrive at the mechanism of the bioreduction reaction. The computational analysis revealed intra-molecular hydrogen bonding to be the major factor for low- diastereoselectivty of the hydroxyl-ketones when subjected to chemical reduction in presence 1OVA for the preparation of diol. Manuscript to be communicated to the Journal of Chemical Informatics and Modeling 9 QSAR studies of parthenin derivatives A library of parthenin derivatives has been created at IIIMJ and several molecules from it have been identified to possess potent anti-cancer activity. In order to arrive at more potent molecules, with less toxicity, QSAR studies of these compounds have been done. Based on the IC50 values of the compounds, the QSAR equation was derived wherein five descriptors were found to have bearing on the overall activity of the molecules. Further studies for the refinement of model are in progress 9 Database on venom PLA2 and its inhibitors Earlier, we have created a library of compounds possessing anti-snake venom (precisely anti-PLA2) activity of the viper venom species. Through molecular docking, we could also arrive at a novel PLA2 inhibitor. Based on the research activities carried out on venom phospholipaseA2, a lot of data is generated. We have also downloaded a lot of information on PLA2 from other venom species including bee, scorpio etc. This information will be combined with the earlier data in order to form a comprehensive source of information on PLA2 and its inhibitors. 9 Human Resource Development. Regular training sessions on Bioinformatics were organized in order to train the students within and around J&K state in the field of Bioinformatics. (Also see point 14) 9 Centre is participating in the mega Vaccine Adjuvants project which is submitted in collaboration with Synthetic Chemistry Dept., RRL-J and Institutes in Norway. 9 The Centre is also a part of the recently proposed Cheminformatics networked project by URDIP, Pune 9 Bioinformatics related Database development undertaken.

5. Infrastructure facilities in the Bioinformatics Centre Computer & Communication facility

174 Silicon Graphics Fuel, PCs & Server; HP laser printer. All computers are on LAN with fiber optics back bone connected with 2Mbps leased line supported with an alternate RF link , CSIRnet &VSAT link. Scientific Software packages - Insight II & Cerius2 - Hyper Chem 7 - NTsys 2.1 - DNA Star, Laser gene - Phylip 3. - Apart from ChemDraw, ISIS etc. and other public domain software. Databases & other information resources MDL Crossfire, Biotechnology Abstract, Medline, Medicinal Plant Database, Dictionary of Natural Products, J-Gate Access.

6. Details about staff members working in the centre (Name of the staff, Designation, Specialization and period of working) Sh. Abdul Rahim Scientist Computer Engineer 01.03.1999 till date Sh. Amit Nargotra Scientist Engg & Bioinformatics 05.07.2001 till date Ms. Monica Gupta Data Entry Operator MCA 17.10.2007 till date

7. Types of services provided i. Assistance to scientists, Research fellows, M.Sc Biotechnology students in accessing, searching and retrieval of biological information. ii. Software installation & demonstration. iii. Human Resource development. iv. Project Guidance to the students from various institutes across the country to complete their bioinformatics and IT related project work. v. Seminars and demonstration of bioinformatics and other software to students of various universities within the state. vi. Maintenance of the computers installed with Gene sequencer, HPLC, Quality Control etc., and peripherals in various departments in the lab. vii. Scientists, Staff and scholars from the following institutes besides RRL Jammu are extensively using the facilities at the Bioinformatics Centre: 1. University of Jammu 2. Sher-i-Kashmir University of Agricultural Science & Technology. 3. Acharya Shri Chander College of Medical Science. 4. State Council of Science & Technology. 5. University of Kashmir 6. GNDU, Amritsar 7. IIIM Srinagar Br. lab 8. Educational activities with details of placement : NA 9. Initiative to validate the outcome of bioinformatics resources The centre works in accordance with various departments in this institute viz., Biotechnology, Pharmacology, Natural Product Chemistry etc. Hence all the outcomes of the Bioinformatics research are validated with the wet lab experiments in the concerned department. Besides this, the wet lab results are also validated theoretically in order to establish a protocol in any new area of study 10. Collaborative works/ initiatives 175 a. The project “Drug Target Development using Insilico Biology” under the Tenth Five Year Plan program with the following Labs : IGIB, Delhi; IMTECH, Chandigarh; IICB, Kolkata; CDRI, Lucknow. (The project is extended for two years [from 2007-2009]) 11. Databases/ Software packages developed • Database on venom PLA2 initiated 12. Papers published or presented in the conferences with reference

¾ Revised manuscript on “QSAR studies of aryl, alky, imine/amide based efflux pump inhibitor” has been sent to the European Journal of Medicinal chemistry. (MS. NO.: EJMECH-D-07-00615R1) ¾ A paper comprising the work on molecular docking on Ovalbumin and its molecular interaction analysis is ready for communication.

13. Initiation of R&D activities in Bioinformatics A lot of research activities on molecular docking, QSAR studies and homology modeling are now going on in the Bioinfomratics Centre IIIM, Jammu. The centre is now participating in other mega research projects of the institute as well as in collaborative projects within and out side the country. The experimental results from various departments of IIIM-J are being validated theoretically at the bioinformatics centre in order to develop a new protocol for any specific area of research involving biomolecular targets of anti-cancer, efflux pump etc.

14. Details of Training/ Workshop organized and total no. of user trained Mar-August 2007: Training programme on “Bioinfomratics & its Application” for Engineering students from several colleges across India (4 students) Apr- June 2007 : Training programme for three months on Database development for B.Tech students (15 students) September 2007: Demonstration of Bioinfomratics work at IIIM Jammu for merit students under CSIR Open Day scheme. (about 105 students in 5 batches) April-October 2007: Training programme on Molecular Modeling and Algorithm development for MSc Bioinfomratics Students for 6 months. (3 students) December 2007: Demonstration of Bioinformatics work at IIIM Jammu for meritorious students under CPYLS scheme. (about 100 students in 5 batches)

15. Impact shown by your centre on the growth of biotechnology and allied areas The centre is now equipped with all the major scientific software packages and hardware and qualified manpower for carrying out the molecular modeling activities. Under this area the major activities taken up were docking studies, homology modeling and QSAR

176 studies. Two papers on homology modeling have already been published, One paper on QSAR is under revision and one paper on molecular docking is ready to be communicated. One patent is also filed (NF0236/2006 dt. 12.10.2006). The centre is also imparting training on various areas of Bioinformatics to the students of Bioinformatics at the DOEACC centre and some of them have been placed in reputed organizations like IGIB, Delhi. The centre is also giving introductory training course to several neighboring institutes like University of Jammu, Sher-I-Kashmir University of Agricultural Sciences and Shri Mata Vaishno Devi University. The centre is constantly in touch with the BIFs created within the state and has always extended a helping hand for any teething troubles faced by those centres.

16. Future activities • QSAR studies on several bioactive compounds on different targets from IIIMJ repository. • Database development on venom PLA2 to be completed. • Refinement of the QSAR model developed for parthenin derivatives. • Docking of selected compounds on PLA2 from different venom species • Threading exercise to determine the 3-D structure of proteins and hence virtual screening of the compounds available in IIIMJ repository. • Algorithm development activities to be carried out as major activity with the collaboration and support of Dr. G.P.S.Raghava, IMT, Chandigarh. • Location-specific databases based on Microbial Biodiversity of North Western Himalayas is to be linked with IIIMJ website. • Frequent workshop and training programmes to expose the latest techniques in Bioinformatics to the scientists as well as students.

Additional Details: Name of the Coordinator: Dr. G.N.Qazi Postal Address: Director, Indian Institute of Integrative Medicine Canal Road, Jammu Phone Number: 2569111/222 Fax No.: 2569333 Email: [email protected] Website: www.iiim.res.in www.rrljammu.org Name of Contact Person(s): Mr. Abdul Rahim, Scientist Mr. Amit Nargotra, Scientist Email: [email protected] Email: [email protected] [email protected]

177 Indian Institute of Chemical Biology, Kolkata Coordinator: Dr. Chitra Dutta

1. Summary of the progress made by the centre from its inception : Since its inception in 2002, various scientific projects on microbial and mammalian genome/proteome analysis have been carried out by the members of the Centre. Among the problems addressed so far are studies on intra- and inter- genomic compositional variations in pathogenic microbes, delineation of molecular mechanisms of adaptation of extremophiles to their specialized niches and analysis of trends in amino acid substitutions between human and mouse orthologs. A number of novel genome data mining software tools have also been developed in course of these studies.

2. Major research activities in Biotechnology and its related fields at your institution IICB is a constituent national laboratory of the Council of Scientific and Industrial Research (CSIR), the premier multidisciplinary Research and Development organization of the Government of India. IICB is engaged in interfacial research on chemical and biological sciences addressing biomedical problems of national importance as well as of global interest. There are six major research groups working in the areas of Cell Biology & Physiology, Chemistry, Molecular and Human Genetics, Structural Biology & Bioinformatics, Drug Development/Diagnostics, Infectious Diseases & Immunology, and Biotechnology. Major objectives of the research activities are to understand the genetic basis and molecular mechanism of the inherited genetic disorders, to have an insight into the pathophysiological basis of metabolic diseases, to develop therapeutics, preventives and diagnostics for diseases intimately associated with impairment of the host immunity, development of herbal medicines, search for effective lead molecules from natural sources etc. Various software are being developed for analysis of macromolecular structures and elucidation of their interactions with bioactive molecules, which will facilitate lead optimization for rational drug design.

3. Area of Specialization of the centre : Genome and Proteome Analysis

4. Major activities of the centre during the year 2007 - 08 :

(A) Polarized trends in nucleotide/amino acid substitution patterns in human and mouse orthologs of two compositional extrema:

A genome-wide analysis of sequence divergence patterns of 12198 human- mouse orthologous pairs revealed that the trends in nucleotide and amino acid substitution patterns in orthologs of high and low GC-composition are highly asymmetric and polarized to opposite directions. As the GC3–contents of human and mouse orthologous pairs exhibit a strong positive correlation (r= 0.86, p<10- 7), the entire dataset was divided into three broad groups on the basis of the GC3–content of human genes: (i) High-GC (GC3>70%), (ii) Medium-GC (70%≥GC3≥50%) and (iii) Low-GC (GC3<50%). The analysis showed that at nucleotide level, the high-GC orthologs have undergone a large excess of AT→GC substitutions over GC→AT substitutions from mouse to human individually in all three codon positions, while for low-GC orthologs, the reverse is 178 true. Consistent with these trends, the amino acid substitution also exhibit definite, but opposite patterns in high-GC and low-GC orthologs. High GC- orthologs exhibit significant bias in favor of Thr→Ala , Ser→Ala, Ser→Pro, Val→Ala, Lys→Arg, Asn→Ser, Ile→Val etc from mouse to human,, while in low Gc-orthologs, the reverse trends prevail. The members of the GC-even group share some trends with the high-GC group and some with the low-GC group. These observations imply that there is a definite directionality in substitution patterns towards increasing compositional divergence in human protein-coding regions as compared to mouse. Surprisingly enough, the trend Asp→Glu from mouse to human is shared by the members of all three groups of orthologs irrespective of their GC-bias, the structural/functional implication of which is not very clear.

(B) Analysis of Gene and Protein Architectures of Extremely Halophilic Microorganisms - Molecular Signature of Hypersaline Adaptation :

A large scale comparative study of the compositional characteristics of genomes and proteomes of the extreme halophilic and non-halophilic microorganisms has revealed the conspicuous characteristics relevant to life in an extreme environment distinguished by hypersalinity. These are (i) distinct synonymous codon usage, (ii) enhanced usage of negatively charged residues on protein surface, (iii) decreased frequencies of hydrophobic residues, and (iv) higher propensities for formation of random coil region in proteins, as compared to their orthologs in non-halophilic organisms. Comparison of 124 orthologous protein sequences from halophilic and non- halophilic species of comparable genomic G+C contents has shown a strong bias towards replacement of positively charged and hydrophobic residues of non- halophilic proteins by Asp and Glu in halophiles. Higher propensity of formation of random coil region and surface negative charge distribution are evident from the previously reported experimentally determined three dimensional orthologous structures of halophiles and non-halophiles. The analysis not only demonstrates that genes/proteins of the extreme halophilic organisms are magnificently engineered in order to survive in the high salt condition, but also offers an insight into the nitty-gritty of the molecular strategies adopted by the microbial world to optimize between their functional activities and structural stability in such a specialized niche.

(C) Other activities: Members of the Centre regularly take classes in Calcutta University, Jadavpur University & Visva-Bharati and also in the pre-Ph.D. course at IICB. Hands-on training is provided to the students and scholars of local Universities/Institutes. Students from various Universities /Institutes perform short-term projects at the Centre.

5. Infrastructure facilities in the Bioinformatics Centre A. Computer & Communication facility SGI Octane Workstations High End Server (Itenium II Hp Integrity Server 4640), Linux OS Mail Server (Xeon server), Ftp Server (Xeon server) 179 P4 PCs, Laser Printers, DeskJet Printers High speed Network Printer with Copier and Scanner function High Resolution Scanners 4 mbps uncompressed leased line Internet connection from VSNL B. Scientific Software packages : Insight II Platform in Silicon, Graphics Octane (Version 2000.1) GCG Wisconsin Package (Version 10.3) & SeqWeb (Version 2.1) DNA Star Laser gene, DS Gene (Version 1.5) Statistica (Version 6), Corel Draw Visual Studio .NET, End Note (Version 8.0.2) Adobe Creative Suite Sigma plot (Version 9.0)

6. Details about staff members working in the centre : Mr. S. Chatterjee Senior Tech. Asst. Bioinformatics Mr. S. K. Bag Junior Tech. Asst. Comp. science Mr. S. Paul Junior Tech. Asst. Bioinformatics

7. Types of services provided : The sequence analysis using different software available in the centre, bibliography search facility and web-based services from our local server are provided to scientists and students of IICB and of other local Research Organizations/Universities. The members of the Centre also actively take part in organizing major events in IICB such as Open house or exhibitions.

8. Educational activities with details of placement : Members of the Centre regularly take classes in Calcutta University, Jadavpur University & Visva-Bharati, NIPER-Kolkata and in the pre-Ph.D. course at IICB. Students from different Institutes/Universities of our country carry out short-term projects at the centre.

9. Initiative to validate the outcome of bioinformatics resources : Research papers have been published in International Journals, Novel genome data mining software tools like SPAST, Gensyn have been posted in the web.

10. Collaborative works/ initiatives : A database on “Genetic Diseases among Indian Population” is being developed with the collaboration of Dr. Kunal Ray, Human Genetics & Genomics Group of this Institute. Analyses of microbial genomes are being carried out in collaboration with Prof. J. Chakrabarti, Indian Association for Cultivation of Sciences, Kolkata.

11. Databases/ Software packages developed : Among the novel algorithms and programs currently being developed by the members of the centre for macromolecular sequence analysis are SPAST (Substitution Pattern Analysis Software Tool), GeneSyn – A program for analysis of gene synteny in genomes of two or more related species and an integrated software tool for prediction of cases of horizontal transfer.

12. Papers published :

180 (i) Bag SK, Paul S, Ghosh S, Dutta C.(2007) Reverse polarization in amino acid and nucleotide substitution patterns between human-mouse orthologs of two compositional extrema. DNA Res., 14:141-54.

13. Initiation of R&D activities in Bioinformatics :

During the reporting period, the following initiatives have been taken on : (i) Development of novel software tools on Gene Synteny, HGT etc. (ii) New collaborative projects on structural analysis of transcription factors of hyperthermophiles (with Prof, S. Roy & Dr. T. Chakraborty, IICB)

14. Details of Training/ Workshop organized and total no. of user trained: No. of Short-term (3-6 months) trainees : 12

15. Impact shown by your centre on the growth of biotechnology and allied areas: No. of papers published by the Centre : 1 No. of papers published with the help of the Centre : 4 No. of Ph. D. thesis completed with the help of the Centre : 4 No. of Software tools developed/under development : 3 No. of database under construction : 1 No. of persons trained in the Centre (short-term projects) : 12 No. of collaborative research projects being carried out : 3

16. Future activities : (i) Development of the database on “Genetic diseases among Indian Population”. (ii) Development of novel genome analysis tools (iii) Comparative genome/.proteome analysis of microbial (especially extremophiles and pathogens), fungal and mammalian organisms.

Additional Details Name of the Coordinator: Dr. Chitra Dutta Postal Address: Bioinformatics Centre, Indian Institute of Chemical Biology 4, Raja S.C. Mullick Road, Kolkata – 700 032 Phone Number: 91 33 2473 3491 (ext. 212) Fax Number: 91 33 2473 0284 / 5197 Email: [email protected];

181 Institute of Bioresources and Sustainable Development, Imphal Coordinator : Shri. Sunil. S. Thorat

1. Summary of the progress made by the centre from its inception: The Distributed Information Sub-centre (DISC), Imphal has constituted an Executive Committee for the proper functioning of the Bioinformatics centre, The First Executive Committee meeting consisting five members was held on 4th December 2006 at Conference Hall of the Institute of Bioresources and Sustainable Development (IBSD). The Centre has started functioning with the recruitment of one Information Officer, one Technical Assistant, and one Data Entry Operator. For the establishment of the Centre, necessary infrastructure development was made by procuring two servers (Mail/Web and Power Database Solution), scanner, color laser printer, 5 KVa UPS, Mac Book, 4 PCs, Plasma TV Screen for presentation a Digital camera and Handycam for Documentation. In addition to this the centre has few scientific software like Genocluster and other software’s like Linux AS4, NOD 32 Antivirus, Microsoft Windows and Office Professional edition along with paper license and a Microsoft Visual Studio 2005 Standard version. The centre has subscribed three e-journals namely Conservation Genetics, Plant Genetics Research and Conservation biology and two databases namely AGRIS and AGRICOLA for the students and researchers of the Institute. The centre has organized 3 (three) training programmes for the Teachers/Lecturers, Researchers/students on 24-25 January, 2007, 29th - 30th March, 2007 and 17- 18th August 2007.Altogether 48 participants were benefited from the trainings. Under Database development programme three Databases, namely Birds database of Sikkim, Zingiberaceae database of NE with special reference to Manipur and Cyanobacteria database have been developed. Currently more than 400 records have been added to these databases and database updating is in progress.

2. Major Research Activities in Biotechnology and its related fields at your institution: • Invitro propagation and mass multiplication of plant resources of selected medicinal, aromatic and horticultural plants for conservation and sustainable development. • Isolation, identification and characterization of medicinal and aromatic oils and bioactive principles from the plants used in traditional/folklore medicines and their value added products. • Isolation, physiological and biochemical characterization isolates of North-Eastern region of India for sustainable utilization and development of cyanobacterial value added products. • Standardization of microbial fermentation for fermented food products of North East Region and value addition for commercial exploitation.

3. Area of Specialization of the centre: Environment & Biodiversity

4. Major activities of the centre during the year 2006-2007: • An Executive Committee of the DISC was constituted.

182 • Training is provided to the Teachers, Researchers & Students from time to time. • Three Databases namely Birds database of Sikkim, Zingiberaceae database of NE with special reference to Manipur and Cyanobacteria database have been developed. Currently more than 400 records have been added to these databases and database updating is in progress. • One poster presentation on “Ethnobotanical plant database of NE India” was presented in the International Conference on Bioinformatics, 2007, HKUST, Hong Kong.

5. Infrastructure facilities in the Bioinformatics Centre: A. Computer and communication facility: Two Servers (Mail/Web and Power Database Solution) , Scanner, Color laser printer, 5 KVa UPS, Mac Book, 4 PCs, Plasma TV Screen for presentation a Digital camera and Handycam for Documentation.

B. Scientific Software packages: The Center has scientific softwares like Genocluster and other software’s like Linux AS4, NOD32 Antivirus, Microsoft Windows and Office Professional edition along with paper license and a Microsoft Visual Studio 2005 Standard version.

C. Database & other information resources: Three Databases, namely Birds database of Sikkim, Zingiberaceae database of NE with special reference to Manipur and Cyanobacteria database have been developed. Currently more than 400 records have been added to these databases and database updating is in progress.

6. Details about staff members working in the centre (Name of the staff, Designation, Specialization and period of working. Please indicate their absorption status) Sl. Name Designation Working Absorption No Since status 1. Shri. Sunil S. Thorat Coordinator Core staff 2. Dr. S. Subharani Devi Information December Not Officer 2006 absorbed 3. Ms. N. Abem Devi Technical December Not Assistant 2006 absorbed 4. Shri. L. Amitkumar Data Entry December Not Operator 2006 absorbed

7. Types of services provided: • E-Journals subscribed by DISC are open accessed to users. • Internet facilities to the Scientists and Researchers. • Printing, Scanning and Photocopying facilities are provided. • Technical assistance is provided for search & troubleshooting.

8. Educational activities with details of placement: Not applicable 183

9. Initiative to validate the outcome of bioinformatics resources: Not yet initiated

10. Collaborative works/initiatives: Manipur University and Colleges affiliated to MU are in touch for necessary support and help from DISC, Imphal.

11. Databases/Software packages developed: Three Databases, namely Birds database of Sikkim, Zingiberaceae database of NE with special reference to Manipur and Cyanobacteria database have been developed. Currently more than 400 records have been added to these databases and database updating is in progress.

12. Papers published or presented in the conferences with reference: Title of the Paper: Ethnobotanical plant database of NE India., Proceedings of Incob2007, HKUST, Hong Kong. Authors: Sunil. S. Thorat, Nilima Huidrom and Rajiv Das Kangabam

13. Initiation of R&D activities in Bioinformatics: Yet to begin

14. Details of Training/Workshop organized and total no. of user trained Workshop/Trainings: • Application of Computer for Bioresources Conservation for Teachers: 24-25 January, 2007 • Application of Computers for Bioresources Conservation for Researchers: 29th - 30th March, 2007 • Application of Bioinformatics for biodiversity conservation: 17- 18th August 2007. No. of Personnel Trained/Educated: 48

15. Impact shown by your centre on the growth of biotechnology and allied areas (In this you may highlight the details like number of paper published/number of papers published with the help of your centre, how your centre is promoting various activities of your organization and neighbouring institutions, manpower trained, tools developed, patents & copyrights acquired and other services offered etc). • One poster presentation on “Ethnobotanical plant database of NE India” was presented in the International Conference on Bioinformatics, 2007, HKUST, Hong Kong. • Three trainings were conducted on different topics for the teachers, Researchers and students. Altogether 48 participants were benefited. • Three databases are developed and updation is in process. • Collaboration with Government Institutes and Universities are initiated.

16. Future activities : • Providing access to scientific information in the area of specialisation of the centre to the scientific community. 184 • Programme for the Development of Database and Software on Biodiversity Conservation and Documentation. • To conduct certain awareness programme on biodiversity and bioresources conservation for school children of the entire north east. • To organize suitable workshops/training programmes in bioinformatics • Plant biodiversity database: Separate database will be developed on certain important plant families covering most of the important characteristics available through the primary and secondary data from the region. • Fauna Biodiversity database: Database will be developed on the Insects and Fishes of Manipur followed by the data from the entire north east. • Microbial biodiversity database: In addition to the existing database of Cyanobacteria, more databases will be developed following the authentic database format followed by the other Institutes.

Additional Details: Name of the Coordinator: Shri. Sunil. S. Thorat Postal Address: Distributed Information Sub centre, Institute of Bioresources and Sustainable Development (IBSD), Takyelpat, Imphal. Phone Number :( 0385) 2446122 Mobile: 09436065265 E-mail: [email protected] Website: ibsd.gov.in

Name of Contact Person(s): As above E-mail: As above

185 Institute of Microbial Technology, Chandigarh Coordinator: Dr G P S Raghava

1. Summary of the progress made by the centre from its inception

Over a period of time since its establishment in 1987, Bioinformatics centre at IMTECH has shown consistent growth in the different areas of bioinformatics whether in carrying out peer reviewed research or providing services to the world wide. Centre has developed databases and softwares both for in house use and for scientist’s world over. BIC has developed a number of web servers based on peer reviewed research carried out at the bioinformatics centre. BIC staff has published more than 70 research papers in reputed international journals and more than 30 abstract/poster/papers presented in national and international conferences (http://imtech.res.in/raghava/pub.html). Our servers are getting more than 15000 hits per day.

We have developed a number of programs/web servers for predicting secondary structure of proteins. Our regular secondary structure (Helix & Sheet) prediction method has been classified in category of highly accurate methods in the world (CASP5, CAFASP3 & EVA). Centre has established the Genome Wide BLAST and FASTA searching facility with integrated sequence analysing tools. It is a world-wide facility for sequence similarity search over large number of databases including genome and proteome. As of today we have genomes and annotated proteomes of all prokaryote and Eukaryote (including human genome) sequenced so far. Centre has developed following databases in biology i) MHCBN: A curated database of MHC binders/non-binders & T-Cell epitopes (~23000 entries); ii) Public Domain Software in biology (more than 500 software); iii) Free software for general purpose (more than 1500 entries); iv) BCIPEP: A curated database of antigenic, immunogenic and non-immunogenic peptides including B cell epitopes (more than 2300 entries); and v) HaptendB: A database of small molecule which are antigenic but not immunogenic.

2. Major research activities in Biotechnology and its related fields at your institution

• Fermentation Technology & Applied Microbiology: Scale-up processes which requires the specific skills of a fermentation technologist are also involved in tackling problems related to stability of recombinant plasmids, when cultivated at high density. • Cell Biology & Immunology: Development of monoclonal antibodies (MAbs) in order to identify disease specific antigenic and molecular targets for malaria, leishmaniasis and tuberculosis and to selectively eliminate infected cells. • Molecular Biology and Microbial Genetics: Molecular Biology & Microbial Genetics with special reference to infectious diseases & bioremediation of environmental pollutants: In this area several different projects are being pursued, aimed directly to address some of the problems alluded to above, there are others which focus on problems related to basic molecular biology. tc. • Protein Science & Engineering: The protein science and engineering group at IMTECH combines on overt set of interests of a fundamental 186 nature with an equally overt leaning towards the finding of applications.

3. Area of Specialization of the centre: Protein Modeling and Protein Engineering

4. Major activities of the centre during the year 2007-08

This year our centre developed methods for - i) Analyzung and predicting antibacterial peptides ii) Subcellular localization of Mycobacterial proteins iii) Identification of RNA interacting residues in a protein iv) Prediction of DNA binding domain and proteins and v) Tertiary structure of bioactive peptides.

5. Infrastructure facilities in the Bioinformatics Centre • Computer facility

1. BioCluster from Apple Computers 2. Apple X-server with 10.5TB storgae 3. SUN Fire v240 Server. 4. SUN Enterprise 420R & 420E Server. 5. SGI ORIGIN 350 Server and Workstation SGI O2 R12000 6. Apple G5 Servers with 3TB RAID 7. DEC ALPHA Servers and worstations 8. Personal Computers; Printers; DVD Server

• Communication Facilities:

1. Electronic Mail; Local Area Network 2. Two internet Connections (1MBPS [1:1] and 2MBPS[1:1] bandwidth) 3. Virtual Private Network (VPN) 4. Domain/Proxy Servers/ FireWalls.

B. Scientific Software packages

BIC have a number of software packages for protein Modeling like AMBER, CHARMm, GROMOS, X-PLOR, BOSS, Modeller, INSIGHTII, RasMol, WHATIF, Midasplus, Pymol, GROMOS, GAMESS, DSSP, MICROGenie etc. We have recently added sequence analysis software such as, CLUSTALW for multiple sequence alignments, ALSCRIPT for analysis of multiple sequences, PHYLIP for evolutionary analysis etc. In addition, we have also procured software MOLSCRIPT and RASTER 3D for presentation of protein structures.

C. Databases & other information resources

Mirror sites of following databases/information resources i) Biological Databases (e.g. genomes, proteomes, PDB, SWISSPROT); ii) Biological software (EBI & Indian Univ.); and iii) General software (GNU, PostgreSQL & SUN Freeware). We are the only official mirror sites in India, for a number of sites. 187

6. Details about staff members working in the centre (Name of the staff, Designation, Specialization and period of working)

S. Name of staff Designation Specialization No. 1. Dr. GPS Raghava Scientist Bioinformatics 2. Dr. Balvinder Singh Scientist Bioinformatics 3. Dr. Manoj Kumar Scientist Bioinformatics 4. Sh. Harvinder J. Tech. Asstt. Computers

7. Types of services provided

• Biocomputing: Centre has expertise in the field of biocomputing, Protein Modeling and Protein Engineering. The softwares are being developed in the above areas on users request. • Consultation Services: Centre also provides consultation services in the field of Protein Modeling, Protein Engineering, Biocomputing and Networking (LAN, WAN, INTERNET, E-MAIL). • Thesis: 5 student completed and 10 students are doing PhD in bioinformatics. A number of trainees has completed their projects as a partial fulfillment of their degrees. • Collaborative Research: BIC staff has solved a number of biological problems in collaboration with biologist. • Other Facilities: ¾ Installing, implementing and maintaining software packages on computers. ¾ Preventive maintenance of computers. ¾ Updates the user with recent advances in computers/Internet.

8. Educational activities with details of placement

• Regular workshops and training programmes in Bioinformatics at the centre. • BIC staff is regularly taking classes in universities, delivers lectures in workshops, conferences and training programmes. • Ph.D. students (More than 80 per year) and others are heavily using facilities at BIC. • BIC staff participates in the pre Ph.D. course in Bioinformatics at IMTECH.

9. Initiative to validate the outcome of bioinformatics resources

The research work is published in peer-reviewed journals and is available on world-wide-web. Servers developed at the centre are receiving more than 15,000 hits per day. The research work has been initiated in collaboration with wet lab scientists so as to test and validate predictions and results obtained using computational tools.

188

10. Collaborative works / initiatives

• Under NMITLI, centre has provided technological information/ know how about various software in the development of BIOSUITE to TCS Ltd., New Delhi. • BIGTECH, a US based company has also signed MOU with IMTECH in the area of bioinformatics. • Centre has also signed MOU for providing consultancy to Opportunia, New Delhi in Bioinformatics. As part of this, centre has provided two weeks training to a few personnel of Asia Privacy, Korea.

11. Databases / Software packages developed Databases Developed This centre have developed more than 70 webserver and a number of curated databases (http://www.imtech.res.in/bic/). Following is the list of web databases. • PRRDB: A database of pattern recognition receptors and pathogen associated molecular patterns. This is important database for innate immunity. • MHCBN: A comprehensive database of MHC binding and non-binding peptides. This is a curated database compiled from literature. • BCIPep: A database of immunodominant B cell epitopes or peptides that can activate the B cell response. This is a curated database compiled from literature. • HaptenDB: A database of haptens which are antigenic non-immunogenic small molecules that can activate immune system with carrier proteins. This is only database of its kind. • PDRB (Public Domain Resources in Biology): It is database of public domain biological resources. • RFSB (Repository of Free Software in Biology): It is a database of public domain software in biology and is available for distribution via on- line as well as off-line modes. • PDWPB (Public Domain Web Pages in Biology): PDWPB consists of the information about web pages in biology. • FSGP (Free Software for General Purpose): The database contains software which is freely available for non-commercial users.

12. Papers published or presented in the conferences with reference

The BIC staff of this centre has published more than 70 research papers in reputed international journals. Following is list of papers published/accepted in year 2007.

1. Vivona, S., Gardy J.L., Ramachandran, S., Brinkman, F.S.L., Raghava, G. P. S., Flower, D.R. and Filippini, F. (2007) Computer aided biotechnology:

189 from immunoinformatics to reverse vaccinology Trends in Biotechnology (In Press) 2. Muthukrishnan S., Garg A. and Raghava, G. P. S. (2007) OxyPred: Prediction and Classification of Oxygen-Binding Proteins Genomics, Proteomics & Bioinformatics (In Press) 3. Kumar, M., Gromiha, M.M. and Raghava, G. P. S. (2007) Prediction of RNA binding sites in a protein using SVM and PSSM profile. Proteins: Structure, Function and Bioinformatics. (In Press) 4. Pashov A., Monzavi-Karbassi B., Raghava, G. P. S. and Kieber-Emmons, T. (2007) Peptide mimotopes as prototypic templates of broad-spectrum surrogates of carbohydrate antigens for cancer vaccination CRITICAL REVIEWS IN IMMUNOLOGY 27 (3): 247-270 5. Saha, S. and Raghava, G. P. S. (2007) Prediction of allergenic proteins and mapping of IgE epitopes in allergens Nature Protocols 10.1038/nprot.2007.505 (Online) 6. Singh, H. and Raghava, G. P. S. (2007) Prediction and mapping of promiscuous MHC class II binders in an antigen sequence Nature Protocols 10.1038/nprot.2007.502 (Online) 7. Lata, S., Sharma, B.K. and Raghava, G. P. S. (2007) Analysis and prediction of antibacterial peptides Nature Protocols 10.1038/nprot.2007.503 (Online) 8. Kumar, M. , Verma, R. and Raghava, G. P. S. (2007) Mitpred2: An improved method for predicting mitochondrial proteins using SVM and HMM Nature Protocols 10.1038/nprot.2007.488 (Online) 9. Kumar M., Gromiha M.M. and Raghava, G. P. S. (2007) Identification of DNA-binding proteins using support vector machines and evolutionary profiles BMC Bioinformatics 8:463 10. Kaur, H., Garg, A. and Raghava, G. P. S. (2007) PEPstr: A de novo method for tertiary structure prediction of small bioactive peptides. Protein Pept Lett. 14:626-30 11. Rashid M., Saha S. and Raghava, G. P. S. (2007) Support Vector Machine-based Method for Predicting Subcellular Localization of Mycobacterial Proteins Using Evolutionary Information and Motifs BMC Bioinformatics 8: 337 12. Raghava, G. P. S. (2007) Prediction of subcellular localization of proteins using machine learning techniques and evolutionary information Amino Acids 33(3): X-XI 13. Lata, S., Sharma, B.K. and Raghava, G. P. S. (2007) Analysis and prediction of antibacterial peptides BMC Bioinformatics 2007, 8:263 14. Mishra, N., Kumar, M. and Raghava, G. P. S. (2007) Support vector machine based method for predicting Glutathione S-transferases proteins. Protein Pept Lett. 6:575-80 15. Vidyasagar et al...... Raghava, G. P. S...... (2007) BioSuite: A comprehensive bioinformatics software package (A unique industry- academia collaboration). CURRENT SCIENCE 92 (1): 29-38 16. Saha, S. and Raghava, G. P. S. (2007) Prediction of bacterial proteins. In Silico Biology 7: 0028 17. Saha, S. and Raghava, G. P. S. (2007) Prediction of neurotoxins based on their function and source. In Silico Biology 7: 0025

190 18. Saha, S., Zack, J., Singh, B. and Raghava, G. P. S. (2007) VGIchan: Prediction and classification of voltage-gated ion channels. Genomics Proteomics & Bioinformatics 4:253-8 19. Greenbaum et al...... Raghava, G. P. S...... (2007) Towards a consensus on datasets and evaluation metrics for developing B cell epitope prediction tools. Journal Molecular Recognition 20:75-82 20. Bhasin, M. and Raghava, G. P. S. (2007) A hybrid approach for predicting promiscuous MHC class I restricted T cell epitopes. J. Biosci. 32:31-42 [PDF]

13. Initiation of R&D activities in Bioinformatics

Same as in 4

14. Details of Training / Workshop organized and total no. of user trained

BIC organize minimum one workshop every year with average 30 participants per workshop. Every year we have different theme, following is detail of workshops organized in last five years.

1. National Workshop on “Subunit Vaccine design”, April, 2003 2. Training to the trainers of DOEACC centre in the northern region, July, 2003 3. Database management and Analysis of Microarray, Oct., 2003 4. Protein simulations and docking, Oct., 2004 5. Machine Learning Techniques in Bioinformatics”, Oct., 2005 6. Training Programme on GCG, sequence analysis software in Dec., 2005 7. Training Programme on InsightII, by Accelrys. Inc., in March, 9th & 10th, 2006 8. Bioinformatics resources on miRNA and siRNA, Nov. 14-17, 2006 9. Computational approaches for predicting molecular interactions. Oct. 9-12, 2007

15. Impact shown by your centre on the growth of biotechnology and allied areas. In this you may highlight the details like number of papers published/number of papers published with help of your centre, how your centre is promoting various activities of your organization and neighboring institutions, manpower trained, tools developed, patents and copyrights acquired and other services offered etc.

Number of papers published/Number of papers published with help of your centre: Solely based upon Bioinformatics approach, the number of publication from the centre are more than 70. Papers published by BIC got high citations more than 700 citations. Dr Raghava’s name appear in hot 100 authors in Biomed journals. This shows that BIC at IMTECH is making big impact on society. It is difficult to calculate the number of papers published with help of bioinformatics from the staff of institute. However, this number is increasing as publishing in good journal/high impact factor journals requires the application of bioinformatics tools.

191 Promotion of various activities of our organization and neighboring organizations: As in 14 and 10.

Manpower Trained: Manpower is being trained by a. Organizing workshops/training programmes by the centre; b. Recruiting project assistants and sharpening their skills in Bioinformatics

Tools Developed: As in 11.

Patents/ Copyright obtained/ filed by your centre:

1. Raghava, G.P.S. (1996) ASSP: A computer program for comparision of observed and predicted protein secondary structure. L-15582/96. 2. Raghava, G.P.S. (1996) A computer program for analysing and creating protein secondary structure database. L-15658/96. 3. Raghava, G.P.S and Agrawal, P. A (1997) Software for phylogcncitic identification of microorganisms. C R. 1/97, date 11.3.97 4. Raghava, G.P.S (2001) A computer program for assisting the user in using protein modelling software package (PMOD 1.0) . SW-393/2001, date 08/02/2001 5. Kaur, H. and Raghava, G.P.S. (2002) BETATPRED: Software for predicting b -turns using statistical algorithm. SW-1162/2003. 6. Raghava, G.P.S. (2002) DNASIZE: A software package for computing DNA/Protein fragments. SW-1156/2003. 7. Issac, B., Singh, H., Kaur, H. and Raghava, G.P.S. (2002) FTG: Software Package for Predicting Gene in DNA using Fast Fourier Transform. SW- 1154/2003. 8. Issac, B. and Raghava, G.P.S. (2002) GWBLAST: Software Package for Genome Wide Similarity Search using BLAST. SW-1149/2003. 9. Issac, B. and Raghava, G.P.S. (2002) GWFASTA: Computer program for genome wide FASTA search. SW-1143/2003. 10. Raghava, G.P.S. (2002) LibInet: Software Package for Managing Library Resources and Accessing via Internet. SW-1155/2003. 11. Singh, H. and Raghava, G.P.S. (2002) MHCBench: Evaluation of MHC Binding Peptide Prediction Algorithms. SW-1160/2003. 12. Singh, H. and Raghava, G.P.S. (2002) MOT: Matrix Optimization Technique for identifying the MHC binding core. SW-1159/2003. 13. Raghava, G.P.S. (2002) PCLASS: Computer Program for predicting structural class of protein via Internet. SW-1157/2003. 14. Raghava, G.P.S. (2002) PDSB: Software Package for Managing Public Domain Software in Biology. SW-1148/2003. 15. Raghava, G.P.S. (2002) PDWSB: Software Package for creating and managing Biological Web Servers. SW-1152/2003. 16. Singh, H. and Raghava, G.P.S. (2002) ProPred: Software package for predicting promiscuous MHC class-II binding peptides. SW-1163/2003. 17. Singh, H. and Raghava, G.P.S. (2002) ProPred-I: Software package for predicting promiscuous MHC Class-I binding peptides. SW-1161/2003. 18. Raghava, G.P.S. (2002) PSAweb: Software package for Analyzing of Protein Sequence and Multiple Alignment. SW-1158/2003.

192 19. Bhasin, M. and Raghava, G. P.S. (2003) MHCBN: A software package for managing data of Immunologically related peptides. SW-1151/2003.

Services Offered: As in 7.

Technologies Developed/Transferred:

• Vaxiprep: A software package for predicting potential vaccine candidates has been developed. This package integrates 14 web servers developed at IMTECH in the field of immunoinformatics. The integration and user interface was developed by Biomantra a informatics company. This has been inaugurated by Dr R. A. Mashlekar, Ddirector General, CSIR on 15th December 2004. • Under NMITLI, centre has provided technological information/ know how about various software in bioinformatics to TCS Ltd., Hyderabad. The software BIOSUITE has been launched by honourable president of India in July 2004.

16. Future activities

The future activities will focus on research as mentioned in 4. Additional Details: Name of the Coordinator: Dr G P S Raghava, Scientist Postal Address: Bioinformatics Centre, Institute of Microbial Technology, Sector 39A, Chandigarh-160 036, INDIA Phone Number: +91-172-2690557 & +91-172-2695225 Fax No.: +91-172-2690632 & +91-172-2690585 Email: [email protected] Website: http://www.imtech.res.in/bic/ ; http://www.imtech.res.in/raghava/ Name of Contact person: Dr G P S Raghava, Scientist Email: [email protected]

193 Karnataka Veterinary, Animal & Fisheries Sciences University, Mangalore Coordinator : Dr. Indrani Karunasagar

1. Summary of the progress made by the center from its inception: The Bioinformatics Centre (Sub-DIC) at the College of Fisheries, Mangalore since its inception in 2000, is actively involved in carrying out research, preparing databases and conducting training programmes in bioinformatics applied to aquatic marine biotechnology The Centre initiated research pertaining to a major shrimp pathogen, the White spot syndrome virus (WSSV), a scourge to aquaculture. Based on a bioinformatics study, a comparative analysis of the three complete genome sequences for WSSV available in GenBank was made wherein we identified a number of repeats of different sizes and composition. Our study showed that three of the minisatellite repeats could be used for genotyping WSSV strains. This was further assessed by experimental studies and our laboratory has been the first to show the use of the all the three minisatellites as epidemiological markers in distinguishing isolates from different geographical regions. This study is particularly useful in monitoring of WSSV infections for shrimp health certification and in forensics and also in epidemiological and ecological studies for tracing the movement and route of infection. We are also the first to characterize the evolutionary lineage of Indian WSSV strains based on regions prone to deletion and recombination and the presence /absence of transposase sequence which has led to the identification of a novel putative ancestral strain of WSSV. The outcome of this research has resulted in three publications. Several new sequences deposited have been assigned Genbank accession numbers. We have been studying the outer membrane proteins of the bacteria, Aeromonas hydrophila, which is the most common warm water fish pathogen. Based on in silico analysis we could identify two outer membrane proteins Omp48 and OmpTS, which could be used as potential vaccine candidates. Our lab based experiments further confirmed the above study, wherein the cloned and expressed recombinant protein proved to be highly immunogenic to fish and resulted in high relative percent survival on experimental challenge. Our work also involves the study of virulence genes in human pathogens such as Vibrio parahaemolyticus and Vibrio vulnificus associated with the aquatic environment. A number of sequences pertaining to the virulence genes of these organisms have been generated. Further, the sequences corresponding to the genomic regions of the fish borne trematodes, Opisthorchis viverrini and Clonorchis sinesis associated with cholangiocarcinoma have been deposited in GenBank and accession numbers assigned. These sequences have helped in the development of PCR based diagnostics for the above parasitic trematodes. Another major work is in the study of the phylogenetic relationship of bacterial groups associated with the marine sponge Halichondria nigricans. 35 unidentified bacterial groups based on the 16S rRNA sequences have been assigned GenBank accession numbers.

194 Antimicrobial peptide molecules such as lysozyme and ferritin from shrimps were identified using bioinformatics based tools. They have since been cloned, expressed and their activity studied. Studies on more molecules are in progress. In a major project on Functioinal genomics of shrimp, several hundred ESTs have been generated and submitted to GenBank.

2. Major research activities in Biotechnology and its related fields at your institution The major research activities include: • Development of rapid DNA based methods for the detection of pathogens and application of these methods for diagnosis of diseases • Development of molecular diagnostics for fishborne trematodes • Development of vaccines, immunostimulants, probiotics for use in aquaculture systems. • Study of marine toxins, harmful algal blooms and public health aspects of fish and fishery products. • Development of DNA based methods for rapid detection of harmful algae and cysts, blooms and their toxicity • Development of monoclonal antibodies to shrimp and fish pathogens • Development of microsatellites as molecular markers to study disease resistance in Penaeus monodon (tiger prawn) and Macrobrachium rosenbergii (freshwater prawn) • Genotyping white spot syndrome virus • Development of subtraction libraries to study differential gene expression with respect of infection with viral and bacterial pathogens and salinity in larval and adult stages of development. • Studying and characterizing antimicrobial compounds from marine bacteria • Studying the expression of genes involved in immune function of shrimp

3. Area of specialization of the center Aquatic Biotechnology

4. Major activities of the center during the year 2007-08 The centre conducted successfully a National Symposium on Bioinformatics during February 1-2, 2006. The Symposium was well attended with over 200 participants. The Centre also took initiative in training rural women in the operation of computers. Women were taught computer fundamentals and the basic softwares such as MS-Word, MS-Excel, and word processing software in local language.

5. Infrastructure facilities in the Bioinformatics Centre a. Computer and Communication facility NT Server - 1 no. Computers(Desktop) - 16 nos. 195 Laser printers (B/W) - 1 no. Laser printer (colour) - 3 nos. Inkjet printers - 2 nos. Epson Dot Matrix Printer - 1 no U.P.S. - 2 nos (3 KVA) Photocopier - 1 no. Internet - Lease line connectivity of 512 kbps b. Scientific software packages Software Application Gel Compare II software - Comparision of DNA/Protein gels and cluster analysis of RAPD and RFLP’s, Phylogenetic analysis • Discover Studio Gene ver 1.5 - DNA and Protein sequence analysis • Systat Version 10.2 - Statistical analysis • Exhome BLAST - Sequence alignments and analysis • GenoCluster - A suite of programs for comparative proteomics c. Databases and other information resources : Nil

6. Details about staff members working in the center Name of the Staff* Designation Specialization Period of working Dr.Malathi Shekar Information Officer Ph.D in Microbiology and from Aug. 2001 Advanced Diploma in Computer Applications Mr. Madhukrishna Technical Assistant Diploma in Computer from Jan. 2007 hardware and software Ms. Mohini M Data Entry Operator Advanced Diploma in from Dec. 2006 Computer Applications Mrs. Prathiba H. Data Entry Operator Certificate course in Microsoft from Dec. 2006 Office Ms. Aparna Data Entry Operator Bachelor in Computer from May 2007 Sharma Application *All Not absorbed

7. Types of services provided a. Use of computational softwares both online and stand alone - BLAST, FASTA, CLUSTAL W, EMBOSS, DS-Gene, SYSTAT, GELCOMPARE II, Exhome Blast, GenoCluster, SEQUENCE QUICKIE, Rasmol, TRF software etc. in routine research b. Web based data mining and prediction studies on available sequences in Genbank. c. Primer designing, uploading sequences to GenBank, e-submission of journal articles for publication etc. d. Providing e-journals such as Aquaculture journal to the university library for benefit of students and staff.

196 e. Maintaining e-manuals such as FDA manual, FAO risk assessment documents, AAPQIS etc. f. Designing, updating and maintaining of website for university involving teaching campuses and research stations of Mangalore, Bangalore, Bidar, Shimoga and Hassan. Assisting researchers from neighbouring medical colleges in analysis of data

8. Educational activities with details of placement We have been conducting only short term training courses. However, our graduates, who worked in the Centre as data entry operators/technical officers have found placement in Bioinformatics/ Biotechnology related areas abroad eg. USA, Germany and Japan.

9. Initiative to validate the outcome of bioinformatics resources There is a close interaction between Bioinformatics Centre and various biotechnology related project in our University and other neighboring Universities like Manipal Academy of Higher Education, Rajiv Gandhi University of Health Sciences, Mangalore University. Predictions made using bioinformatic tools are validated by lab experiments carried out in various projects. The centre has been successful in depositing a total of 76 sequences in GenBank and obtaining accession numbers.

10. Collaborative works/initiatives The Centre is collaborating with the following Centres and Universities • UNESCO Microbial Resources Centres • Wurzburg University, Germany • University of Goteborg, Sweden • Centre for Tropical Marine Ecology, Bremen, Germany • University of Kristianstad, Sweden • James Cook University, Townsville, Australia • Ghent University, Belgium

11. Databases/software packages developed Database on: a. Complete genome & protein sequence of whitespot syndrome virus b. Genomics of Vibrio parahaemolyticus c. Genomics of Aeromonas hydrophila d. Genomics of Vibrio vulnificus e. India Tiger shrimp Penaeus monodon f. SOP for Antibiotic residues in shrimp g. Bibliography of human food pathogens

12. Papers published or presented in the conferences with reference Using bioinformatics facility – the following papers were published

197 1. Divu, D., Khushiramani, R., Malathi, S., Karunasagar, I. and Karunasagar, I. (2007). Isolation, haracterization and evaluation of microsatellite DNA markers in giant freshwater prawn Macrobrachium rosenbergii, from South India. Aquaculture (in press).

2. Pradeep, B., Malathi S., Karunasagar, I. and Karunasagar, I. (2007). Genotyping of white spot syndrome virus prevalent in shrimp farms of India. DAO. (in press).

3. Maiti, B., Rekha, K., Karunasagar, I. and Karunasagar, I. (2007). Cloning and expression of ferritin from Penaeus monodon with a potential for application in aquaculture. Prot. Exp. Pur. (submitted).

4. Bhowmick, P.P., Rekha, K., Raghunath, P., Karunasagar, I. and Karunasagar, I. (2007). Molecular typing of Vibrio parahaemolyticus isolated from seafood harvested along the southwest coast of India. Lett. Appl. Microbiol. (submitted).

5. Anuj, T., Rekha, K., Karunasagar, I. and Karunasagar, I. (2007). Antivibrio activity of recombinant lysozyme expressed from black tiger shrimp, Penaeus monodon. Aquaculture, 272:246-249.

6. Rekha,,K., Girisha, S.K., Karunasagar, I. and Karunasagar, I. (2007). Cloning and expression of an outer membrane protein ompTS of Aeromonas hydrophila and study of immunogenicity in fish. Prot. Exp. Pur. 51, 303-307.

7. Rekha, K., Girisha, S.K., Karunasagar, I. and Karunasagar, I. (2006). Protective efficacy of recombinant OmpTS protein of Aeromonas hydrophila in Indian major carp. Vaccine 25, 1157- 1158.

8. Godhe, A., McQuoid, M.R., Karunasagar, I., Karunasagar, I. and Rehnstam Holm Ann S. (2006). Comparison of three common molecular tools for distinguishing among geographically separated clones of the diatom Skeletonema marinoi sarno et zingone (Bacillariophyceae). J. Phycol. 42, 280-291.

9. Parvathi, A., Sanath K. H., Bhanumathi, A., Ishibashi, M., Nishibuchi, M., Karunasagar, I. and Karunasagar, I. (2006). Molecular characterization of thermostable direct hemolysin-related hemolysin (TRH) positive Vibrio parahaemolyticus from oysters in Mangalore, India. Environ. Microbiol. 8, 997–1004.

10. Parvathi, A., Sanath K. H., Karunasagar, I. and Karunasagar,I.(2005). Study of occurrence of V.vulnificus by RAPD and gyrB sequence analysis. Environ. Microbiol 7, 995-1002.

11. Manjanaik, B., Umesha, K.R., Karunasagar, I. and Karunasagar, I. (2005). Detection of hepatopancreatic parvovirus (HPV) in wild shrimps in India by nested polymerase chain reaction (PCR). DAO. 63, 255-259.

12. Parvathi, A., Sanath, K.H., Karunasagar, I. and Karunasagar, I.. (2004). Detection and enumeration of Vibrio vulnificus in oysters from two estuaries along the south west coast of India using molecular methods. Appl. Environ. Microbiol. 70, 6909-6913. 13. Shahadat, H. Md., Otta, S.K., Chakraborty, A., Sanath, K.H., Karunasagar, I. and Karunasagar, I. (2004). Detection of WSSV in cultured shrimps, captured brooders, shrimp postlarvae and water samples in Bangladesh by PCR using different primers.Aquaculture, 237, 59-71.

14. Sanath, K.H., Karunasagar, I., Karunasagar, I., Teizou, T., Shima, K. and Yamasaki, S. (2004). Characterisation of Shiga toxin-producing Escherichia coli (STEC) isolated from seafood and beef. FEMS Microbiol. Lett. 233, 173-178.

198

15. Manivannan, S., Bob, K.M.D., Karunasagar, I. and Karunasagar, I. (2004). Prevalence of monodon baculovirus (MBV) in wild Metapenaeus species along the south west coast of India. Aquaculture, 232, 63-67.

16. Umesha, R.K, Uma, A., Otta, S.K., Karunasagar, I and Karunasagar, I. (2003). Detection by PCR of hepatopancreatic parvovirus (HPV) and other viruses in hatchery reared Penaeus monodon postlarvae. DAO. 57, 141-146.

17. Sanath, K.H., Sunil, R. Venugopal, M.N., Karunasagar, I. and Karunasagar I. (2003). Detection of Salmonella spp. in tropical seafood by Polymerase chain reaction (PCR). Int. J. Food Microbiol. 88, 91-95.

18. Dhanashree, B, Otta,S.K., Karunasagar, I. and Karunasagar, I.(2003). Typing of Listeria monocytogenes isolates by random amplification of polymorphic DNA. Ind. J. Med. Res. 117, 19-24.

19. Dhanashree, B., Otta, S.K., Karunasagar, I., Goebel, W. and Karunasagar, I. (2003). Incidence of Listeria spp. in clinical and food samples in Mangalore, India. Food Microbiol. 20, 447-453.

20. Karunasagar, I., Karunasagar, I. and Otta, S.K. (2003). Disease problems affecting fish in tropical environments. J. Appl. Aqua. 13, 231-249.

21. Dhanashree, B., Otta, S.K., Karunasagar, I. and Karunasagar, I. (2003). Protein profile analysis of Listeria monocytogenes strains from tropics. Curr. Sci. 84, 628-630.

22.Karunasagar, I., Rivera, B., Joseph, B., Kennedy, V.R., Shetty, A., Huq, I., Karunasagar, I. and Colwell R.R. (2003). OmpU genes in nontoxigenic V. cholerae associated with aquaculture. J. Appl. Microbiol. 95, 338-343.

23. Dilip, H., Sanath, K.H., Kumar, Y., Karunasagar, I., Nishibuchi, M. and Karunasagar, I. (2003). Application of polymerase chain reaction for detection of Vibrio parahaemolyticus associated with tropical seafoods and coastal environment. Lett. Appl. Microbiol. 36, 423-427.

24. Otta, S.K., Karunasagar, I. and Karunasagar, I.. (2003). Detection of Monodon Baculovirus (MBV) and whitespot syndrome virus (WSSV) in apparently healthy Penaeus monodon postlarvae from India by polymerase chain reaction. Aquaculture. 220, 59-67.

25. Godhe, A., Rehnstam –Holm, A., Karunasagar, I. and I. Karunasagar I. (2002). PCR detection of dinoflagellate cysts in field sediment samples from tropic and temperate environments. Harmful Algae (Elsevier), pp. 361-373.

26. Chakraborty, A., Otta, S.K., Joseph, B., Sanath, K.H., Shahadat, H. Md.., Karunasagar I., Venugopal, M.N. and Karunasagar I. (2002). Prevalence of white spot syndrome virus (WSSV) in wild crustaceans along the coast of India. Curr. Sci., 82, 1392-1397.

27. Manivannan, S., Otta, S.K., Karunasagar, I. and Karunasagar, I. (2002). Multiple viral infection in Penaeus monodon shrimp postlarvae in an Indian hatchery.DAO. 48, 233-236. Papers presented at conferences: 1. Malathi, S., Pradeep, B., Karunasagar, I. and Karunasagar, I. Genotyping of White spot syndrome virus of shrimps and its significance. Lecture presentation at the 48th Annual Conference of the Association of Microbiologists of India, December 18-21,2007, Chennai, India. 199

2. Malathi, S., Karunasagar, I. and Karunasagar, I. A bioinformatics based study of the thermostable hemolysin (tdh) gene in Vibrio parahaemolyticus and related vibrios. Presented at the 5th International Conference on Bioinformatics, December 18-20, 2006, Delhi, India

3. Rekha K., Malathi, S., Karunasagar, I. and Karunasagar, I. A bioinformatics based study of ompTS protein of Aeromonas hydrophila. Presented at the 5th International Conference on Bioinformatics, December 18-20, 2006, Delhi,India.

4. Malathi, S., Karunasagar, I. and Karunasagar, I. Tandem repeats within white spot syndrome virus genome sequences: Distribution and compositional analysis for comparative studies. Presented at National Bioinformatics Symposium, February 1-2, 2006, Mangalore, India

5. Rekha, K., Souche,Y. and Mourya, D.T. Bioinformatic based phylogenetic analysis of Dengue1 and Dengue 2 virs serotypes isolated from different parts of India. Presented at National Bioinformatics Symposium, February 1-2, 2006, Mangalore, India

6. Akash, N., Malathi, S., Karunasagar, I. and Karunasagar, I. Bioinformatics based study on the outer membrane proteins (OMP) of Aeromonas hydrophila for DNA vaccine design. Presented at National Bioinformatics Symposium, February 1-2, 2006, Mangalore, India 13. Initiation of R & D activities in Bioinformatics a. Comparative study of three complete nucleotide sequences of White spot syndrome virus – analysis for the distribution and composition of tandem repeats and look for VNTR regions which could serve as markers b. Comparative analysis of nucleotide sequence of thermostable direct hemolysin gene in Vibrio parahaemolyticus and related Vibrio spp. c. Comparative study of nucleotide sequence of outer membrane proteins of aquatic aeromonads d. Genotyping of the white spot syndrome virus e. Characterization and evaluation of microsatellite markers in giant freshwater prawn Macrobrachium rosenbergii .

14. Details of Training/workshop organized and total no. of user trained The following six training programmes (consisting of lectures and demos) and one National symposium on Bioinformatics has been conducted

Topic Month/Year Participants Application of Bioinformatics March 21-23,2002 15 Application of Bioinformatics in March 19-21, 2003 15 Marine culture and Marine resource utilization Application of Bioinformatics in March 22-24, 2004 15 Fisheries Sciences Bioinformatics and its applications March 21-23, 2005 15 in marine sciences Computer fundamentals and March 27-28, 2006 26 Basics ( for women 200 empowerment) Basic Bioinformatics and its March 15-17,2007 35 application National Symposium on Feb.1-2, 2006 200 Bioinformatics

15. Impact shown by your center on the growth of biotechnology and allied areas: - The Centre has been able to deposit over 300 sequences in GenBank and accession numbers have been assigned. - One Ph.D thesis in the area of Bioinformatics submitted and two are registered for PhD in Bioinformatics of Mangalore University . - The major impact is both in terms of service and primary data generated by the Centre using bioinformatics. This is evident from the publications in bioinformatics and related areas (listed in item 12). - The DBT has submitted 2 patents and two technologies based on the patents is ready for transfer . The BCL has written to the university for the commercialization rights. - Based on the DBT project support and the Bioinformatics facility, PCR based diagnostics has been developed for the White spot syndrome virus and this kit was selected for the technology development award in 2003 by the DBT.

16. Future activities The Bioinformatics Centre will be involved in the following research areas: • Studies on gene expression and development of EST Bank in the tiger shrimp P. monodon to be continued

• Identify the type III secretion system in Vibrio vulnificus using Genomics and Proteomics approach

• Comparative analysis of all the Omp genes in Aeromonas hydrophila for vaccine studies.

• Bioinformatics based analysis of virulence and omp genes for the development of a rapid test kit for Salmonella

• Bioinformatics study of sequences of shrimp viruses such as HPV and WSSV for RNAi studies.

• Genotyping of Indian shrimp viruses

• Genotyping of Indian Nodavirus of prawns

• In silico studies to predict immunoreactive peptides and candidate vaccines

• Development of test kits for seafood pathogens

Additional details: Name of the Coordinator : Dr. Indrani Karunasagar Postal Address : Department of Fishery Microbiology

201 KVAFSU, College of Fisheries, Mangalore Phone Number : 0824-2246384; 2243755 Fax No. : 0824 - 2246384 E-mail : [email protected]; [email protected] [email protected]; Website : www.mircenbiotech.com

Name of contact Person(s): 1. Dr. M.N.Venugopal (Professor) Email: [email protected] 2. Dr. Malathi Shekar (Information Officer) Email: [email protected]

202 Kerala Agricultural University, Thrissur Coordinator : Dr R Keshavachandran

1. Summary of the progress made by the centre from its inception: Bioinformatics Centre at KAU, Thrissur started functioning as a 23rd Distributed Information Sub Centre (DISC) since 1995 under BTISnet programme. The Centre was upgraded to DIC during 2004. The centre has shifted to new premises in September 2006 which also has facilities for wet lab work. Since its inception, the centre is carrying out research, preparing databases, conducting training programmes in the area of bioinformatics, and supporting plant biotechnology activities. A (2+2) credit course in Bioinformatics is offered to the Postgraduate students of Centre for Plant Biotechnology and Molecular Biology. 2. Major research activities in Biotechnology and its related fields at your institution: The work carried out at the Centre for Plant Biotechnology and Molecular Biology include isolation and characterization of genes encoding disease resistance to bacterial wilt and leaf curl virus in tomato, genomic library construction and cloning of genes for PR proteins in black pepper, isolation of novel strains of Bacillus thuringiensis from Western Ghats, assessing the molecular diversity, the insecticidal activity of the crystal proteins and cloning of novel cry and vip genes, genetic transformation for biotic stress tolerance in bell pepper and hairy root induction in medicinal plants. 3. Area of specialization of the centre: The main area of specialization is Plant Biotechnology. Apart from acting as a supporting centre for Biotechnology research, the Centre is involved in creating databases relevant to agriculture. 4. Major activities of the centre during the year 2007-08: • Selection of 2 Research Associates, 1 Senior Research Fellow and 1 Junior Research Fellow. • Conducting training programmes. • Insilico work mainly focusing on sequence analysis, molecular modeling, protein structural analysis and Docking studies. • Establisment of leased line connectivity of 6Mbps speed at the Bioinformatics centre, from AIRTEL. • Creation and maintenance of website for the College of Horticulture. 5. Infrastructure facilities in Bioinformatics Centre: A. Computer and Communication facility The centre has one IBM server, 6 Intel Core 2 Duo PCs, 7 PIV PCs, 7 AMD 64 Bit PCs, One Thermal Cycler, 2 HP Inkjet Printers, 2 HP LaserJet Printers (One Monochrome and One color), One HP All in One (Printer, Scanner, Fax & Copier), 1 Scanner, 1 LCD Projector, 1 Digital Photocopier, 1 Fax Machine. Communication Facilities - 6 Mbps Leased Line Broadband Internet connection from Airtel. B. Scientific software packages Omiga 2.0, Ligplot, LigandScout, Chem Axon, Maestro 8.0, Rasmol, Rastop, Qmol, Cn3D, VMD, PyMol, MDL Chime, KING, Marvin View, Swiss PDB Viewer, Chimera, Modeller 7v7, Genedoc, Bioedit, Treeview, Phylodraw, Mega 3.0, Clustal X, Phylip, Python, Perl, Argus lab, Hex, AutoDock tools, Molegro Virtual Docker, Marvin Sketch 203 ISIS Draw. C. Databases and other information resources Derwent Biotechnology Abstracts, Biological and Agricultural Index, Agricola, Agrisearch. 6. Details about staff members working in the centre: Name of the Staff Designation Specialization Period of Absorption working status Dr.R.Keshavachandran Professor & Plant 1-4-02 KAU staff Coordinator Biotechnology onwards Alishya Joy Research Bioinformatics 11-10-07 till Temporary Associate date Dileep K.V Research Bioinformatics 11-10-07 till Temporary Associate date Reena.N Senior Research Bioinformatics 11-10-07 till Temporary Fellow date Abhilash Joseph Junior Research Bioinformatics 9-03-07 till Temporary Fellow date Tintu George Junior Research Bioinformatics 17-10-07 till Temporary Fellow date 7. Types of services provided: • Training programmes for agricultural scientists, technical staff, students of KAU and staff & students of other educational institutions. • Literature search by means of CD ROM and Internet. • Offering courses in Bioinformatics to PG students. • Support to R&D activities for PG projects in Biotechnology. 8. Educational activities with details of placement: As a part of the M Sc program, the centre conducts a [2+2] credit course in Bioinformatics for M.Sc students of the Centre for Plant Biotechnology and Molecular Biology. As a part of the Ph.D program offered by the university, a course on Bioinformatics has been sent for approval. An initiative for E-print facility will be one among the future activities of the centre. Students who have completed the course are well placed with various Biotech companies. 9. Initiative to validate the outcome of bioinformatics resources: The research activities and regular training programmes validate the outcome of bioinformatics resources. Scientists in the university are regularly benefitted by the facilities of this centre. Bioinformatics resources are made use by the M.Sc. students for their research works. 10. Collaborative works / Initiatives: Nil 11. Databases/Software packages developed: The databases that are being developed include Database on Improved Crop varieties at KAU, Tissue culture protocols, Database on Indian Spices, Database on Rice Info. 12. Papers published or presented in the conference with Reference: 1. Keshavachandran,R., Nazeem P.A.,Girija, D., John P.S and Peter K.V. 2007(Eds) Recent trends in Horticultural Biotechnology.Vol.I, Vol.II New India Publishing Agency,New Delhi. 2. Nazeem P.A., Keshavachandran,R.,Babu T.D.,Achuthan C.R., Girija, D and Peter K.V.2007.Assessment of Genetic Variability in Black Pepper (Piper nigrum L.) Varieties through RAPD and AFLP Analyses. Recent trends in Horticultural Biotechnology. (eds. Keshavachandran et al.), New India Publishing Agency, New Delhi. pp 485-490.

204 3. Keshavachandran,R., Nazeem P.A., and Karihaloo J.L. 2007. Genetic Fingerprinting of Piper nigrum L. and Piper longum L. Cultivars Using RAPD Markers. Recent trends in Horticultural Biotechnology. (eds. Keshavachandran et al.), New India Publishing Agency, New Delhi. pp 635-640. 4. Rema Menon., Sunny K.M., Nisha Jose., Nazeem P.A., Keshavachandran,R., and Shakunthala Nair. 2007. Study of Isozyme Polymorphism in Musa Cultivars of Kerala. Recent trends in Horticultural Biotechnology. (eds. Keshavachandran et al.), New India Publishing Agency, New Delhi. pp 649-651. 5. Suma, B and Keshavachandran,R. 2007. Factors affecting Agrobacterium tumefaciens Mediated Transformation in Ginger (Zingiber officinale Rosc). Recent trends in Horticultural Biotechnology. (eds. Keshavachandran et al.), New India Publishing Agency, New Delhi. pp 721-726. 6. Karmarkar S.H and Keshavachandran,R. 2007. Induction of Hairy Roots in Holostemma ada-kodien With Agrobacterium rhizogenes. Recent trends in Horticultural Biotechnology. (eds. Keshavachandran et al.), New India Publishing Agency, New Delhi. pp 769-772. 7. Keshavachandran,R., Ajitha, R and Lavina C.V., Deepthy P.S., Nazeem P.A., and Girija, D. 2007. Bioinformatics: a KAU Perspective. Recent trends in Horticultural Biotechnology. (eds. Keshavachandran et al.), New India Publishing Agency, New Delhi. pp 967-969. 8. Fatima A.G., Girija, D., Meera C.S., Nazeem P.A. and Joseph L. 2007. Agrobacterium mediated genetic transformation in bell pepper. Recent trends in Horticultural Biotechnology. (eds. Keshavachandran et al.), New India Publishing Agency, New Delhi. pp 909-916 9. Sambasivam P.K. and Girija, D. 2007. Molecular characterization of Ralstonia solanacearum infecting ginger in Kerala. J. Ecobiol. 20:229- 237 13. Initiation of R&D activities in Bioinformatics: The centre is actively engaged in plant based research on gene & protein sequence analysis, protein structure prediction and metabolic pathways. In silico projects carried out include: • In Silico analysis of proteins of importance and interactions in Biocontrol agents like Trichoderma spp,. • Study of Functional Residues and Phylogenetic Analysis of Cystine Protenases involved in programmed cell death of plants • An evolutionary analysis and structural validation of Auxin Response Factors • Insilico analysis of insulin like proteins in plants • Bioprospecting of Chitinolytic microorganisms focusing on Serratia marcescens Chiting binding Protein(CBP21) • In Silico study of antimicrobial properties of Ginger against Epstein Barr virus, Aspergillus flavus and Helicobacter pylar 14. Details of Training / Workshops organized and total no: of users trained: Three DBT funded training programmes were conducted this Year. They include: 1. Bioinformatics in Data Analysis of Genes and Proteins. 2. Structural Bioinformatics :Exploring Macromolecular structures 3. Bioinformatics: Current approaches & Applications. 205 Other trainings conducted include: • Training programme on Sequence Analysis • Training on Emerging Trends in Bioinformatics. Total number of persons trained till date is 463. 15. Impact shown by the centre on the growth of biotechnology and allied areas: The usage of Bioresources by the students have increased notably and the facilities of the Centre are widely being made use of for research, paper presentations and other research activities of the University as well as for interpretation of molecular marker analysis data and sequence related work . Papers published with the help of Bioinformatics Centre : 10 No. of papers presented in conferences : 5 No. of scientists trained till date : 418 As a supporting centre for Biotechnology division, the Centre is in charge of the Gel Documentation system [BioRad] which is widely used by the staff and students for molecular marker analysis. 16. Future activities: • To train faculty, students & research workers to make use of bioinformatics techniques in scientific research. • Purchase softwares to strengthen R&D activities in Bioinformatics. • Publish practical and theory manual in Bioinformatics. • Introduce a course in bioinformatics to B.Sc and Ph.D students of KAU. • Continuation of teaching of Bioinformatics to M.Sc Plant Biotechnology students • Propose an E-newsletter from the Bioinformatics Centre. • To enable a E print facility to act as a repository for research articles by integrating data generated from Biotechnology division and other affiliated research stations Additional details: Name of the Coordinator : Dr R Keshavachandran Postal address : Bioinformatics Centre, (DIC) Kerala Agricultural University, Vellanikkara. Thrissur, Kerala -680 656. Phone number : 0487-2371994 Mobile : 9388987121 Email : [email protected] Website : www.kaubic.in Name of contact person(s) : Dr R. Keshavachandran Email : [email protected]

206 Madurai Kamaraj University, Madurai Coordinator : Prof. S.Krishnaswamy

1. Summary of the progress made by the centre from its inception The Centre of Excellence in Bioinformatics at School of Biotechnology, Madurai Kamaraj University, Madurai functions as a reputed centre for research and manpower development in bioinformatics apart from providing service. The centre has been established as a Distributed Information Centre (DIC) in 1986. The Centre was elevated to a Centre of Excellence in Bioinformatics in 2003. From 1996, the centre started its extensive manpower development activities with the initiation of the one year Advanced Diploma Course in Bioinformatics. The centre also submitted a proposal to DBT to upgrade the Advance Diploma course in Bioinformatics to M.Sc program in Computational Biology from the next academic year (2008-2009) onwards. The National High Resolution Graphics Facility started in 1993, cater to the need of structural biologists and molecular modelers. The Centre has been focusing its attention mainly on development of research and manpower development as well as services in the areas of structural bioinformatics, proteomics, database development, data mining, molecular modeling and dynamics. The Centre has an acclaimed reputation for service, teaching and research in the area of Bioinformatics. The staff of the center, as an integrated activity, with the faculty of the School of Biotechnology performs research and teaching. The Center has been a catalyst for the growth of Bioinformatics in this region and has contributed significantly to manpower development.

2. Major research activities in Biotechnology and its related fields at the institution ¾ Structural bioinformatics of membrane proteins ¾ Structural Genomics of prophage proteins ¾ Genome analysis for non coding RNAs ¾ Computational biology of macromolecular interactions ¾ Molecular Modeling and Drug design ¾ Data mining and text mining ¾ Proteomics and biomarkers discovery ¾ Genetic Engineering and Strain Manipulation of industrially important microorganisms ¾ Genomics of antibiotic biosynthesis ¾ Plant genetic engineering for disease resistance and stress tolerance ¾ Structural virology ¾ Fungal biotechnology ¾ Xenobiotics

3. Area of Specialization of the centre Structural Bioinformatics and Genetic Engineering

4. Major activities of the centre during the year 2007-08 1. Ten students completed Advanced Diploma in Bioinformatics (2006-07) and Ten ongoing (2007-08). 207 2. Five PhD students completed till 2007. Seven new students registered. 3. Participation in local workshops and academic staff training. 4. In house seminars and workshops related to Bioinformatics. 5. Elective courses as part of CBCS on Programming for Computational Biology, Structural biology and molecular modeling apart from Core courses on Biophysics and Bioinformatics for M.Sc. Biotechnology 6. Courses on Bioinformatics, Structural genomics, proteomics for M.Phil

5. Infrastructure facilities in the Bioinformatics Centre A. Computers and Communication Facility Systems PCs, SGI systems, Sun workstations, Multiprocessor cluster and server Dedicated 2Mbps RF VSNL connectivity, Structured intranet network connecting entire School of Biotech. with Print/backup/UPS facilities.

B. Scientific Software Packages Programs for sequence analysis and molecular modeling/dynamics including GCG, Biosym, Accelrys Discovery Studio, GROMACS and Clementine 10.0

C. Databases and other information resources Databases Beta barrel membrane porins, Prophage database, HNH database and Noncoding RNAs Software Information calculation for genomes, HNH domain subclassification, PCR primer design for whole genome, Structure analysis of Porins, Consensus based validation of porins and a software to detect Non-coding RNAs All databases and mirrors are available through (http://bicmku.in:8081, http://bicmku.in:8082, http://bicmku.in:8083, http://bicmku.in:8084) .

6. Details about staff members working in the centre: Except for Dr. Sanjeev K. Singh in the teaching staff and all in hired under CoE such as Database Admin, Programmer and JRFs, rest of the staff have been taken over by the Govt. of Tamil Nadu.

Teaching Staff Name Designation E-mail Id Dr.K.Dharmalingam Sr Professor [email protected] Dr.S.Krishnaswamy Sr. Professor and [email protected] Coordinator Dr.Z.A.Rafi Reader [email protected] Dr.N.Jeyakumar Lecturer [email protected]

Dr. Sanjeev K. Singh Lecturer [email protected]

Non-Teaching Staff Database admin, Programmerand JRFs Name Designation Name Designation

Mr.M.Raghuram Sr. Technician Mr. Krishnamohan Database Administrator 208 Mr.B.Shivakumar Sr. Technician Mrs. Mohana Priya Programmer

Mr.S.Prabakar Jr. Technician Mr. Nagoor Meeran System Administrator Mr.K.Rajendran Accountant Ms. Ranjana Chellam JRF (resigned)

Mr.C.Raja Stenographer Mr. Sankara Narayanan JRF

Mr.P.Muthupandi Clerk/Typist Mr.Sridharan JRF

Mr.P.Natarajasundara Data Assistant m Mr.M.Nagarajan Messenger/peon

7. Types of services provided Service Database access, Sequence analysis, Information retrieval, Molecular modeling and Project advice Manpower Development Advanced Diploma Course in Bioinformatics, Elective and Core Courses under CBCS to MSc and MPhil Biotech. students, In house workshops/seminars and Project trainees – MSc, MPhil, ADCB and PhD Research The Centre provides research services to college teachers, students from other Schools in the Universities and Industries.

8. Educational activities with details of placement Eighty seven students have successfully completed the ADCB till 2007. Eighty percent of the students are placed in different organizations – from Industries to higher education both in India and abroad. The current ADCB batch has 10 students. The students are placed in various institutions such as IARI, IBAB, IIT, AUKBC, TN govt, local Colleges, Molecular Connections, Meta Helix, CCMB, and also in UK, US, Canada, Germany and Switzerland. As part of the CBCS, an elective in Programming for Computational Biology with a revised syllabus to include perl programming has been introduced for the post-graduate and MPhil courses.

9. Initiative to validate the outcome of bioinformatics resources The industry and academia utilize the services and research advice on a regular basis. The industrial consultancy is done through the University. The research findings are published in national and international journals.

10. Collaborative works/ initiatives Weizmann Institute, Israe; University of Bath, UK; University of Aalborg, Denmark; Aravind Eye Hosptial - Medical Research Foundation, Madurai; NCBS, Bangalore; IISc, Bangalore; AIIMS, New Delhi; Genotypic Technologies, Bangalore; Avesthagen, Bangalore; HLL, Bangalore and CSIR NMITLI.

11. Databases/ Software packages developed Databases

209 F. Beta barrel membrane porins , Prophage database, HNH database and sRNABase. G. Software Information calculation for genomes, HNH domain subclassification, PCR primer design for whole genome, SCOMPS – Structure analysis of Porins, Consensus based validation of porins and Non-coding RNA detection

12. Papers published or presented in the conferences with reference 1. Nishma, N. P. Sankarnarayan and K. Dharmalingam (2007). Serum proteome of leprosy patients undergoing erythema nodosum leprosum reaction: regulation of expression of the isoforms of haptoglobin. Journal of Proteome Research (Available online) 2. N.S. Baalaji, M.K. Mathew and S. Krishnaswamy (2006). Functional assay of S.typhi OmpC using reconstituted large unilamellar vesicles: A general method for characterization of outer membrane proteins. Biochimie (doi:10.1016/j.biochi.2006.05.010) 3. K.V. Srividhya, V.R. Geeta, L. Raghavenderan, M. Preeti, J. Prilusky, M. Sankarnarayanan, J.L. Sussman, and S. Krishnaswamy 2006. Database and Comparative Identification of Prophages In ICIC 2006, LNCIS D.-S. Huang, K. Li, and G.W. Irwin (Eds.), Springer-Verlag., 344, pp. 863 – 868. 4. The NMITLI Bio-Suite Team (2007) BioSuite: A comprehensive bioinformatics software package (A unique industry–academia collaboration) Current Science 92: 29-38 (S.Krishnaswamy and group were part of the NMITLI team) 5. K. V. Srividhya and S. Krishnaswamy (2007). Sub classification and targeted characterization of prophage encoded two-component cell lysis cassette. J. Biosci. 32 (in Press). 6. J. Kagavalli, P.J. Eswari, S.R. Krishnadas and S. Krishnaswamy, P. Sundaresan 2007. In vitro and in vovo study on the secretion of the Gly367Arg mutant myocillin protein, Muscular Vision, 13, 1161-1168. 7. Sridhar and Z.A. Rafi (2007) Small RNA identification in Enterobacteriaceae using synteny and genomic backbone retention. OMICS: A Journal of Integrative Biology, 11, 74-99. 8. Sridhar and Z.A. Rafi (2007) Identification of Genomic Islands using small RNAs. In Silico Biology 7, 0053. 9. N. Jeyakumar, C. Haines, B. Berglund . DeSesa C, C.J. Hack, W. Dubitzky and E.G. Bremer. GetItFull – A Tool for Downloading and Pre- processing Full-text Journal Articles, Proc. Intl. Workshop on Knowledge Discovery in Life Science Literature (KDLL) in PAKDD 2006, Singapore, 139-145. 10. N. Jeyakumar, B. Daniel, W. Dubitzky, H. Catherine , Z. Yonghong, D. Catherine, R.V.B. James and E.G Bremer. (2006) Text mining of full-text journal articles combined with gene expression analysis reveals a relationship between sphingosine-1-phosphate and invasiveness of a glioblastoma cell, BMC Bioinformatics, 7:373. 11. N. Jeyakumar and R. Jawahar (2007) Functional Gene Clustering via Gene Annotation Sentences and MeSH Keywords, INCOB, Hong Kong. 12. S.K. Singh and N.S. Ram (2007). Theoretical Studies on Cyclin Dependent Kinase (CDK4) Inhibitors and drug receptor interaction analysis Med. Chem. Res. 15, 367.

210 13. S.K. Singh, N. Dessalew and P.V. Bharatam (2006) 3D-QSAR CoMFA studies on Indenopyrazole as CDK2 Inhibitors. Eur. J. of Med. Chem. 41, 1310-1319.

13. Initiation of R&D activities in Bioinformatics Comparison of Proteome Profile with Transcriptome Profile in E.coli Growing under Oxygen Stress (K.Dharmalingam) Infection proteomics of fungal keratitis (K.Dharmalingam) Comparison of Homology Modeled 3D structure of M. Laprae 18KDa small heat shock protein and its mutant (K. Dharmalingam and S.K. Singh) Structural genomics of prophage proteins (S. Krishnaswamy) Sub classification of HNH domain proteins (S. Krishnaswamy) Struct. bioinformatics of membrane proteins and complexes (S. Krishnaswamy) Detection of small RNAs in bacterial genomes ( Z. A. Rafi) Structural bioinformatics of Protein-RNA binding proteins (Z A Rafi) Bioinformatics Analysis of Protein Kinase Relations and Pathways from Biomedical Data and Literature (N. Jeyakumar) Theoretical Studies on Cyclin Dependent Kinase Inhibitors (S.K. Singh) Modeling Studies on Non-Nucleosidic HIV-RT Inhibitors (S. K. Singh)

14. Details of Training/ Workshop organized and total no. of user trained Workshop on Trends in Systems Biology and Bioinformatics, March 6-8, 2007 - 75 participants (and) Local workshop on Bioinformatics software September 11- 12, 2007 - 20 participants.

15.Impact shown by centre on growth of biotechnology and allied areas. The usage of the centre has resulted in a number of research publications over the years in referred journals, Ph.D. dissertations and project reports by the users. The host institution and more than 80 different nearby institutions have extensively used the infrastructure facilities of the centre. The centre is accessible to users from different parts of the country. The National Facility on High Resolution Graphics has acted as a catalyst to several of the south Indian institutions. The centre has been involved in assisting several research publications and completion of research thesis within the university and nearby universities and colleges.

16.Future activities New initiatives in manpower development - E-learning and content development - Eprints archives - Bioinformatics Portal - Bioinformatics Teacher Training - Research and Software testing for industries

Additional Details: Name of the Coordinator: Prof. S. Krishnaswamy Postal Address: School of Biotechnology, Madurai Kamaraj University, Madurai 625021 Phone Number:0452 2459141 Fax No.:0452 2459105 Email: [email protected],[email protected] Website: www.biotechmku.org , http://bicmku.in:8081

211 Name of Contact Person(s): Dr. Z. A. Rafi, Dr. N. Jeyakumar Email: [email protected] , [email protected]

212 Mahatma Gandhi Institute of Medical Sciences, Sevagram (Wardha) Coordinator: Dr. B. C. Harinath

1. Summary of the progress made by the centre from its inception Bioinformatics Centre at JB Tropical Disease Research Centre, Mahatma Gandhi Institute of Medical Sciences was established in March 1999 with support from Department of Biotechnology, as part of National Bioinformatics Network. The Centre has thrust on Medical / Health Informatics since inception and is actively involved in research and providing academic bibliography service. In addition to In-house Training programme for staff involved in Hospital Information service, the Centre organizes yearly National level Workshop / Seminar / Symposia etc. So far 10 have been organized which were well appreciated. Further, this Centre also publishes SEVAMED, a Quarterly Update on Infectious Disease Research and Traditional Medicine in its 9th year of publication, has been well received by the medical teachers and scientists through out India. Centre has developed database software TbDB, FilaDB, ObSoft, GynSoft, PsySoft for recording & retrieval of data on Tuberculosis, Filariasis, Obstetrics & Gynecology and Psychiatry patients’ related information. The Centre has also developed CaDB a database on cancer patients registry for Pathology department and JBTDRC-Res- Pub, a database on Centre’s 170 research publications which are convenient for end users. Proceedings of National Symposium on Medical Informatics & CME on Hospital Information System as a reference book including the basics of computer to advances & its application in Medical Informatics has also been published and available on www.jbtdrc.org. Centre has recently launched a web portal MGIMS- JBTDRC – Health Update under its e - health info services related to emerging infectious diseases, life style health problems and medical tourism.

2. Major research activities in Biotechnology and its related fields at our institution JBTDRC, an advanced Centre for Tropical Disease Research is the result of sustained problem based research activity by the Biochemistry department for more than three decades at MGIMS, with support from ICMR, CSIR, DST, WHO/TDR, Indo US-STI, DBT, UGC & KHS. Research in tropical diseases with thrust on diagnostics and vaccines in filariasis and tuberculosis is being carried out at this Centre conducting Ph.D and M.D. programmes. Filaria Repository: A National Repository facility for filarial parasites and reagents has been set up with the support from DBT for more than 10 years. Brugia malayi filarial infection in rodents mastomys and jirds (2nd Centre in India) and a filarial sera bank with collection of about 300 sera of different clinical groups of bancroftian filariasis from various endemic regions are being maintained. Dipstick / strip based enzyme immunoassays (SEVA FILA CHEK) have been developed at this institute using penicillinase / peroxidase enzymes, to detect active filarial infection in different clinical groups. Further protein / DNA vaccine studies using cocktail antigens of ALT- 2 and VAH studies in filariasis supported by DBT are in progress. Tuberculosis: SEVA TB ELISA system for detection of antibody, circulating free and immune complexed (IC) antigen in tuberculosis has been developed in this Institute. The detection of IgG antibody by Indirect ELISA against M. tb. cocktail (ES-31 + ES- 43 + EST-6 Ag) antigen in pulmonary and extra pulmonary tuberculosis and detection of free and immune complexed (IC) antigen using affinity-purified anti cocktail antibody by Sandwich ELISA is routinely used for hospital patients. The test is quite helpful in childhood tuberculosis where it is difficult to obtain sputum samples. Further antigen detection has been found helpful for detecting tuberculosis in patients with HIV co-infection. This test is also useful in confirming tubercular aetiology in extra pulmonary tuberculosis (lymphnode Tb, meningitis Tb, bone & joint Tb, abdominal Tb, plural effusion Tb, occular Tb, genitourinary Tb, milliary Tb etc.). 213 Recently mycobacterial serine protease (ES-31) has been shown to have potential

as drug target for screening new anti tubercular drugs.

Patent Granted – A process for isolation and purification of M. tuberculosis excretory-secretory (M. tb ES-31) protein for use in antibody based assay or antigen based assay by detecting the presence and monitoring of M. tuberculosis infection. Patent No.-184510, granted on June 2, 2001. Patents under active consideration: 1) A process for the preparation of Brugia malayi microfilarial excretory-secretory (mf ES-22) glycoprotein. 2) Antigen detection using antibodies in tuberculosis. 3) TB diagnostics based on Mycobacterium tuberculosis Excretory-Secretory antigens and their specific immunoglobulins.

3. Area of Specialization of the centre The Bioinformatics Centre has thrust on Medical / Health Informatics and is involved in development of databases for patients’ information, Quarterly updates on advances in disease research and Health information on emerging infectious diseases and life style health problems.

4. Major activities of the centre during the year 2007-08 • SEVAMED, has entered 9th year of its publication and is available on www.jbtdrc.org. • 10th National Workshop on Medical Informatics & Biomedical Communication was organized during November 30 - December 1, 2007. Seven Eminent Experts in Medical Informatics, Hospital Information Systems & Biomedical Communication and 43 delegates from all over India attended the Workshop. Mr. Senthil Kumaran Shanmugam, Vice President, Satyam Computer Services Ltd., Chennai delivered the keynote address. • Launching of web portal MGIMS-JBTDRC Health Update on emerging infectious diseases, life style health problems and medical tourism. • Short term project work was carried out by Mr. Rajabrata Bhuyan & Mr. Dibyabhaba Pradhan, in ‘Health Information Resources’ and ‘e - updates on Medical Tourism’ respectively.

5. Infrastructure facilities in the Bioinformatics Centre Computer & Communication facility: Computer Hardware: Server-3, Workstations-3, PCs-14, LAPTOP PC-2, Printers-6, Photoprinter–1, Other equipments available include Cisco Router, Modem (2), Wireless router. Switch, Desktop LCD projector-2, Scanner, Fax machine, Canon B155 plain paper fax machine, Digital copier cum printer (3), Kodak Digital Camera, etc. Bioinformatics Centre, Lab-1 (Immunology) & Lab-2 (Molecular Biology) and Central Library are networked through LAN. Computer Software: Windows NT, Windows 98, 2000, XP; Microsoft Windows NT 4.0 Service Pack 4, Developer Training Service pack 3, MS office 97/ 2000, XP, Adobe PageMaker 6.5, Wings 2000 (Accounting software), Microsoft Visual Studio 6.0 Professional Edition, with MSDN Library. Communication Facility: Centre has got installed 512 kbps leased line from BSNL. Centre has provided 10 nodes for benefit of students in the Library and one node for Hospital Information System. Scientific Software packages: TM4 Microarry software suite 1.5.0, MEGA 4.0, Auto Dock 4.0.1, Dock 6.1, Swiss PDB Viewer 3.7, Cn3D, TreeView, ClustalX.

214 Databases & other information resources: In-house databases developed as detailed in 11. The library collection of Centre includes about 68 Indian & foreign Journals, bulletins, Newsletters etc.

6. Details about staff members working in the centre

Name Desig. Specialization Period of working 1. Lingaraja Jena Information System administration, Program- 5 months Officer ming, Database designing & Bioinformatics tool development. 2. Mr. P. Deshmukh Technical Programming, Database manage- 7 Years Assistant ment, web designing and update-ion, assistance in publications. 3. Mrs. S. Rao DEO Data entry, retrieval, Accounting, and 3 years Library Management 4. Mrs. T. Das DEO Data entry, assistance in Sevamed 1 ½ years publication Information Officer and Technical Assistant posts have been absorbed by the host Institute. Further absorption of other staff is under consideration.

7. Types of services provided b. Publication of ‘SEVAMED’ – Quarterly Update on Infectious Disease Research and Traditional Medicine. c. Research & academic related information retrieval by the staff & Students. d. Yearly National level workshops on ‘Medical Informatics & Biomedical Communication’. e. Short term in-house training for teaching, non- teaching staff for HIS of this Medical Institute.

8. Educational activities with details of placement Centre also extended training and research facility to the students doing post graduation in Bioinformatics / Biotechnology for doing short term projects. So far 21 students from various Universities such as Bharathiyar University, Coimbatore, Orissa University of Agriculture and Technology, Bhubaneswar, Madras University, Chennai, Anna University, Chennai, RTM Nagpur University, Bundelkhand University, Jhansi, Amravati University etc. have successfully carried out their projects.

9. Initiative to validate the outcome of bioinformatics resources We are taking initiatives to assess the effect of e-health info services portal, MGIMS- JBTDRC Health Update to bring awareness in the people about the management of emerging infectious diseases and lifestyle health problems and usefulness of ‘SEVAMED’ quarterly update to medical researchers.

10. Collaborative works / initiatives: Collaborating with SVIMS University to develop syllabus in Medical Informatics for 6 months certificate course.

11. Databases/ Software packages developed The Centre has developed certain user-friendly database softwares: i. FilaDB, TbDB, PsySoft, GynSoft, ObSoft, CaDB for recording and retrieving patients’ information for better patient management. ii. JBTDRC-Res-Pub a Research Publications 215 (1970-2007, full paper) have been developed. iii. SEVAMED bibliography database for the year 2001 – 2007 has also been developed.

12. Papers published or presented in the conferences with reference i. Pramod Deshmukh, Jayant Jumde, Satish Kumar, MVR Reddy and BC Harinath. FilaDB – Database software for information storage and retrieval on detection and management of filaria patients. Bioinformatics India. Oct-Dec 2005;3(4): 36- 46. ii. Pramod Deshmukh, Jayant Jumde, Satish Kumar and BC Harinath. TbDB – A database software for storage and retrieval of tuberculosis patients’ information. - National Bioinformatics Symposium held at KVAFSU, Mangalore, February 1-2, 2006. iii. BC Harinath. Keynote address on ‘Medical Informatics in Health Care and Research’ - All India Medico Informatics Society (AIMIS), Nagpur, April 15 -16, 2006. iv. Pramod Deshmukh, Satish Kumar and BC Harinath. Development of database software for storage and retrieval of information related to tuberculosis and filarial patients in tertiary hospital setting. - 5th International Conference on Bioinformatics (InCob-2006) held at New Delhi, December 18-20, 2006. v. Rajabrata Bhuyan, Satish Kumar and BC Harinath. Virtual Reality in Health Care: Robots replacing Clinicians - National Conference on Healthcare Biotechnology at IISc, Bangalore organized by Innovative Centre for Biosciences (ICBio), Bangalore, April 20-21, 2007.

vi.Dibyabhaba PradhanSatish Kumar and BC Harinath. Medical Tourism: An emerging area in Healthcare. - National Conference on Healthcare Biotechnology at IISc, Bangalore organized by Innovative Centre for Biosciences (ICBio), Bangalore, April 20-21, 2007. 13. Initiation of R&D activities in Bioinformatics e - health info services web portal MGIMS – JBTDRC Health Update will help in epidemiological research related to emerging infectious diseases and lifestyle health problems.

14. Details of Training/ Workshop organized and total no. of user trained Sr. Date Title of the Training / Workshop No. of No. Participants attended 1 8 Apr. 2000 Introduction to computer Basics & Access to Biomedical 24 Information 2 24-26 Nov. 2000 Bioinformatics & Medical Research 14 3. 26-28 Nov. 2001 Medical Informatics, Research & Communication 13 4. 23-25 Sept.2002 Medical Informatics & Biomedical Communication 30 5. 10-12 Dec. 2002 ICMR-WHO Workshop on Storage & Retrieval of Information 38 6. 29 Oct. 1 Nov, 03 Medical Informatics & Biomedical Communication 29 7. 6-7 Sept. 2004 National Symposium on Medical Informatics & CME on 40 Hospital Information System supported by DBT, MCI, CSIR, DST, ICMR, MoH&FW, IAMI & KHS

216 8. 9 –10 Dec. 2005 National Seminar on Biomedical Informatics 40 9. 1-2 Dec. 2006 National Workshop on Medical Informatics 17 10. 30 Nov. – 1 Dec., National Workshop on Medical Informatics & Biomedical 43 2007 Communication 11. 19 March-3 April , Inhouse computer training course 20 2001 for the non-teaching staff of MGIMS 12. 24 Feb.14 March Inhouse computer training course for the staff of Trauma 15 2003 Centre. 13. 3 May – 9 Oct., Inhouse computer training course for the teaching, non- 205 2004 teaching and nursing staff of MGIMS as a part of establishment of Hospital Information System.

15. Impact shown by the Centre on the growth of biotechnology and allied areas. Bioinformatics Centre since its inception has been actively helping medical teachers, post graduate students and scientists in information search for research, publication of SEVAMED – a quarterly bibliography journal for medical teachers, development of patients’ information based databases & research publications. Centre has trained about 205 of the non-teaching & nursing staff of MGIMS for operating Hospital Information System funded by Ministry of Information Technology. From the inception of centre 67 research papers covering disease diagnostics and vaccines from JBTDRC and Dept. of Biochemistry have been published in Indian and International Journals. 22 Ph.Ds and 20 MDs have been awarded. The Centre has developed customized database software for patients’ information in consultation with Psychiatry, Obst. & Gyne. and Pathology departments and for specific public health problems namely filaria and tuberculosis. Further a database on JBTDRC research publications (full paper) has been developed. The Centre was very helpful in supporting active MD / Ph.D research programme with grants from DBT, DST, UGC, ICMR, CSIR and KHS. One patent for TB antigen of diagnostic interest has been granted. Three patent applications are under active consideration, two in India and one in United States.

Awards:

Year Name Award 2005 Ms. K. N. Krithika GP Talwar Young Scientist (IIS Conference, PGIMER, Chandigarh) 2005 Mr. Vijay Upadhye MGIMS Tropical Disease (ACBICON-2005, Patna) 2006 Dr. M.V.R. Reddy Fellowship of Association of Clinical Biochemists (ACBICON- 2006, Pune) 2006 Mr. V. Anandharaman MGIMS Tropical Disease and ACBI Travel Fellowship (ACBICON-2006, Pune) 2007 Mr. V. Anandharaman Visiting Scholarship for Collaborative study at Illinois University, USA 2007 Dr. M.V.R. Reddy Biotechnology Overseas Associationship by DBT as a visiting Professor at Illinois University, USA 2007 Dr. M.V.R. Reddy APFCB Fellowship for Council Meeting at Beijing, 2007 Mr. Vijay Upadhye APFCB Travel Fellowship, Beijing, China 2007 Mr. Vijay Upadhye GP Talwar Young Scientist (IIS Conference, NARI, Pune)

16. Future activities 217 ‰ Evaluation of the beneficial effects of e-health info services related to Research and Health Informatic updates and Medical Tourism to medical teachers, research students and patients. ‰ Formulation of Online Certificate Course on Health Informatics for health administrators, medical teachers & practitioners and paramedical workers. ‰ Continuation of SEVAMED Quarterly B An Update on Infectious Disease Research and Traditional Medicine to bring awareness and promote research. ‰ Development of Clinical Decision Support System (CDSS) by analysis of the field data of Filariasis, Tuberculosis etc. ‰ Organization of National Level Workshops on Medical Informatics and Biomedical Communication.

Additional Details: Name of Coordinator : Dr. B. C. Harinath, PhD (USA) Director, JBTDRC & Coordinator, BIC Postal Address : Bioinformatics Centre, JBTDRC, Mahatma Gandhi Institute of Medical Sciences Sevagram (Wardha) - 442 102 TeleFax : 07152 - 284038 Mobile: 09890776971 email : [email protected], [email protected] Web: www.jbtdrc.org

Name of Contact Person : Dr. Satish Kumar, MD Professor, Biochemistry & Dy Coordinator, BIC e-mail: [email protected]

218 M.S. University of Baroda, Baroda Coordinator : Bharat B Chattoo

1. Summary of the progress made by the centre from its inception The Bioinformatics Centre at M.S. University of Baroda, facilitates the use of databases and software packages required by biotechnology students and researchers. It provides an upto-date and accurate information in the area of Biotechnology. Apart from answering the bibliographic queries and supplying the sequence data, the centre also offers unique facilities for data analysis, in addition to the use of E-Mail and internet facilities to the students and faculties. Software package like GCG and Seqweb from the Wisconsin Genetics Computers Group, enables us to purse several sequence analysis projects. This also serves as a major tool in our research initiative in the area of Genomics through the use of advance methods for database searching, molecular modeling, sequence editing and comparison, visualization of molecular structures, gene mapping, plasmid and primer design. NTSYPC software has proved to be an important tool for the statistical analysis of the quantitative biological data obtained from our studies on microbial biodiversity and the study of population structure and dynamics of microorganisms. The molecular modeling software of the centre, helps our users in theoretical studies and visualizing of molecules. The Centre provides the computing support for users in Bioprocess simulation, prediction of trends in a process under altered parameters. MATLAB and SIMULINK are currently being used to substantiate experimental data of the bioprocess. We also serve as the regional node under the ICCB-net collaboration with the Weizmann Institute of Science, Israel. This contact has helped us to use new approaches to data analysis in our current research and research initiatives in Genomics and Proteomics. We jointly organized a national level workshop, with participation of the scientists from the Weizmann Institute on the use of contemporary methods of computer based information processing for analyzing the structure and function of biological macromolecules. The Centre has trained several bioinformatics students through their dissertation project work in the area of computational biology, microarray data analysis etc. within and from the outside institutions.

2. Major research activities in Biotechnology and its related fields : Biotechnology training at M.S. University emphasizes the areas of Microbial technology and the main features of the programme are Genetics, Molecular Biology, Industrial Microbiology and Immunology. The basic training is given in Microbiology, Biochemistry, Genetics, Developmental biology, Genetic Engineering, Biochemical Engineering and some aspects of Biophsysics, biostatistics, plant tissue culture and environmental biology.

- Our work in the past few years has focused on the study of molecular basis of disease, using the interaction of the rice blast pathogen Magnaporthe grisea with rice as a model system. We have utilized new and emerging tools of Molecular Biology to analyse the genome and proteome of this fungus, initiated work on functional genomics in this fungus and in a complementary approach, we have mapped important genes for resistance to blast fungus 219 and also generated transgenic plants showing enhanced resistance to bacterial and fungal pathogens. - The study of genomic flux in the blast fungus, use of novel bioinformatics tools for genome analysis, bioprocess development for important therapeutic molecules, using non-conventional yeasts as hosts, and the use of molecular biological tools for the documentation of microbial diversity.

3. Area of Specialization of the Centre : Crop Biotechnology and Molecular Biology, Genome and Proteome Analysis, Bioprocess Development

4. Major activities of the centre during the year 2007-08 : • Several bioinformatics dissertation projects were carried out in the area of genome sequence analysis and microarray data analysis for M.Sc / B.Tech students from various institutions. • A tool for genome-wide microRNA prediction has been developed and is being validated. • Upgraded GCG package and implemented high speed internet line at the centre. • A bioinformatics project has been introduced as a part of the practical training of M.Sc biotechnology students. • We initiated activities as a regional node under the ICCB-net in collaboration with the Weizmann Institute of Science, Israel. The focus of this collaboration is in the specific analysis of genes and proteins involved in plant disease. Several proteins of potential interest are being analysed for their structural information and possible significance in host-pathogen interactions.

5. Infrastructure facilities in the Bioinformatics Centre : The Centre has created the necessary infrastructure for Bioinformatics activities under Genome Research Centre. The Centre is equipped with Computers and Communication facility. More than 20 desktop computers and 2 servers are available for students and faculty of the department of microbiology and biotechnology programme. The softwares available in the centre include GCG and Seqweb from the Wisconsin Genetics Computers Group and NTSYPC software. This facilities are also being accessed by other departments as well as colleagues from the local industries.

6. Details about staff members working in the Centre: Sl. Name of the Staff Designation Working sinc Absorption No. status (Yes/No)* 1. Mr. Ramesh Menon Information September No officer 2005 2. Mr. Amwillsu VargheseTechnical April 1991 No Assistant

220 3. Mr. Nitesh D Bhatt Data Entry November No operator 1998

7. Types of Services Provided:

Apart from answering the bibliographic queries and supplying the sequence data, the centre also offers unique facilities for data analysis, in addition to the use of E-Mail and internet facilities to the students and faculties. The Centre support the use of bionformatics tools in teaching and research programmes, particularly in newly emerging areas of genomics and proteomics and in studies on microbial diversity and bioprocess development.

The Centre has trained several bioinformatics students through their dissertation project work in the area of computational biology and bioinformatics. Following students from various institutions have carried out their dissertation work in our centre during 2006-08:

Sl. Name of the Course University / Project Title Duration No student Institute

1 Mr. Salabh M.Sc S.P Computational 6 months Takkur Bioinformatics University identification of microRNA in M.grisea

2 Ms. Vidhita B.Tech Rajasthan Analysis of MPSS 4 months Sinha Biotechnology Vidyapeeth data for University upregulated genes in aspersoria formation 3 Mr. Purvil B.Tech Rajasthan Cluster analysis of 4 Sukhadia Biotechnology Vidyapeeth top 20 upregulated months University appresoria genes in M.grisea 4 Mr. Bhavesh B.Tech Rajasthan Microarray data 4 Dharmani Biotechnology Vidyapeeth analysis of months University M.grisea genes using Genespring software. 5 Ms. Darshna M.Sc S.P Expression data 3 months Ramrakhyana Bioinformatics University analysis of top 50 upregulated genes of M.grisea in Nitrogen starvation.

8. Educational activities with details of placement:

Our Department started a master’s level course in Microbiology in 1964. We started a post graduate course in Biotechnology in 1985 with the support from UGC and the Dept. of Biotechnology. Over the years, we have developed a strong base in microbial technology and molecular biology. We have started one year Post M.Sc. Diploma Course in Genetic Engineering and Bioprocess Development to cater to the merging needs of the industry in these areas. This course is aimed at providing training to both in-service candidates from industry as well as fresh students in specific application areas. 221 Most of the students are pursuing higher studies in institutes within the country as well as abroad. Several students from the earlier batches have been offered independent faculty or research positions in various prestigious academic and research institutions. The department maintains a fairly close contact with it’s alumni. In 2007, 19 M.Sc students passed out of a batch of 20 and 6 Post M.Sc. Deiploma students passed out of a batch of 6. Following are the percentage of placement: Higher Studies (India) 52% Higher Studies (Overseas) 28% Working in other field 4% Working in BT related area 12% Information not available 4%

9. Initiative to validate the outcome of bioinformatics resources: In a span of 18 years of its existence, the centre has emphasized the research on Genetic Engineering and Bioprocess Development. The resources available under the centre will be utilized for this purposes. It is planned to increase the component of bioinformatics in this programme as well as our ongoing M.Sc. Biotechnology Course and Post M.Sc diploma course.

10. Collaborative works/initiatives: We have initiated activities as a node under the ICCB-net in collaboration with the Weizmann Institute of Science, Israel. The focus of this collaboration is in the specific analysis of genes and proteins involved in plant disease. Several proteins of potential interest are being analysed for their structural information and possible significance in host-pathogen interactions. i. Sterling Biotech: Emphasis of collaboration is on data base development, bioprocess development and process optimization.

ii. Tel-Aviv University, Dept. of Plant Sciences, Life Science, Israel : Plant SUMO conjugates – its role in biotic stress , supported by DST under Indo- Israeli collaboration iii) John Innes Centre, Norwich, UK: Molecular analysis of disease resistance signaling, supported by DBT under Indo-UK Bilateral Collaboration

11. Databases/Software packages developed: Software: MIST (MicroRNA Search Tool): A tool for genome-wide microRNA prediction using sequence and structure based strategies has been developed.

12. Papers published or presented in the conferences with references 1. Gupta, A & Chattoo, B.B. (2007) A novel gene MGA1 is required for appressorium formation in Magnaporthe grisea. Fungal Genetics and Biology. 44:1157-1159 2. Tendulkar S.R., Saikumari Y.K., Patel V., Raghotama,S.,T.Munshi, P.Balaram and Chattoo,B.B. (2007) Effect of surfactin from Bacillus licheniformis BC98, a soil isolate, on the phytopathogenic fungus Magnaporthe grisea, J. of Applied Microbiology 103(6):2331-2339. 3. Gupta, A & Chattoo,B.B. (2008) Functional analysis of a novel ABC transporter ABC4 from Magnaporthe grisea, FEMSLE 278:1, 22-28.

222 4. Munshi, T. and Chattoo,B.B. (2008) Bacterial Community analysis of the Jute Retting Water Environment. Applied and Environmental Microbiology (press)

13. Initiation of R&D Activities in Bioinformatics: R & D activities related to ongoing projects in Genomics and Proteomics, particularly the analysis of micro-array data as well as 2-D protein gels are being initiated.

14. Details of Training/Workshop organized and total No. of user trained: Nil

15. Impact shown by our centre on the growth of biotechnology and allied areas. Developments in the emerging fields of Genetic Engineering, Immunology, Plant tissue culture, Animal cell cultures and biochemical engineering are leading to new products and applications in the area of Health, Agriculture, Industry, Energy etc. Progress in these areas depend on the availability, analysis and dissemination of information. Every year 2-5 papers with the support of bioinformatics resources were published by the faculty in international journals. A Centre of Excellence in Microbial Genomics has been established by the Gujarat State Biotechnology Mission (GSBTM) and providing support for establishing micro array facilities. The centre plans to develop the facilities as a resource centre for gene expression studies in close cooperation with local industry and academic institutions. One of the main projects being undertaken at the Centre is the study of crop disease with focus on the study of rice-blast diseases.

16. Future Activities Development of data bases for research in the following areas : • High significant datasets on resistance genes from eukaryotes (with reference to different domains found in resistant gene products). • Sub datasets of protein spots and their complete annotation for proteomics research purpose. • Databases with reference to Biomedical importance. • Industries involved in R & D for therapeutic recombinant molecules, projects undertaken, field trials, products patented and other data. R & D institutions involved in promoting science and technology in Gujarat and also the institutes directly working on communicable diseases, which are prevalent in the areas of Gujarat.

Additional Details:

Name of the Coordinator: Bharat B Chattoo Postal Address: Distributed Information Centre, Department of Microbiology and Biotechnology Centre, Faculty of Science, M.S. University of Baroda, Baroda – 390 002, Gujarat Phone Number: 265-2794396/2750498 Fax No.265-2792508 E.Mail. [email protected] ; [email protected] Web site: www.bcmsu.ac.in, www.msubiotech.ac.in

223

Name of Contact Person(s): Prof. B.B.Chattoo [email protected]

224 National Brain Research Centre, Manesar, Haryana Coordinator: Dr. Nandini C.Singh

17. Summary of the progress made by the centre from its inception Formatted: Bullets and Numbering The Distributed Information Centre has set up state of the art high speed computing facilities at NBRC. High-end SUN and IBM servers function as Web Servers (www.nbrc.ac.in), (www.nbrc.res.in) Mailserver (http://mail.nbrc.res.in), DNS Server and FTP server. Centralized Network Attached storage worth 11 TB space has been made available for high end computing requirements. Windows 2003/ Windows 2000, Red Hat Enterprise Linux loaded IBM servers act as File Server, Mail Server, Proxy Server with content filters, Web Server & Application Servers respectively. In order to access and share resources all knowledge-based systems are connected to these servers through LAN. Pool of PCs are clustered to provide internet access to students with their individual user Profiles. DIC has also expanded its internal network by adding several desktops/workstations loaded with heterogeneous operating systems, establishing interconnectivity between buildings by using a fiber optic backbone. WiFi connection has been implemented within the campus alongwith enhanced Internet bandwidth to 2 Mbps. The DIC staff works as a team and focuses on in-house development, assists in technical problem solving, in addition to helping the scientists, handling the servers and network.

18. Major research activities in Biotechnology and its related fields at your Formatted: Bullets and Numbering institution Computational neuroscience and neuroinformatics, which deals with the analysis, characterization and modeling of neural data is a new emerging area. NBRC is the only institute pursuing research and imparting training in this area in a focused and dedicated manner. A few highlights of the research and training at NBRC in this area have been summarized below

Image analysis – Headed by Dr. P K Roy, a laboratory focused on developing new techniques of image analysis to enable better diagnosis of MRI images has been set up. The laboratory uses the process of stochastic resonance to amplify the response peak in Magnetic Resonance Imaging/Spectroscopy for characterization/classification procedures of diagnosing tumours and some neurodegenerative processes. Speech analysis – Using methods of spectral analysis, the speech and language laboratory headed by Nandini C Singh has been analyzing speech signals from children and those with different speech disorders. The efforts of this group have been directed at developing novel computational tools that will enable a unified study of speech production skills. This group has been using this approach to study the development of various articulatory features in typically developing children and setting up quantifiers to assess different speech disorders. This laboratory is also interested in studying the phonological organization of different Indian languages.

19. Area of Specialization of the centre : NEUROINFORMATICS Formatted: Bullets and Numbering

20. Major activities of the centre during the year 2007-08 Formatted: Bullets and Numbering The high speed computing facilities at NBRC have been upgraded to support 250 users. High performance SUN and IBM multiprocessor servers have 225 been added to provide Active Directory Services, Mail Services, DNS Services and Web services and high speed computing. Nokia IP390 Checkpoint High availability firewall has been configured at the gateway level to ensure infrastructure security. A 2 Mbps dedicated Internet bandwidth line has been provided to scientists, students and staff. Wireless access inside the campus for roaming laptop users has also been provided. The centralized heterogeneous network attached storage server for data warehousing has grown to 10 Terabyte and is accessible across the network with LDAP authentication for aiding data security and integrity.

21. Infrastructure facilities in the Bioinformatics Centre Formatted: Bullets and Numbering Computer & Communication facility SunFire x4100 Server-(Web server, Application Server FTP Server ) IBM xSeries 346 Xeon–(Active Directory. Application Server, Websense Content filtering) IBM xSeries 3650 Xeon (Linux Mail server) IBM xSeries 235 – Xeon Dual processors Servers with Windows 2003 Server (File server, Mail Server) IBM xSeries 220 server with windows 2000 server (DNS) Network Attached Servers – 11 TB, Tulsiant NAS 8420R Desktops and ThinClients. HP Laserjet 1300,2100,2200,2420,2300, 1020/3030/ 3050, 1320 HP Deskjet 3535, HP 800 PS Design Jet (Plotter) Routers Cisco – 2600 and1700 Switches: 3Com 10/100 Mbps 24 port, 100 Mbps 12 port – 1 No. D-Link 24 Port Xstrack DGS 3426 , D-Link 48 Port DES 3550 D-Link 24 Port DGS 1024 D Nokia IP390 Firewall 2 Mbps Leased Line (BSNL), 512 Kpbs Leased Line (HCL) Scientific Software packages Formatted: Bullets and Numbering Matlab 7.1, SPSS, E-Prime,SPM,Brain Voyager, Neurolusida MriCro, Spot Fire (Micro Array), Silicocyte, Instrument Control Manager, Sequence Analyzer, Phred Phrap, Consensus (Sequencer), DS Modeling Software Databases & other information resources Formatted: Bullets and Numbering Chemical Management System, Cell Lines Status in Lab's Leave Management System 22. Details about staff members working in the centre (Name of the staff, Formatted: Bullets and Numbering Designation, Specialization and period of working. Please indicate their absorption status) Absorption Sl. Working Name of the Staff Designation status No Since (Yes/No)

226 1 Mrs. Reema Saxena Computer Operator 21-12-2000

2 Mr. Jothibasu Information Scientist 23-05-2001 Yes

3 Mr. Hariharan AAO 29-04-2002 Yes

4 Mr. Mahender K. Singh Jr. Information Scientist 21-03-2005 Yes

5 Mr. Kedar Singh Bajetha Computer Operator 17-07-2003 Yes

6 Mr. P.V.S. Shyam Kumar Computer Operator 29-07-2003 Yes

7 Mr. Sanjeev Bhardwaj Computer Operator 28-02-2005

8 Mr. Anoop Singh Computer Operator 28-02-2005 Yes

9 Mr. Ashish Upadhyay Computer Operator 22-03-2005

10 Mr. Punit Kumar Computer Operator 02-04-2007

11 Mr. Jeebanada Chottary Computer Operator 27-07-2007

12 Mr. Sanjay Kumar Gupta Computer Operator 12-11-2007

23. Types of services provided Formatted: Bullets and Numbering DIC is providing diversified services like software development, Internet, intranet, mailing facilities maintenance of servers and network.

24. Educational activities with details of placement Formatted: Bullets and Numbering NBRC is a deemed University and has two training programmes in Neuroscience namely a PhD programme and Integrated PhD programme in Neuroscience.

25. Initiative to validate the outcome of bioinformatics resources – Not Formatted: Bullets and Numbering Applicable

26. Collaborative works/ initiatives Formatted: Bullets and Numbering The project on speech patterns in children with autism in the laboratory of Dr. Nandini C Singh being carried out in collaboration with Dr. Shobha Srinath and Dr. Shivshankar from NIMHANS, Bangalore, Dr. Amit Sen from SBISR, New Delhi. Joint project between Nandini C Singh of NBRC with Dr. Srinivas Chakravarthy of IIT, Madras to explore the possibility of using speech and handwriting patterns as markers for early diagnosis of Parkinson’s disease. Application of Stochastic Activation and Stability analysis for Brain Imaging and Therapy In collaboration with Dr. K. L. Chakrabarty, Institute of Nuclear Medicine & Allied Sciences, Delhi

27. Databases/ Software packages developed Formatted: Bullets and Numbering Chemical Management System, Cell Lines Status in different laboratories in NBRC.

227 Leave Management System

28. Papers published or presented in the conferences with reference Formatted: Bullets and Numbering List Publications and patent applications: Computational Neuro-science and Neuroimaging laboratory o Subramanyam, R, Roy, P. Stochastic Resonance-Based Tomographic Transform for Image Enhancement of Brain Lesions, J. Computer-Assisted Tomography, 2007 (in press). o Subramanyam, R, Roy, P. Magnetic Resonance image enhancement using Stochastic Resonance in harmonic space, Computerized Medical Imaging, 2007 (in revision). o Roy, P. Nature of a Living State from a Thermodynamic Perspective: Information, Fluctuation and Order in the Organism, in S Rangachari (ed). Life and Organism, New Delhi (accepted, with revision). o Subramanyam, R, Budhachandra, K, Upadhyay, A, Roy, P, The Self Looks at its Brain: Symbiosis of Tensor Imaging and Functional Imaging strategies for the Neuroinformatics Initiative, Computer Society Transactions (communicated). Patents o A Medical Image Enhancement Device based on Image Transform Resonance, using a Computational Apparatus consisting of an Embedded System (submitted) Speech and Language Laboratory o Tanusree Das, Latika Singh, Nandini C Singh, Rhythmic structure of English and Hindi – new insights from a computational analysis, Prog. In Brain Research (in press). o Latika Singh, P. Shantisudha, Nandini C Singh, Developmental patterns of speech in children, J. of Applied Acoustics, 68, 260-268, 2007. o Latika Singh and Nandini C Singh, The development of articulatory signatures in children, Developmental Science (in press). o T.Padma Subhadra, Tanusree Das, and Nandini C Singh, Speech rhythms in children learning two languages : From Heart to Brain, Springer Life Sciences Series, (in press). o Mohini Verma and Nandini C Singh, “Cross-cultural language rhythms – effects of emotion recognition in speech”, J. of cross-cultural Psychology, (in revision) o T. Padma Subhadra and Nandini C Singh, Speech production in bilingual children, Int. J. of Language and Commn. Disorders, (submitted) 29. Initiation of R&D activities in Neuroinformatics Formatted: Bullets and Numbering As described above NBRC has initiated research in the area of the image analysis and speech processing. With the organization of CNS workshops every year for the past 6 years than 250 students have been trained in basic techniques of computational neuroscience in different parts of the country. The 3T fMRI scanner recently set up at NBRC will now enable research in the speech and language laboratory to study undertake projects that will allow the investigation of neural correlates of language and speech processing. It would allow the neuroimaging laboratory headed by Dr. Roy to now undertake the development of pulse programming sequences for efficient implementation study of stress tensor imaging.

228 30. Details of Training/ Workshop organized and total no. of user trained Formatted: Bullets and Numbering CNS course at NBRC – Under intra-mural training, students undergoing MSc (Neuroscience), Int. PhD and PhD and NBRC attended 8 week course on computational neuroscience which also consists of tutorials and laboratory sessions. A total of 15 students were trained in this course in 2007. CNS workshop - NBRC has been conducting a national workshop on computational neuroscience since 2001 across different universities and IIT’s in an attempt to encourage and popularize the field of computational neuroscience. A total of 35 student from India and 4 from Bangladesh and Iran kj mbb b vbvcxb vghv b bv students were trained in various techniques of computational neuroscience at the 7th such workshop which was held at Dept. of Computer Science, Delhi University in December 2007.

31. Impact shown by your centre on the growth of biotechnology and allied Formatted: Bullets and Numbering areas. In this you may highlight the details like number of paper published/ number of papers published with the help of your centre, how your centre is promoting various activities of your organization and neighboring institutions, manpower trained, tools developed, patents & copyrights acquired and other services offered etc. The computational neuroscience group at NBRC has published/submitted around 10 publications and patent applications in 2006-07 NBRC digital library access more than 400 online scientific journals. This is the first library of kind in that it allows inter library loan service thereby sharing its resources 48 Network Centres across the nation. NBRC library is currently subscripting to 521 journals of which 444 are online and others are in the hard copy formats. A total of 245 registered users are using the digital library facilities. NBRC conducts Summer Training Programme every year for the Students from different academic backgrounds and varied academic Institutions who are in their penultimate year of their undergraduate / postgraduate course. The summer training projects give students an exposure to neuroscience and to encourage them to consider it as a future career option and a total of 12 students were trained in 2007. DIC personnel actively contributed to the developments of new signal processing tools to study speech and image analysis. The image analysis tools have been directed towards the analysis of MRI images for better diagnosis whilst the speech analysis techniques have been used to study speech and language in typically developing children and those with speech disorders children.

32. Future activities Formatted: Bullets and Numbering • Creation of High end cluster computing environment for Functional MRI analysis and Speech analysis using blade servers. • Developing specialized software for fMRI image analysis and Image processing. • Establishment of Video conferencing facility for conducting lectures of eminent scientist across other centres and universities.

229 • Development of a portal site for neuroscience and neuroinformatics which would provide comprehensive information to various aspects of neurosciences research in India and abroad. This will be useful to illustrate, catalogue and assist the latest research in neuroscience.

Additional Details: Name of the Coordinator: Dr. Nandini C.Singh Postal Address: National BrainResearch Centre, Manesar-122050, Gurgaon Dist., Haryana

Phone Number : 0124-2338921 Extn: 333 Mobile : Email : [email protected] Website : www.nbrc.ac.in

Name of Contact Person(s): Mr. JothiBasu Email: [email protected]

230 National Dairy Research Institute, Karnal Coordinator : Dr. D.K. Jain

1. Summary of the progress made by the center from its inception The Distributed Information Sub-Centre on Animal Biotechnology started way back in 1990 with the objective of inculcating Computer Culture in the Institute; providing literature search facilities to the Scientists and Students; database and software development has taken a leap forward in undertaking research and development in the core area of Bioinformatics. In 1996, the dial up connectivity was established using MODEM and a telephone line. Local Area Network (LAN) and KU Band VSAT was installed in the Institute initially in 1998 which was further expanded in 2002 to cover the main buildings through optical fiber/UTP cabling and distantly located buildings through Remote Access Server (RAS) in order to provide round the clock E-mail/Internet services to all the scientists and other officers numbering around 300 in their Labs/Offices.

2. Major research activities in Biotechnology and its related fields in your Institution The major areas of research include Embryo Biotechnology, Reproduction Augmentation, Livestock Genomics in general and Buffalo Genomics in particular, Probiotic attributes of milk, Development of recombinant dairy enzymes, PCR based test kits for detection of food borne pathogens, and Structural Biology/ Bioinformatics of biological macro-molecules.

3. Area of specialization of the centre Animal Biotechnology.

4. Major activities of the center during the year 2007-08 A leased line of 512 kbps was commissioned by BSNL, Karnal; A Bioinformatics Lab measuring 1200 Sq ft. has come up to house some of the Bioinformatics facilities like Silicon Graphic Workstation. A central facility for the Scientists and research scholars of the Institute; Video-conferencing facility along with IP telephony connections established. Subscription to 18 on-line foreign journals and on-line availability of CD-ROM database and the catalogue of library; the existing databases updated.

5. Infrastructure facilities in the Bioinformatics Centre A. Computer and communication facility Silicon Graphic Workstation, Pentium Computers, Server PII with operating system Window NT4.0, Server DATAMINI E-8000 with operating system Window 2000 with one workstation, Laser jet and Desk jet Printers, Fax Machine, KU Band VSAT, Photocopier-cum-printer, UPS 3KVA and 5 KVA. B. Scientific software packages Vector NTI Advanced TM9.1 Sequence Analysis, VB. NET and Macromolecular Simulation and Dynamics software; SYSTAT, SPSS, LIMDEP, TORA, MATLAB, LIBSYS, Arcview GIS, In house developed application software packages for data analysis and MIS. C. Databases and other information resources ♦ Integrated Information System on Dairying. ♦ Up-to-date CAB and FSTA literature databases. 231 ♦ Digitized inventory of Ph.D. thesis. ♦ On-line availability of information on books and periodicals. 6. Details about staff members working in the center (Name of the staff, Designation, Specialization and Period of working)

Period of Name of Staff Designation Specialization working Dr. A.K. Sharma Scientist (CAA) & Computer June, 1995 to Information Officer Applications in Continuing. (additional charge) Dairying Ms. Aruna Pandey Computer Operator Bioinformatics Since July, 06 Mr. Sunny Bali Computer Operator Electronics & Selected and Commun. Engg. yet to join

7. Types of services provided Literature search (both on-line and off-line); Training and workshops; E-mail / Internet Access; Structure and Sequence Analysis for Proteins & DNA; Assistance in Software development for MIS and data analysis.

8. Educational activities with details of placement The Institute runs M.Sc. and Ph.D. programmes in Animal Biotechnology, Animal Biochemistry and Dairy Microbiology. One course on Bioinformatics for Post- graduate students introduced from the current academic session. Use of Bioinformatics tools in genetic engineering being offered to the students as part of Genetic Engineering course. All the students are getting good placement.

9. Initiative to validate the outcome of Bioinformatics resources The software developed on various aspects are being validated by the users with the sample data and put to effective use by the researchers. Similarly, the information system in the form of ready to use software and database on different aspects of dairying is being used by the researchers, administrators, bureaucrats, policy makers, industrial/ commercial organizations.

10. Collaborative works/initiatives The Centre has made some initiatives towards inter-divisional research at this Institute as well as explored possibility for collaboration with external Institutions of excellence in research such as IITD, JNU, IASRI, Thapar University and Punjabi University, Patiala; BISR, Jaipur and University of Québec, Canada. 11. Databases/Software packages developed Existing Databases were updated.

12. Papers published or presented in the conferences with reference Journal articles 1. Sharma, A. K., Sharma, R. K. and Kasana, H. S., 2007. Prediction of first lactation 305- day milk yield in Karan Fries dairy cattle using ANN modeling. Applied Soft Computing 7(3): 1112-1120. 2. Yadav, Anita and Yadav, B.R. 2007. Genetic diversity among six breeds of Indian goat using RAPD markers. Biotechnology, 6(1): 57-60. Conference papers 3. Ruhil, A.P., Singh, R.R.B., Jain, D.K., Patel, A.A. and Patil, G.R. 2007. Development of an artificial neural network based model for shelf-life prediction of Basundi Mix – an Indian dairy

232 product. In: Proceedings of the 3rd Indian International Conference on Artificial Intelligence, December 17-19, Pune, pp.1517-1524. 4. Sharma, A. K., Sharma, R. K., Kasana, H. S. and Chakarvarty, A. K., 2007. Connectionist vis-à- vis conventional models for predictions of lifetime milk production in Karan–Fries dairy cattle. In: Proceedings of the 2nd International Conference on Advanced Computing and Communication Technologies (ICACCT–2007), Nov. 03-04, Panipat, pp. 492-495. Book chapter 5. Sharma, A. K. and Jain, D. K., 2008. Computational intelligence: state-of-the-art in research and applications to dairying. In: Ahmad R. (editor), WTO and Agriculture Sector – Opportunities, Problems and Challenges. The editor is Professor at Department of Agricultural Economics & Business Management, Aligarh Muslim University, Aligarh-202002

13. Initiation of R&D activities in Bioinformatics Projects were initiated in the following fields of Bioinformatics related to Animal Sciences/Dairying. Genomics ♦ Structural and functional characterization of IGFBP5 gene and exploring its role in truncation of lactation in Farm animals (Institute funded IRC Project) Modeling & Structural analysis of proteins ♦ Energetics and Dynamics of Protein Stability and Iron binding properties and their modulation by domain-domain interactions in lactoferrin from various animal species (DBT funded project). Predictive Modeling ♦ Prediction of economic traits in Murrah buffaloes – a comparative assessment of connectionist and conventional models (Institute funded IRC project).

14. Details of trainings/workshops organized and total number of users trained: A workshop is being planned in the first half of year 2008 the Institute faculty was occupied in other assignments like organizing two International Conferences in Animal Nutrition and Dairy Technology; and CAS Training Programme of 21 days duration each. Also, two sponsored trainees were imparted training on Advanced Computing techniques for Bioinformatics applications.

15. Impact shown by your center on the growth of Biotechnology and allied areas. In this you may highlight the details like number of papers published with the help of your center, how your center is promoting various activities of your organization and neighboring institutions, manpower trained, tools developed, patents & copyrights acquired and other services offered etc. ♦ Increased use of advanced computing techniques for effective data management, visualization, analysis and interpretation. ♦ Regular national level workshops and training programmes for spread of the knowledge on emerging areas of Information Technology and Bioinformatics to the participants drawn from various R&D institutions including NDRI. ♦ Attracted a large number of students for pursuing training and project work as part of their PG degree requirements through studentship. ♦ Availability of databases on different aspects of Dairying. ♦ R&D activities in Bioinformatics and related areas; Publications and presentation of research papers/invited talks.

233 16. Future activities ♦ Genome analysis (QTL) in bovines in relation to milk constituents from existing on-line information search. ♦ Comparative genomics, evolution and functional analysis of aspartic proteases: Implication in milk clotting. ♦ Phylogenetic lineage of indigenous animal resources. ♦ DNA/Protein sequence analysis and genome mapping of farm animals and starter cultures. ♦ Structural biology of macro-molecules ♦ Application of Soft Computing methodologies in Dairying. ♦ Web server based Support Vector Machine to predict protein functions. ♦ Analysis of regulatory pathways regulating mammary gland physiology during mammary gland development, lactation and involution.

Additional Details Name of the Coordinator : Dr. D.K. Jain Postal Address : Principal Scientist & I/c Computer Centre N.D.R.I., Karnal – 132001 Phone Number : 0184-2259014 Fax No. : 0184-2250042 Email : [email protected]; [email protected] : [email protected] Website : http://www.ndri.res.in Name of Contact Person(s) Dr. D. K. Jain, Coordinator Dr. A. K. Sharma, Information Officer.

234 National Institute of Immunology, New Delhi Coordinator : Dr. Dinakar M. Salunke

1. Summary of the progress made by the centre from its inception Bioinformatics Center (BIC) at NII was set up by the Department of Biotechnology with the mandate to serve as an information resource and state of the art computational facility for researchers in the field of molecular biology and immunology. The usage of the facilities provided by the center is reflected in large number of publications from various research groups at NII. The center has also catered to the requirements of researchers from other institutes. The center is also engaged in advanced research in the area of computational and structural biology. The center has contributed to the discovery of new biosynthetic pathways and elucidation of novel mechanisms of immune recognition.

2. Major research activities in Biotechnology and its related fields at your institution The Institute is committed to advanced research addressing the basic mechanisms involved in body defense, host-pathogen interactions and related areas with a view to contribute to the creation of an internationally competitive intellectual knowledge base as a sustainable source of innovative futuristic modalities of potential use in health care. The research interests of the various research groups at NII coalesce in six major areas; Chemical Biology, Genetics & Cell Signaling, Immunity & Infection, Molecular & Cell Biology, Reproduction & Development, and Structural & Computational Biology.

3. Area of Specialization of the centre Structural Biology & Molecular Modelling

4. Major activities of the centre during the year 2007-08 During the year 2007-2008, the center has upgraded its computational resources by addition of a Sunfire X2200 cluster consisting of 16 dual core 2.8 GHz AMD Opteron processors and 5 TB of storage space, and several high end LINUX and MAC OS X workstations. The center has carried out extensive work on molecular dynamics simulations of large proteins.

5. Infrastructure facilities in the Bioinformatics Centre Computer & Communication facility The center has established major computational resources involving Sunfire 2200 cluster with 16 dual core CPUs, Apple G5 workgroup cluster with 16 CPUs, Mac OS X G5 and MacPro workstations, SGI Servers and Intel linux or Windows workstations. The center is linked to INTERNET through two independent 2 Mbps(1:1) leased lines.

Scientific Software packages The center has a large collection of commercial and public domain softwares and they are listed at http://www.nii.res.in/bionfo-software.html .

Databases & other information resources 235 Apart from online access to various databases on the INTERNET, the center also maintains local copies of many databases for fast access by users. The center has online access to all the major journals in biological sciences.

6. Details about staff members working in the centre (Name of the staff, Designation, Specialization and period of working. Please indicate their absorption status)

Name Designation Specialization Status Dr. D. M. Salunke Staff Scientist VII Struct. Biology NII Core Dr. D. Mohanty Staff Scientist V Comp. Biology NII Core Ms. S. Sachdeva Technical Officer System Admin NII Core Mr. M. S. Rao Technical Officer System Admin NII Core Mr. Naveen Technician Comp Operations NII Core

7. Types of services provided BIC, NII manages the entire scientific and administrative computing infrastructure at NII and ensures that most bioinformatics applications are available on the users desktop either from INTERNET or from in house servers. Molecular dynamics, Molecular Graphics and other CPU intensive applications are made available from clusters or high end workstations at the center.

8. Educational activities with details of placement Currently a number of research scholars are carrying out research work for Ph.D. degree in bioinformatics under the supervision of scientists associated with BIC, NII. Three students have completed Ph.D. in Bioinformatics from BIC, NII.

9. Initiative to validate the outcome of bioinformatics resources Exploring the possibility of experimental validation of in silico predictions has always been a major priority of the center. Attempts are being made to validate the results of the structure based predictions for substrates of Ser/Thr kinases.

10. Collaborative works/ initiatives The center is associated with several collaborative projects with other experimental groups at NII as well as other institutes in India. These projects relate to work on Mycobacterium tuberculosis and various other aspects of immunity and infection. The center is participating in a collaborative project involving experimental as well as computational work to understand the molecular basis of the vitiligo disease.

11. Databases/ Software packages developed A major activity of the center has been development of databases and softwares which permit correlating the sequence and structural features of various biosynthetic proteins to the chemical structure of the metabolites they synthesize. Softwares have also been developed for structure based prediction of MHC ligands and substrates for kinases.

236 During the reporting year, several new gene clusters have been added to the NRPS-PKS database. A web based software has been developed for predicting substrate specificity of acyl adenylate superfamily. Most databases/softwares have been made available from NII website.

Software for Motif Discovery http://202.54.249.131/~depak/RegAnalyst.html Software for modeling Protein-peptide complexes http://www.nii.res.in/modpropep.html Substrate Specificity of ACS http://linux1.nii.res.in/~pankaj/poss.html Software for analysis of GTr http://www.nii.res.in/searchgtr.html Database for NRPS/PKS: http://www.nii.res.in/nrps-pks.html Genome analysis tool: http://www.nii.res.in/genome.html

12. Papers published or presented in the conferences with reference

1. Kumar N and Mohanty D* (2007) MODPROPEP: A program for knowledge based modeling of protein-peptide complexes. Nucleic Acids Res 35: W549- 55. 2. Gokhale RS*, Sankaranarayanan R and Mohanty D (2007) Versatility of polyketide synthases in generating metabolic diversity. Curr Opin Struct Biol 17: 736-743. 3. Goyal K, Mohanty D and Mande, S. C.* (2007) PAR-3D: A server to predict protein active site residues. Nucleic Acids Res 35: W503-5. 4. Gokhale RS*, Saxena P, Chopra T and Mohanty D (2007) Versatile polyketide enzymatic machinery for biosynthesis of complex mycobacterial lipids. Nat Prod Rep 24: 267-77. 5. Krishnan L, Sahni G, Kaur KJ and Salunke DM (2007) Role of Antibody Paratope Conformational Flexibility in the Manifestation of Molecular Mimicry. Biophysical J (in press). 6. Kaur KJ, Sarkar P, Nagpal S, Khan T and Salunke DM (2007) Structure- function analyses involving palindromic analogs of tritrypticin suggests autonomy of anti-endotoxin and antibacterial activities. Protein Sci (in press). 7. Krishnan L, Lomash S, Raj BPJ, Kaur KJ and Salunke DM (2007) Paratope Plasticity in Diverse Modes Facilitates Molecular Mimicry in Antibody Response. J Immunol 178:7923. 8. Bhowmick A, Krishnan L and Salunke DM (2007) Structural immunology: Mechanisms of antigen recognition J Ind Inst Sci 87:35-41. 9. Kaur KJ, Pandey S, Salunke DM (2007) Design of a functionally equivalent nonglycosylated analog of the glycopeptide antibiotic formaecin I. Protein Sci 16:309.

13. Initiation of R&D activities in Bioinformatics The center also has a number of ongoing research projects focused on molecular modeling and analysis of protein sequences/structures.

Molecular Basis of functional mimicry (Dinakar M. Salunke) Focus of our research has been on the elucidating the structural basis of functional mimicry among chemically dissimilar molecular systems, 237 highlighting the possible consequences in different biological processes. A distinguishing characteristic of our work has been the judicious combination of structural, biochemical and immunological techniques with bioinformatics applications.

Molecular modelling of protein-ligand complexes (Debasisa Mohanty) The main theme of the research is to understand structural principles that govern binding of ligands to proteins and folding of peptides/proteins to stable conformations, and then use these principles for developing computational approaches for specificities of protein-ligand complexes and structures of peptides/proteins.

14. Details of Training/ Workshop organized and total no. of user trained During the current reporting year, the center has arranged 2 hands-on bioinformatics laboratory sessions for students and teachers of different degree colleges. During April 2007, one day workshop with hands on training on homology modeling and protein-ligand docking was also arranged.

15. Impact shown by your centre on the growth of biotechnology and allied areas The major users of bioinformatics center at NII have been the large number of scientists and researchers working at NII. The impact of the center on the research at NII is reflected in about 50 publications every year in peer reviewed journals. Resources of the center are also used by researchers from JNU, ICGEB, AIIMS, Delhi University etc.

16. Future activities The center plans to expand the scope of the existing research projects to analyze metabolic, regulatory and signaling pathways. Attempts are also being made to initiate projects related to in silico design of drugs/inhibitors. Additional Details: Name of the Coordinator: Dr. Dinakar M. Salunke Postal Address: NII, Aruna Asaf Ali Marg, New Delhi-67 Phone : 011-26717108 Email:[email protected] Website:http://www.nii.res.in Name of Contact Person(s): Dr. Debasisa Mohanty Email: [email protected]

238 National Institute of Oceanography, Goa Coordinator : Dr. P.A. Loka Bharathi

1. Summary of the progress made by the centre from its inception

Marine biodiversity is undoubtedly the most diverse, not only in terms of number of diverse kinds of organisms but also in terms of unique habitats and ecosystems. Compared to terrestrial biodiversity, diversity of the marine organisms attracts more importance due to its fragile nature. Direct and indirect effects of anthropogenic activities have proved to be of serious concern to marine biodiversity. Therefore, conservation of marine biodiversity is very important, particularly in the Indian context.

Bioinformatics Centre at NIO works towards improving the understanding of the marine biota in the Indian waters. Centre has a full-fledged website www.niobioinformatics.in to disseminate the collected data and information. Workshops and training programmes in the emerging areas in marine biodiversity. Recently a National workshop on Ecological Niche Modeling was conducted to train researchers and academicians in species distribution modeling, Remote Sensing and GIS.

2. Major research activities in Biotechnology and its related field at your institute

a. Bioactive molecules from marine environment b. Identification and preparation of extracts of pharmacological importance from marine organisms c. Identification of marine organismsm for compounds with industrial applications d. Bioprospecting and biotechnology of marine microorganisms. e. Habitat ecology, controlled reproduction and conservation of marine organisms with food and medicinal values. f. Evaluation, mechanisms and control of biofilm and biofouling

3. Area of specialization of the centre : Marine Biodiversity Informatics

4. Major activities of the centre during the year 2007 – 08

• Website launched for dissemination of marine biodiversity data and information www.niobioinformatics.in • Developed DigiMus-0.1, a software to digitize marine biodiversity specimen collections. • Trained several researchers and academicians in ecological niche modeling, through National Workshop on Ecological Niche Modeling in Biodiversity Management, in Dec,2007. • Training imparted to students from colleges in areas such as protein sequence analysis and various bioinformatics softwares. • Special feature on Indian Coral reefs launched on www.niobioinformatics.in for commemorating International Year of the Reef (IYOR), 2008. • Papers in different aspects of marine biodiversity informatics have submitted in scientific journals.

239 • Initiated work on marine heat shock proteins, drug designing and databases on protein derived from marine organisms.

5. Infrastructure facilities in the Bioinformatics Centre a. Computer & Communication facility The resources available at the centre Computer Systems 6 Nos. Notebooks 2 nos. Printers 3Nos. Fax 1 No.

b. Scientific Software packages : DigiMus 0.1- Marine biological specimen digitization software.

c. Databases & Other information resources • Aquatic Science & Fishery Abstracts • Science Direct online database

6. Detailed about staff members working in the centre (Name of the staff, Designation, specialization and period of working

Name Designation Period of working Absorption status 1 Shri Devanand Kavlekar Tech. Officer 17 Years Absorbed 2. Vishwanath Kulkarni Lab. Assistant 17 years Absorbed 3. Aditya Kakodkar Proj. Assistant 3 years Not Absorbed 4. Sarika Kerkar Proj. Assistant 1 year (Aug,06- Not absorbed Aug,07) 5. Neena Verghese Proj. Assistant 1 year Not absorbed 6. Ambily Nath I.V. Proj. Assistant 1 Year Not absorbed 7. Akshata Arolnekar Proj. Assistant 1 Year Not absorbed

7. Type of services provided Main function of the centre is to provide information to the interested users on topics pertaining to the relevant areas of marine biodiversity.

8. Educational activities with detailed of placement Post-graduate students in bioinformatics are given facilities to complete short term project work.

9. Initiative to validate the outcome of bioinformatics resources : NA

10. Collaborative works /initiatives The Bioinformatics Centre of NIO and NCL, Pune have collaborated to form the Indian Ocean Biogeographic Information System (IndOBIS) which is the Indian Ocean regional node of the Ocean Biogeographic Information System (OBIS).

11. Databases /Software packages developed

• Web based information services through www.niobioinformatics.in

240 • Biological specimen digitization software DIGIMUS Ver 0.1

NIO's digital herbarium: The NIO's Digital herbarium, is an online source of accessing the specimen in the Herbarium collection of the National Institute of Oceanography, it contains 741 specimen records of 142 species of marine algae.

Indian Ocean Node of Ocean Biogeographic Information Systems (IndOBIS): Bioinformatics Centre in association with NCL, Pune has developed a database of known organisms of the Indian Ocean. The database contains about > 40,000 species, with their metadata.

12. Papers published or presented in conferences with reference

13. Initiation of R & D activities in Bioinformatics

At present the centre has not initiated any R & D activities in Bioinformatics.

14. Details of training/ Workshop organized and total number of users trained The Centre has organized a “National Workshop on Ecological Niche Modeling in Biodiversity Management” from 13th to 15th December 2007 at NIO, Goa. The workshop was attended by ~25 participants from different institutions and universities.

15. Impact shown by your centre on the growth of biotechnology and allied areas • C. T. Achuthankutty and Kakodkar A. P., (2007), Applications of informatics in marine biodiversity conservation in the Indian Context. Marine Biodiversity, (Eds.) S. Kannaiyan & R. Venkataraman, submitted to National Biodiversity Authority. • Kakodkar A. P., Kerkar S. S., Kavlekar D. P.Kavlekar and C.T. Achuthankutty, (2007), Marine Biological Museums in Real Time - from Shelves to Screens: A Case Study, Communicated to Biodiversity conservation. • Kakodkar A. P., C. T. Achuthankutty and V. S. Chavan, (2007) Ocean Biodiversity Information Infrastructure” for India: Opportunities and challenges, Communicated to Current Science. • Vishwas Chavan, Chandan Badapanda, Aditya Kakodkar, SwapnaPrabhu, C.T. Achuthankutty and IndOBIS Team (2007), IndOBIS: Development of web based informatics infrastructure todocument known Indian Ocean biodiversity, Communicated to Marine ecology.

16. Future activities

• Database on Heat Shock Proteins from Marine organisms • Database on Marine Drugs & Designing Tools. • Databases on bio-molecules derived from marine organisms.

241 • Ecological Niche Modeling in Marine Environment and its applications in biotechnology.

Additional Details : Name of the Coordinator : Dr. P.A. Loka Bharathi Postal Address : Bioinformatics Centre National Institute of Oceanography Dona Paula, Goa 403 004 Phone number fax number Email website (0)832- 2450281 (0)832-2450606 [email protected] www.nio.org Name of Contact Person(s) : Shri Devanand kavlekar Email : [email protected]

242 National Institute for Plant Genome Research, New Delhi Coordinator : Dr. Gitanjali Yadav

1. Summary of the progress made by the centre from its inception The Sub-DIC at NIPGR is in its first year of inception, and it has already successfully installed, operationalized and established major computational, networking and scientific resources. Staff intake for two positions has been completed. Installation of major computational resources, including institute’s own web & academic emailing servers is complete.

2. Major research activities in Biotechnology and its related fields at your institution Development of Genetically modified crops with increased yield and nutrition quality. Generation of ESTs and DNA based molecular markers for Molecular Mapping and Genome analysis. Genetic Diversity analysis, Functional Genomics and Proteomics in Plants. Differential Gene expression and analysis of plant stress responses

3. Area of Specialization of the centre Plant computational Biology, Molecular Evolution of protein families involved in stress response

4. Major activities of the centre during the year 2007-08 Inception and infrastructure establishment of Sub-DIC. Staff Intake

5. Infrastructure facilities in the Bioinformatics Centre Computer & Communication facility High end Linux and Mac Workstations & Servers, Laser Printer, Copier and Scanner, Tape Drives for data Back up. Scientific Software packages Accelrys Discovery Studio v 2.0 Databases & other information resources

6. Details about staff members working in the centre Sl. NAME DESIGNATION WORKING STATUS No. 1 Subhashish Mondal Data Entry Operator Since 7-1-08 Just Joined 2 Swarupa Pradhan Tech asst Since 3-1-08 Just Joined 3 Info Officer In process

7. Types of services provided

243 Sequence and structural analyses, Installation of scientific software packages, Assistance with genome sequencing efforts in Tomato. 8. Educational activities with details of placement To be started w.e.f current year 9. Initiative to validate the outcome of bioinformatics resources To be started w.e.f current year 10. Collaborative works/ initiatives To be started w.e.f current year 11. Databases/ Software packages developed To be started w.e.f current year 12. Papers published or presented in the conferences with reference : NA 13. Initiation of R&D activities in Bioinformatics: Analysis of protein domain fusions, plant Transcription factors, and Gene Mapping 14. Details of Training/ Workshop organized and total no. of users trained Five Students have been trained to date. Six students are undergoing training currently.

15. Impact shown by your centre on the growth of biotechnology and allied areas. 16. Future activities To conduct annual workshops and discussion meetings. Expansion of center infrastructure.

Additional Details: Name of the Coordinator: Dr. Gitanjali Yadav Postal Address: National Inst of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg. New Delhi -110067 Phone Number: 26735103 Email: [email protected] Website: http://www.nipgr.res.in Name of Contact Person(s): Dr. Gitanjali Yadav Email: [email protected]

244 National Institute of Technology, Raipur Coordinator : Dr. M. K. Verma

8. Summary of the progress made by the centre from its inception.

1) Procurement of Server, Computers, software’s, Internet facilities and other important necessary items for the development of Bioinformatics Laboratory facilities in the center 2) Development of Bioinformatics Laboratory. 3) Development of Wet Laboratory. 4) Organized courses for students. 5) Provided center facilities to pursue research and project work in Bioinformatics to the students of B.Tech (Bio-Medical, Bio-Technology, Chemical Engineering, Computer Science Engineering) and M.Tech. Computer Technology.

9. Major research activities in Biotechnology and its related fields at your institution.

1) Research work in Bioinformatics was carried by students of M.Tech. Computer Technology. 2) Research work initiated and carried in the biotechnology especially in Environmental Biotechnology and Biotransformation. 3) Data base generation and Data mining were initiated by center. 4) Research work carried in the field of ANN and Medical Bioinformatics.

10. Area of Specialization of the centre: Environmental Biotechnology, Medical Bioinformatics and Biotransformation.

4. Major activities of the centre during the year 2007-08 ¾ Development of Center to cater the needs for the researchers, students and teaching faculties related to biotechnology, biomedical, computer technology and Bioinformatics including other basic science. ¾ Development of Infrastructure facilities in center. ¾ Initiated the research environment in related field by providing the necessary research facilities.

5. Infrastructure facilities in the Bioinformatics Centre. 9 Computer & Communication facility 9 Scientific Software packages: MATLAB TOOL BOX, Genechek, Genowitch. 9 Databases & other information resources Under Generation.

6. Details about staff members working in the centre (Name of the staff, Designation, Specialization and period of working. Please indicate their absorption status)

245 S.no Name of the staff Designation period of absorption working status 1. Dr. M.K.Verma Coordinator Oct-2006 Regular 2 Mr. R.R. Janghel Information officer Dec-2005 Non-Regular

1. Dr. M.K.Verma (Coordinator, Sub-DIC Bioinformatics centre) 2. Mr. R.R. Janghel (Information officer ) 3. Interviewed (Technical Assistant) 4. Interviewed (Data Entry Operator) 5. Interviewed (Trainee ship)

7. Types of services provided. ™ Provided infrastructure facilities to pursue research and development work in allied discipline. ™ Provided various short-term courses and workshop in Bioinformatics.

8. Educational activities with details of placement. Facilities provided to in-house and other institute to pursue research activities including carrying their project works.

9. Initiative to validate the outcome of bioinformatics resources. Students including U.G., P.G and other research scholar were benefited by the center.

10. Collaborative works/ initiatives. Collaborative research works were carried out with Pt. J.L.N.M Medical College Raipur. Like Development of expert system for the diagnosis of cancer and diabities.

11. Databases/ Software packages developed. 1. Database under process for the cancer and diabities.

12. Papers published or presented in the conferences with reference.

List of Research Publications: 1. One paper has published in National conference on “Innovation in Science and Technology towards Industrial Development” in Rungta College of Engineering and Technology Bhilai (C.G.)

13. Initiation of R&D activities in Bioinformatics. 1. Research work has been initiated and ongoing in the field of Environmental Biotechnology, Biotransformation, and Medical Bioinformatics etc. 2. Under development an expert system for the diagnosis of cancer and diabities.

246 14. Details of Training/ Workshop organized and total no. of user trained. 1. National conference/ Training are going to be organized during the month of January-2007, i.e. on 28-29 Jan 2007.The total no of trained user are 30. 2. One week training programme on “Tools and Technique in Bioinformatics” from 23-28 July, 2007. The total no of trained user are 30. 15. Impact shown by your centre on the growth of biotechnology and allied areas. In this you may highlight the details like number of paper published/ number of papers published with the help of your centre, how your centre is promoting various activities of your organization and neighboring institutions, manpower trained, tools developed, patents & copyrights acquired and other services offered etc.

1. Center has been involve in various research activities and providing training program to the students of B.E. biotechnology, B.E. Biomedical Engineering and M.Tech Computer Technology by providing facilities to carry out their research, projects etc. to the students of various nearby and in-house institutes/ university.

16 Future activities.

1. Center will organize various short-term courses and conferences. 2. Center will continuously going to develop the basic infrastructure facilities to make benefiting the students/ Researchers/ Faculty members etc.

Additional Details:

We have conducted Executive meeting on 21/12/2007. We have conducted interview for the post of Information Officer, Technical Assistant and trainee ship.

Name of the Coordinator: Dr. M.K. Verma Postal Address: Coordinator, SUB-DIC Bioinformatics Center National Institute of Technology Raipur Raipur-492010. Phone Number: 07714062385 Fax No.:07714062385 Email: [email protected],[email protected]

247 North-Eastern Hill University, Shillong Coordinator : Prof. Pramod Tandon

1. Summary of the progress made by the Centre from its inception The Bioinformatics Centre (BIC) at North-Eastern Hill University (NEHU) has been setup and funded by Department of Biotechnology (DBT), Ministry of Science & Technology under the Biotechnology Information System Network (BTIS) program. The Centre started functioning from November 1999 with a view to catering to the needs of the scientific community in the far-flung northeastern region of the country and to augmenting their research activities through information inputs. Rich in great variety of flora and fauna, the north- eastern part of the country has been identified as one of the bio-diversity ‘hotspots’. The forest wealth includes numerous orchids, timber-yielding trees, medicinal and aromatic plants, animals and microbes and some unique plants and animals from the region. For the bio-resource development, its exploration, conservation and proper utilization, an urgent need was felt for linkage with the Bioinformatics network. The Centre is part of the national Bioinformatics Network and functions as an information base in various areas of Biosciences.

The Centre has been considered for upgradation to DIC with ‘Excellent’ remarks during the XIth Plan period as per the Sub-DICs’ 2nd review meeting report.

2. Major research activities in Biotechnology and its related fields at your institution The School of Life Sciences comprises four Departments: Botany, Biochemistry, Biotechnology & Bioinformatics and Zoology, catering to the varied research interests of faculty members at NEHU. Some of the important areas of research are molecular characterization, genome organization and expression in plants, animals and microbes, oncology, parasitology, crop improvement, microbial genetics etc. The most important area of research relevant to the northeastern region being biodiversity, the facilities of the Centre are extensively used for preparation of databases. Besides, some work on genomics, proteomics and metabolomics has also been initiated, apart from providing support to all disciplines of research in biotechnology.

3. Area of Specialization of the Centre The Centre’s activities focus on developing databases of scientific relevance on biological resources of the region, training of manpower and dissemination of information and technical knowhow (Computer Support Services) to the end users of national community working in the arena of Biotechnology and allied sciences.

4. Major activities of the Centre during the year 2007- 08 i) Workshop and Interaction meeting on ‘Mapping and Quantitative Assessment of Geographic Distribution and Population Status of Plant Resources of Eastern Himalayan Region’ dated April 17-18, 2007 248 ii) A lead talk on ‘Eco-informatics in Conservation and Database Management’ by Prof. K. N. Ganeshiah, UAS, GKVK, Bangalore on April 18, 2007 iii) Organized EDUSAT Interaction for the North-East Region Vision Document 2020 on August 10, 2007 iv) Lectures- cum- hands on training to participants of the UGC-sponsored Refresher Course – a) in Zoology on “Recent Trends in Bioinformatics” during September, 2007, b) in Botany on “Ancient internet: Information flow in Cells” during Nov-Dec 2007 and c) in Political Science on “E-governance and Basic Applications in IT” during December 2007. v) Training course on “Inferring Biological Relationships: A Bioinformatics Approach” during November 27- December 1, 2007 vi) Training course on “Molecular Biology Databanks and Integrated Data Analysis Tools: A Bioinformatics Approach” (scheduled to be held during March, 2008).

5. Infrastructure facilities in the Bioinformatics Centre The Centre is functioning from a small building of its own, which has the facilities and capacity to hold Trainings Courses and Seminars. i. Computer & Communication facility i. Leased Line Internet Connectivity (512 kbps) ii. Implementation of LAN on a Structured CAT 5 UTP Cabling Network using Switches and Hubs iii. Servers, PCs & Workstations, Printers, Scanner, UPS, Projector, etc. ii. Scientific Software packages i. Accelrys Gene 2.5 (Sequence Analysis Work Bench) ii. Matlab 7.0 (A high-level technical computing language and interactive platform for algorithm development, data visualization, data analysis, and numeric computation iii. Winspirs ver 4.1 for the Biotechnological Abstracts iv. Reference Manager for downloading and organizing data from available online Journals. iii. Databases & other information resources i. Derwent Biotechnological Abstracts (July 1987 - March 2006) ii. Reference Update Delux Edition (July 2002 - June 2004) iii. Parasitology Database obtained through MOE&F. iv. Other Softwares • Windows 2003 Small Business Server, Windows 2000 Professional Server, Microsoft Small Business Server 2000, Red Hat Linux, SQL Server 2005, Winproxy 6.0 • Windows XP, Windows Millennium Edition • Macromedia Director Shockwave Studio 8.5, Dreamweaver CS3, Adobe Photoshop 6.0, Adobe Acrobat 5.0 • Microsoft Visual Studio .NET 2005, Microsoft Visual Studio 6.0, Microsoft Office Professional 2000, Microsoft Office Frontpage 2000, iWork 2006 6. Details about staff members working in the Centre Prof. Pramod Tandon, Coordinator and Vice-Chancellor, NEHU Prof. Veena Tandon, Dy. Coordinator and Dean, School of Life Sciences,

249 NEHU WORKING ABSORPTION S.NO. NAME OF THE STAFF DESIGNATION SINCE STATUS 1. Mr. Devendra Kumar Information July 2006 The process of Biswal Officer selection for absorbed position is on. 2. Mr. Manish Debnath Senior November Absorbed Technical 1999 since July Assistant 2006 3. Mr. Hamarbamutlang Computer March 2007 Additional Kharshiing Operator posts were 4. Mr. Welfrank Computer March 2007 sanctioned by Thongnibah Operator UGC for the 5. Mr. Graciously Technical March 2007 Bioinformatics Kharumniud Assistant Centre and 6. Mr. Santosh Kumar Technical March 2007 recruitments Vishwakarma Assistant have been made. 7. Mr. Pradeep Kumar Data Entry November Absorbed Kar Operator 2005 since July 2006

7. Types of services provided a) Training b) Database & Software Development c) Assisted in teaching of Bioinformatics course to the Post graduate students of Department of Biotechnology and Bioinformatics at the University by way of conducting lectures and providing hands on training to them. d) Internet Access e) Access to Journals Subscribed (Users and on request) f) Technical Support to University g) Printing & Scanning 10,500 users (approx.) as per the log book maintained by the Centre. 8. Educational activities with details of placement Names of the trainee students who did their project work at BIC, NEHU Sl. Name Affiliation Title & details of the Remarks No. project work undertaken 1 Mr. Allen Freddy M.Sc. (Zoology), Madras Listing of polymorphic Pursuing Ph.D at (06-07) University microsatellite markers for NEHU chromosomes 1-7, 9 and 22 in H. sapiens 2 Mr. Donald Jyrwa M.Sc. (Zoology), NEHU Helminth Parasite of Pursuing Ph.D at (06-07) Freshwater Fishes in India NEHU 3 Mr. Lingaraj Jena Pursuing M.Sc.(Bioinfo), a) Helminth Parasite of Working as IO, BIC, (07-08) OUAT Freshwater Fishes in India MGIMS, JBTDRC b) Phylogenetic analysis Wardha on ITS1 & ITS2 sequences in pathogenic zoonotic trematodes 4 Mr. P. Ravikumar Pursuing M.Sc. (Bioinfo), Have joined on January 14, 2008 (07-08) Bharatiyar University 5 Mr. Eric Sandor Pursuing M.Sc. (Bioinfo), Have joined on January 14, 2008 Pakma (07-08) Bharatiyar University 250 6 Mr. Budheswar Pursuing M.Sc.(Bioinfo), Will be joining on February 15, 2008 Dehury (07-08) OUAT 7 Ms. Chinmayee Pursuing M.Sc.(Bioinfo), Will be joining on February 15, 2008 Priyadarshini OUAT Mandhata (07-08)

9. Initiative to validate the outcome of Bioinformatics resources The quality of research has tremendously improved with the facilities of the Centre being used by many faculty members, research scholars and M.Sc. students of not only NEHU but neighboring institutions as well in Northeastern region. 10. Collaborative works/ initiatives i) Preparation of data base on mosquito fauna of Northeastern region in collaboration with RMRC (ICMR), Dibrugarh. ii) Database on Seed Mycoflora of local variety of Phaseolus vulgaris Linn. in collaboration with Department of Biotechnology and Bioinformatics, NEHU. iii) With reference to the zoonoses of worm origin, a consortium-based programme is supposed to be taken up by the Bioinformatics Centre at NEHU with Public-Private Partnership (PPP) venture such as TCGA (an IGIB-IMM collaboration) emphasizing on Whole Genome Sequencing and Analysis of the lung fluke, Paragonimus sp. (a worm parasite), the infection of which prevails in crab-eating populations in Near- and Far Eastern Asian countries and which mimics symptoms of Tuberculosis.

11. Databases/ Software packages developed i. The Helminth Parasite Spectrum in Northeast India ii. Mosquito Fauna of North East India – with Special Reference to the Medically Important Vectors iii. Traditional Fermented Foods and Beverages of the Sikkim Himalayas iv. Medicinal Plants of Meghalaya v. Helminth Parasite of Freshwater Fishes in India 12. Papers published or presented in the conferences with reference

Prasad, P. K., Tandon, V., Biswal, D. K., Goswami, L. M. and Chatterjee, A. (2007) In silico molecular phylogenic location of the Indian liver fluke, Fasciola gigantica (Cobbold, 1855) based on the ribosomal internal transcribed spacer regions presented at 77th Annual Session of the NASI, Mysore during December 2007.

Tandon V., Prasad P.K., Chatterjee A. and Bhutia P.T. (2007) Surface fine topography and PCR-based determination of metacercaria of Paragonimus sp. from edible crabs in Arunachal Pradesh, Northeast India. Parasitology Research, 102: 21-28. DOI 10 1007/s00436-007-4.

Prasad P.K., Tandon V., Chatterjee A. and Bandyopadhyay S. (2007) PCR- based determination of internal transcribed spacer (ITS) regions of ribosomal DNA of giant intestinal fluke, Fasciolopsis buski (Lankester, 1857) Looss, 1899. Parasitology Research 101(6):1581-7.

Tandon P., Rathore, T.S. and Kumaria S. (2007) Micro-propagation of Coptis teeta Wall.-Threatened medicinal plant of Arunachal Pradesh, India. Indian Journal of Biotechnology 6: 280-282

251 Tandon P., Kumaria S. and Choudhury H. (2007) Plantlet regeneration of Pinus kesiya Royle ex. Gord. from mature embryos. Indian Journal of Biotechnology 6: 262-266.

Tandon P., Bhowmik, S. K. D., Mao, A. A. and Kumaria, S. (2007) Rapid in vitro clonal propagation of Mantisia spathulata Schult, A rare and endemic plant of Northeastern India for recovery. Biotechnology 6(1): 68-71.

Das, M.C., Kumaria, S. and Tandon, P. (2007) Protocorm regeneration, multiple shoot induction and ex vitro establishment of Cymbidium devonianum Paxt. Asian Journal of Plant Sciences 6(2): 349-353.

Tandon, P., Kumaria, S. and Abrol, Y.P. (Eds.) (2007) Biodiversity and its Significance. I.K. International Publishers, New Delhi 370 p.

Tandon, P. and Bhattacharjee, P. (2007) Bioinformatics: An overview. In: Plant Biotechnology and its Applications in Tissue Culture. (Eds. A. Kumar, N.S. Shekhawat and I.D. Arya). I.K. International Publishers, New Delhi.

Tandon, P. and Bhattacharjee, P. (2007) Bioinformatics in biodiversity mangement. In: Biodiversity and its Significance (Eds. P. Tandon, Y.P. Abrol and S. Kumaria) I.K. International Publishers, New Delhi, pp 332-353.

Stadwelson, D., Das, M.C., Kumaria, S. and Tandon, P. (2007) Conservation of Splendid Orchids of North-East India (Eds. P. Tandon, Y.P. Abrol and S. Kumaria) I.K. International Publishers, New Delhi, pp 354-365.

Bhatt, B.P., Pathanaik, A. and Tandon, P. (2007) Shifting cultivation: Issues and Strategies in N.E.H. region (Eds. P. Tandon, Y.P. Abrol and S. Kumaria) I.K. International Publishers, New Delhi pp 262-273.

Tandon, P. and Kumaria, S. (2007). Conservation of biodiversity of North-east India using biotechnological approaches (Eds. P. Tandon, Y.P. Abrol and S. Kumaria) I.K. International Publishers, New Delhi, pp 157-166.

Tandon, P. and Bhattacharjee, P. (2007). Bioinformatics in bio-technological research. In: Biodiversity and Environmental Biotechnology (Eds. P. Dwevedi, S.K. Dwevedi and M.C. Kalita) Scientific Publishers (India), Jodhpur, pp 225-250.

13. Initiation of R&D activities in Bioinformatics The BIC at NEHU, which is being considered for upgradation to DIC, proposes to initiate specific teaching programmes in Bioinformatics relevant to the needs as well as undertake R & D activities pertaining to development of dedicated and derived databases and development of innovative softwares addressing genomics and proteomics applications.

14. Details of Training/ Workshop organized and total no. of participants trained I) National Training Courses i. Basic Computer Concepts and Applications, 12-14 June 2000, 22 nos.

252 ii. Introduction to Computer Networks and Internet, 26th -29th September 2000, 16 nos. iii. Application of Basic IT Resources, 20th -23rd June 2001, 15 nos. iv. Basic Computer Concepts and Applications, 23rd-26th April 2002, 13 nos. v. Application of Basic IT Resources, 21-23 January 2003, 7 nos. vi. Introduction to Basics of Retrieval & Creation of Scientific Databases, 23-25 February 2004, 22 nos. vii. Database Creation with Emphasis on Biodiversity, 29-31 March 2004, 17 nos. viii. Database Creation with Emphasis on Biodiversity 22nd – 24th February 2005, 22 nos. ix. Computer Basics & Application in Bioinformatics (Internet & Databases)” April 18 - 20, 2005, 10 nos. x. Database Creation & Internet in Biological Applications, February 06 - 10, 2006, 16 nos. xi. Computer & Internet Applications in Bioresource Development, March 01 - 03, 2006, 14 nos. xii. Applications in Bioinformatics, February 13-15, 2007, 29 nos. xiii. Bioinformatics: Recent Trends in Sequence Analysis March 28-30, 2007, 31 nos. xiv. Inferring Biological Relationships: A Bioinformatics Approach, November 27- December 1, 2007, 22 nos.

II) Workshop & Seminars i. Hosted the DBT National Roving Seminar on Patenting in Biotechnology on October 26, 2002. ii. National workshop on ‘Conservation and Sustainable Utilization of Medicinal Plants of North-East India’ during May 27-28, 2004.

III) In-house Training & Resources i. Services of providing access to Internet and Journal Abstracts Subscribed. ii. Young Scientist Workshop on “Identification & Diagnosis of Parasites of Biomedical and Zoonotic Importance” 6th July 2000 iii. Young Scientist National Workshop on Water Quality Assessment Bio- monitoring and Zooplankton Diversity (Zoology Department) 5th Dec 2001 iv. Training for NEHU Ministerial Administrative Staff - 19th February - 19th March, 2002 v. Training for NEHU Ministerial Administrative Staff - 1st - 31st May, 2002, 3rd June - 2nd July, 2002 vi. Workshop and Interaction meeting on ‘Mapping and Quantitative Assessment of Geographic Distribution and Population Status of Plant Resources of Eastern Himalayan Region’ dated April 17-18, 2007 vii. A lead talk on ‘Eco-informatics in Conservation and Database Management’ by Prof. K. N. Ganeshiah, UAS, GKVK, Bangalore on April 18, 2007 viii. Organized EDUSAT Interaction for the North-East Region Vision Document 2020 on August 10, 2007 ix. Lectures and hands on training in Refresher Courses in 253 • Botany: October 21-23, 2000, September 25, 2001, November- December 2007 • Zoology: December 6, 2000, December 7, 2001, November 23-24, 2004, March 5-26, 2007, August 27-September 18, 2007 • Political Science: “E-governance and Basic Applications in IT” during December 2007 x. Regular training on awareness and familiarization of benefits of IT imparted to faculty members, research scholars, College teachers & students through regular training programmes. xi. Taking Bioinformatics theory Classes and providing hands on practical training of the same to the Post-graduate students of the Department of Biotechnology and Bioinformatics of the university.

15. Impact shown by your Centre on the growth of biotechnology and allied areas. i. The Centre started functioning from November 1999 with a view to catering to the needs of the scientific community in the far-flung northeastern region of the country and to augment their research activities through information inputs. ii. The BIC at NEHU provides the scholars with latest information in their respective fields and brings them closer to the rest of the world as far as scientific advancements are concerned. The Centre is part of the National Bioinformation Network and functions as an information base in various areas of Biosciences. iii. Bioinformatics Training programmes, which have always been an integral part of the Centre’s activity and for which connoisseurs in the field are always invited to act as resource persons, have greatly benefited the students and researchers of the region who otherwise because of the location could not attend such trainings elsewhere. iv. Successful Database preparation and information resource development in biological sciences and Computer assisted cutting edge research in functional annotation of bio-molecules, thereby leading to emanation of quite a good number of publications in peer reviewed journals. v. The Centre at NEHU, Shillong has been inducted as one of the Examination Centers for conducting the National Level Bioinformatics Certification Exam (BINC), 2008 onwards,catering to the much needed facility for the aspirant students from the north-eastern region of the country.

16. Future activities The areas of Functional genomics, proteomics, metabolomics, and evolutionary bioinformatics and developing e-learning bioinformatics modules will figure prominently in our list of items for research in future. Besides, the ongoing activity of cataloguing the biodiversity informatics will continue. The future of bioinformatics both in teaching and research at NEHU is highly promising. The manpower development in the discipline in a rather neglected region will be given top priority. The following teaching/research programmes are envisaged; A. Teaching Programmes • Advanced P.G. Diploma in Bioinformatics (18 months) • Certificate Courses (5 months)

254 • Credit Course in Bioinformatics that can be offered to the Postgraduate and Doctoral students of the University B. Research Programmes Plant Sciences • Developing Grid-based Platform for Quantitative Trait Loci Analysis with Hi-Density Molecular Markers in Orchids of North-East India • Ecological Genomics of Orchids (of medicinal importance) specific to North-East India & Modeling of Flowering Time Control and Circadian Oscillator in Orchids Animal Sciences 1. Bioinformatics and Health Care 9 Database development on health issues specific to North-East India, with special reference to Malaria, Thalassaemia, Malnutrition and Zoonoses of worm origin. 9 Nutritional Genomics, which has a major role to play in Health Care Informatics, giving special emphasis on dietary guidelines. 9 With reference to zoonoses of worm origin, consortium - based programmes can be taken up by the Bioinformatics Centre at NEHU with Public-Private Partnership (PPP) venture such as TCGA (An IGIB IMM Collaboration). 2. Major Bioinformatics Tools to be developed at the Centre 9 Developing Eukaryotic Gene Prediction tools, Gene nomenclature, functional characterization, genome browsing and genome database development specific to worms and Insilico study of Paragonimus under broader areas like Proteome analysis with a focus on revelation of gene families and duplicated genes and Evolutionary Modeling and Phylogeny Reconstruction.

255 Additional Details:

Name of the Coordinator: Prof. Pramod Tandon Name of the Deputy Coordinator: Prof. Veena Tandon Postal Address: Bioinformatics Centre North-Eastern Hill University Shillong 793 022 Phone Number: (0364) 255 0150/ 272 1242/ 272 2214/ 272 2244 Fax No.: (0364) 255 0150/ 255 0300 Email: [email protected]; [email protected] Website: http://www.nehu.ac.in/bic Name of Contact Person(s): Email: Prof. Veena Tandon [email protected]; [email protected]

256 Pondicherry University, Pondicherry Coordinator : Dr. P.P. Mathur

1. Summary of the progress made by the centre from its inception

The Centre for Bioinformatics in Pondicherry University was started as Sub Distributed Information Centre of the Department of Biotechnology, Govt. of India (DBT) in 1991. The mandate of the Centre was to provide biological information to the end users. The Centre became a focal point for providing various communication and computational facilities to the users from the university and also from other institutions. The Centre provides training to teachers and students of the university, affiliated colleges and other institutions. The Centre has so far organized 24 training National level programs. The Centre has periodically arranged lectures by many eminent scientists working in the areas of bioinformatics and biotechnology. Several professionals from Industry have also delivered lectures on the opportunities and challenges in the sector of Bioinformatics.

The Centre has been offering an Advanced PG Diploma course in Bioinformatics with financial support from Department of Biotechnology (DBT), Govt. of India since 2001. The also offers a Ph.D program in Bioinformatics. The Centre has started offering M.Sc. in Bioinformatics since 2007 which is funded by the University Grants Commission (UGC) under its scheme of Innovative Program in Emerging Areas. The Centre has been offering a 4-credit course in Bioinformatics since 1994 to the Masters students of Life Sciences and Biotechnology.

In the past few years, the Centre has taken up research activities in the areas of sequence analysis, molecular modeling, database development etc., and several papers have been published in peer-reviewed national and international journals.

Most of the past students have got placements in various leading / research institutions and industries.

The Centre has been identified as a Centre for Excellence in Bioinformatics Teaching and Research by the Department of Information Technology, Ministry of Communication & Information Technology, New Delhi.

2. Major research activities in Biotechnology and its related fields at your institution

The University has several departments and affiliated institutions which are having major research activities in Biotechnology. Some of the important areas are DNA Protein Interactions, X-ray Crystallography Macromolecular (Proteins), Molecular Modeling / Simulation of Biomolecules for targeted Drug Discovery, Database & Software Development and Development of Bioinformatics Educational Materials

3. Area of Specialization of the centre

257 Plant and Animal Biotechnology

4. Major activities of the centre during the year 2006-07

Faculty and non teaching positions have been advertised and two lecturers have joined. The Centre started offering a Ph.D program in Bioinformatics. The Centre started offering a Masters program in Bioinformatics (M.Sc) in 2007 which is funded by the University Grants Commission (UGC) under its scheme of Innovative Program in Emerging Areas. The Centre has undertaken several projects in the areas of Computational Genomics, development of Database on Zinc Finger Proteins, Homology Modeling, Molecular Docking and Computer-based Tutorial on Bioinformatics. The Centre has conducted various training programmes in Bioinformatics and arranged several invited lectures.

5. Infrastructure facilities in the Bioinformatics Centre

A. Computers and Communication facilty Xeon Cluster Servers, Itanium-Email Server, AMD Opteron Server-DS Modeling Server, Wipro [email protected] Ghz-Web Server, Silicon Graphics Fuel Machine, Apple IMAC, HCL Laptops, HCL Pentium Core Duo/ Dual Core/ Pentium IV Workstations (55 nos.) – Works on both Windows and Linux Operating Systems. The Centre has a dedicated 2 Mbps internet connectivity exclusively for the Centre for Bioinformatics from Videsh Sanchar Nigam Limited, Pondicherry The students have the modern computing facilities and round the clock internet facility to meet their academic and research needs. B. Scientific Software packages

Insight II, Amber, DS Modeling suite, Autodock, Dock, Modeller, Gromos 96, Whatif, EMBOSS, BioEdit, Phred, Consed, GeneScan, Statistica, Endnote,

C. Resources & Services A separate website has been maintained by the Centre for Bioinformatics. This website was designed in-house and hosted in the web server maintained in the Centre, can be accessed at www.bicpu.edu.in. Information about course, admissions, syllabus, seminar notifications & various opportunities for traineeship/ studentship / JRF are updated periodically. Bioinformatics related tools can be downloaded from the site

D. Databases & other information resources Books 400 books (In addition to the books available in the Central Library) Journals Science, Nature, Scientific American, Bioinformatics & Computational Biology, Briefings in Bioinformatics, Bioinformatics, Nature Structural Biology, Nature Chemical Biology, Cell, Bioinformatics Trends, Current Science 258 Magazines Linux for U, PC Quest, PC World Access to E-Journals Access to Science Direct, Access to EBSCO Databases 6. Details about staff members working in the centre (Name of the staff, Designation, Specialization and period of working)

Posts Sanctioned Date of Joining Sl. Name of the Area of From To No. Employee Specilization 1 Lecturer Dr. D. Sundar Bioinformatics, June Continuing Proteomics & 2005 Genomics

2 Lecturer Dr. R. Krishna X-ray Dec, Continuing Crystallography 2007 (Proteins), Molecular Modeling (Protein & DNA) 3 Lecturer Dr. M . Suresh Structural Decemb Continuing Kumar Studies on Viral er, 2007 Proteins, Promiscuity of Antibodies, Inhibitors for Viral Proteases 4 Information Officer M. Sundara Mohan Computer March, Continuing Networks, 1992 Database Management 5 Sr. Technical Ms. V. Amouda Mathematics March Continuing Assistant Modeling and 1992 Simulation 6 Computer Assistant Ms. D. Venmathi - Novemb Continuing er 2007

* All the above positions including the vacant posts of Reader and Technical Assistant are already absorbed by the University 7. Types of services provided

The Centre has been providing computational and internet facilities to the faculty and students of the University and nearby institutions.

8. Educational activities with details of placement

The Centre started an Advanced PG Diploma course in Bioinformatics with financial support from Department of Biotechnology (DBT), Govt. of India from

259 2001. The Centre started offering a Masters program in Bioinformatics (M.Sc) in 2007 which is funded by the University Grants Commission (UGC) under its scheme of Innovative Program in Emerging Areas. The also offers a Ph.D program in Bioinformatics. The Centre has been offering a 4-credit course in Bioinformatics since 1994 to the Masters students of Life Sciences and Biotechnology. Most of the students of the previous batches have been placed suitably. Some of the Institutions/ Industries who have recruited our students are as follows Industry Placements HCL Infosystems, Pondicherry, Molecular Connections, Bangalore, Institute of Bioinformatics, Bangalore, Protein Lounge, Bhubaneswar, Genemines, Chenna, BIOBASE Databases Indian Pvt. Ltd., Bangalore Teaching/ Research Placements Pusan National University, South Korea, Sungkyunkwan University, South Korea, University of Madras, Chennai, Central Sericulture Research & Training Institute, Mysore, Institute of Microbial Technology Institute, Chandigarh, Aravind Eye Hospital, Madurai, Indian Institute of Technology, Chennai, Jawaharlal Nehru University, New Delhi

9. Initiative to validate the outcome of bioinformatics resources

The Bioinformatics resources created and procured in the Centre has been subjected to peer review and suggestions have been taken from various experts in the field. The University has nominated a Committee with external experts to monitor the teaching/ research programmes of the Centre. 10. Collaborative works/ initiatives The Centre completed the following projects during the year Sl. No. Project Comparative sequence analysis & homology modelling 1. studies on factors involved in the rubber biosynthesis in rubber plant Hevea brasiliensis & Parthenium argentatum. A comparative homology modeling study on alcohol 2. dehydrogenase I enzyme in Oryza sativa indica and Oryza sativa japonica 3. Comparative genome analysis and molecular modelling studies of Clostridium novyi with other Clostridium spp. for the production pf phospholipase C. Crystal structure of putative dipeptidase form Pyrococcus 4. horikoshii OT3 Molecular docking of lead anti-retroviral non-nucleoside 5. reverse transcriptase inhibitors (NNRTI) compounds to HIV-I reverse transcriptase. Homology Modelling and Molecular Docking studies of 6. nsp2 protease of Chikunguniya virus. Structural Analysis of Green Fluorescent Proteins 7. 260 11. Databases/ Software packages developed • EnZif : A tool for targeted Genome Engineering • EnZif-dB : A database of DNA binding proteins (more information available in Biobytes-November 2007 issue) • Molecular Visualization and Homology Modeling tools – • Educational Kit on Bioinformatics • Database of Genomic Information of Sequenced Bacteria 12. Papers published or presented in the conferences with references • Kandavelou, K., Sundar, D and S. Chandrasegaran (2008). Custom- designed molecular scissors for targeted manipulation of the plant and mammalian genomes. Methods in Molecular Biology (in press). • Kandavelou, K., Sundar, D and S. Chandrasegaran (2008). Plasmids for gene therapy. In: Plasmids: Current Research and Future Trends, Georg Lipps (Ed.). Horizon Press, UK (in press). • Sundar, D (2008). An improved method for interrogation of DNA-protein interactions. Proceedings of the International Conference on Trends in Cellar and Molecular Biology, Jawaharlal Nehru University, New Delhi, January 2008, p. 36. • Anmol J. Hemron, J. Muthukumaran and D. Sundar (2007). Comparative modeling of cis_IIPS domain in cis-prenyl transferase from Hevea brasiliensis. Protein Model Data Base (PMDB identifier : PM0075092 • Shankar Prasad Kanaujia, Chellamuthu Vasuki Ranjani, Jeyaraman Jeyakanthan, Seiki Baba, Lirong Chen, Zhi-Jie Liu, Bi-Cheng Wang, Masami Nishida, Akio Ebihara, Akeo Shinkai, Seiki Kuramitsu, Yoshitsugu Shiro, Kanagaraj Sekar, Shigeyuki Yokoyama. Crystallization and preliminary crystallographic analysis of Molybdenum cofactor biosynthesis protein C from Thermus thermophilus. Acta. Cryst. 2007, F63, 27-29. • Shankar Prasad Kanaujia, Chellamuthu Vasuki Ranjani, Jeyaraman Jeyakanthan, Seiki Baba, Akio Ebihara, Akeo Shinkai, Seiki Kuramitsu, Yoshitsugu Shiro, Kanagaraj Sekar, Shigeyuki Yokoyama. Cloning, expression, purification, crystallization and preliminary X-ray crystallographic study of DHNA synthetase from Geobacillus kaustophilus. Acta. Cryst. 2007, F63 • Gowthaman, U., Jayakanthan, M. and Sundar, D (2007). Molecular docking studies of DTNB and its related compounds to Protein disulphide isomerase. Proceedings of the International Conference on Bioinformatics, University of Hyderabad, Hyderabad, December 2007. • Sundar, D (2007). Engineering DNA-binding proteins for modification of mammalian genomes. Proceedings of the International Conference on Cellular and Molecular Bioengineering (ICCMB 2007), Nanyang, Singapore, December 2007, p.56. • Sundar, D. (2007). Unraveling the supply from primary to secondary carbon metabolism. Proceedings of the International Conference on Light and Life, Hyderabad, India, August 2007, p.21.

261 • Sundar, D. and A.R. Reddy (2008). Detection of a rapidly accumulating 50 kDa polypeptide and increased rubber accumulation in guayule under low temperatures. (Submitted) • Jayakanthan, M. and Sundar, D. (2008). Computer Aided Drug Design for H-Ras P21 Mutant Protein: Molecular Docking of H-Ras P21 Mutant Protein with Ligand Molecules. (Submitted) • Anmol J. Hemron, J. Muthukumaran and Sundar, D. (2008). Comparative protein modeling of CIS_IPPS domain in cis-prenyl transferase from Hevea brasiliensis. (Submitted)

13. Initiation of R&D activities in Bioinformatics A number of sponsored research projects for the period 2006-2009 are carried out by the faculty of the Centre. Some major funding agency include the Department of Biotechnology (DBT), Department of Science and Technology (DST), Department of Information Technology (DIT), Govt. of India 14. Details of Training/ Workshop organized and total no. of user trained (2006-2007) • National Seminar on “Computations in Bioinformatics”, February 14-16, 2007. No. of participants : 100 • National Seminar on “Applications of Bioinformatics in Genome Research”, February 13-15, 2008. No. of participants : 100 (Proposed)

15. Impact shown by your centre on the growth of biotechnology and allied areas. In this you may highlight the details like number of paper published/ number of papers published with the help of your centre, how your centre is promoting various activities of your organization and neighboring institutions, manpower trained, tools developed, patents & copyrights acquired and other services offered etc. • The Centre started offering a Master’s program in Bioinformatics (M.Sc) in 2007 which is funded by the University Grants Commission (UGC) under its scheme of Innovative Program in Emerging Areas. • The Centre has been identified as a Centre for Excellence in Bioinformatics Teaching and Research by the Department of Information Technology, Ministry of Communication & Information Technology, New Delhi.

• The Centre has been able to achieve many targets towards training and manpower development in bioinformatics • The Centre has been able to advertise positions and recruit a few staff members • Completed projects in the areas of comparative genomics, homology modeling, molecular docking and Computer Based Tutorial on Bioinformatics • The Centre has created a big impact in Pondicherry University and surrounding Institutions towards teaching and research in Bioinformatics.

262 Our Centre is collaborating with many other institutions like Vector Control Research Centre, IICT, Hyderabad and Industries. • A CD on free software on Internet has been prepared and is available for distribution • Conducted various training programmes in Bioinformatics and arranged several invited lectures • The Centre has helped various Universities/ Colleges for curriculum development & training

16. Future activities • Strengthening of R&D activities in the areas of comparative genomics, homology modeling, molecular docking, development of Databases • Computational Analysis of Rubber biosynthetic Genes from different plant species • Development of Database on Zinc Finger Proteins • Development of teaching aids in Bioinformatics • Strengthening and expansion of teaching and research programme

Name of the Coordinator: Dr. P.P. Mathur Postal Address: Centre for Bioinformatics, Pondicherry University, Pondicherry – 605 014 Phone Number: +91-413-2655212 Fax No.: +91-413-2655211 Email : [email protected] Website : www.bicpu.edu.in

Name of Contact Person(s): Dr. P.P. Mathur Email: [email protected] ; [email protected]

263 Punjab Agricultural University, Ludhiana Coordinator : Dr.(Mrs.) Parveen Chhuneja

1. Summary of the progress made by the centre from its inception: ¾ Developed a database Pedigree Retrieval cum Morphological Diversity in Wheat Version 1.0 ¾ Developed an online database of cultivars of wheat, rice, cotton, maize, pulses and fodders released by PAU since 1960 ¾ Developed a database of molecular markers of wheat, Barley and Triticale consisting of 3160 markers ¾ Provided Leased Line Internet connectivity of 1 Mbps speed to the researchers ¾ Provided various information retrieval services both offline and online to the students, research scholars and the faculty ¾ Provided services for standardization of the mapping and the statistical software ( IRRISTAT, J/QTL, R/QTL, Map Maker, Map Manager QTX, ICImapping, QTLnetwok etc.) for the use of research workers ¾ Developed an online database of Publications of the faculty of Plant Breeding, Genetics & Biotechnology.

2. Major research activities in Biotechnology and its related fields at your institution The major emphasis of Agbiotech Center of Excellence at Punjab Agricultural University is the germplasm enhancement in field crops using wide hybridization, molecular marker and transgenic technology. ¾ Introgression and mapping of new alien disease resistance genes and productivity traits using molecular markers and molecular cytogenetic techniques in wheat and rice ¾ Mapping of QTLs for disease resistance, quality and domestication traits in wheat ¾ Pyramiding of rust resistance genes in wheat and bacterial blight resistance genes in rice using marker assisted selection (MAS) ¾ Improving architecture of Basmati rices using MAS ¾ Isolation of new genes ¾ Developing transgenic plants in rice and sugarcane

3. Area of Specialization of the centre : Bioinformatics & Agriculture 4. Major activities of the centre during the year 2007-08 ¾ Developed an online database of cultivars of wheat, rice, cotton, maize, pulses and fodders released by PAU since 1960. ¾ Developed a database of molecular markers of wheat, Barley and Triticale consisting of 3160 markers. ¾ Standardization of the scientific softwares (IRRISTAT, J/QTL, R/QTL, Map Maker, Map Manager QTX, ICImapping, QTLnetwok etc.) for the use of research workers. ¾ Maintenance of Local Area Network of (approx. 200 nodes) in the Department of Plant Breeding, Genetics & Biotechnology. ¾ Maintenance and updating the Sub-Distributed Information Centre and university websites. 264 ¾ Computing and networking facilities to the students, research scholars and the faculty. ¾ Conducting training on the “Bioinformatics: Basics and its use in gene cloning” for molecular biologists and biotechnologists of the university. 5. Infrastructure facilities in the Bioinformatics Centre 2) Computer & Communication facility Table : List of computer and communication facilities available in the Bioinformatics Centre

Item Total No. Item Total No. Lease Line Internet 1 Mbps Scanner 1 connectivity Computer System (PC) 18 Photo copier 2 Laptop (IBM) 1 Network Switch 3 Server 2 UPS Online 3 kva 2 LCD Projector 1 UPS Online 1 kva 1 Printer Laserjet 2 Computer Table 18 Printer Deskjet 1 Furniture –Chairs 18 Dot Matrix Printer 1 Filing Cabinets 2 Book Case 1 3) Scientific Software packages Bio-Chemical Interactions Primer 3 (primer design) J/QTL (QTL mapping) Glimmer M QTX Map Manager (QTL NTSYS 2.0 (diversity analysis) mapping) IRRISTAT (statistical analysis) Map Maker (mapping) SPSS Statistical Software ICIMaping (QTL mapping) (statistical analysis) QTLnetwork (QTL interactions) Gencheck (sequence analysis) 4) Databases & other information resources ¾ IRIS - International Rice Information System ¾ IWIS - International Wheat Information System ¾ ICIS- International Crop Information System ¾ Rice Genome Sequence from TIGR Database

6. Details about staff members working in the centre

Sl. Name of the Designation Working Since Absorption No. Staff status 1. Parminderdeep Information 1st Dec.2006 till Not absorbed Singh Mangat Officer date 2. Jasbir Singh Bioinformatic 24thNov.2006 till Not absorbed Sandhu Assistant date 3. Gurbax Singh Data Entry 24th Dec.2001till Not absorbed Operator date

7. Types of services provided 265 ¾ Internet connectivity and computing services provided to faculty, students and research workers of various departments of the university

¾ Standardization of the scientific softwares (IRRISTAT, J/QTL, R/QTL, Map Maker, Map Manager QTX, ICImapping, QTLnetwok etc.) for the use of research workers ¾ Searching and downloading the scientific softwares for making these softwares available to research workers ¾ Maintenance of Local Area Network of (approx. 200 nodes) Department of Plant Breeding, Genetics & Biotechnology ¾ Facilities of typing, printing, scanning and photocopying etc., are provided in the Bioinformatics Centre, LCD, Laptop facility extended during workshops held in different departments of the university and during the seminars.

8. Educational activities with details of placement M.Sc & Ph.D. courses in Biotechnology will commence from next academic session

9. Initiative to validate the outcome of bioinformatics resources Research workers are utilizing Bioinformatics tools in their research endeavors extensively

10. Collaborative works/ initiatives Providing help in the use of various mapping softwares and information retrieval from public domains to the faculty of Genetics and Biotechnology of PAU, Ludhiana.

11. Databases/ Software packages developed ¾ Pedigree Retrieval cum Morphological Diversity in Wheat Version 1.0 ¾ Online Database of varieties of wheat, rice, cotton, maize, pulses and fodders released by PAU since 1960 ¾ Molecular marker database of wheat, Barley and Triticale consisting of 3160 markers ¾ Online database of Publications of the faculty of Plant Breeding, Genetics & Biotechnology ¾ Developed website of Sub-DIC PAU, Ludhiana (www.bicpau.org) ¾ Online database of Bio-Tools 12. Papers published or presented in the conferences using Bioinformatics support Cheema K K, N S Bains, G S Mangat, A Das, D S Brar, G S Khush, and K Singh (2007) Introgression of quantitative trait loci for improved productivity from Oryza rufipogon into O. sativa. Euphytica (Accepted) Chhuneja P, S Kaur, R K Goel and H S Dhaliwal (2006) Mapping of leaf rust and stripe rust resistance QTLs in bread wheat X synthetic RIL population under Indian field conditions. Indian J. Crop Science 1: 49-54. Chhuneja P, S Kaur, T Garg, MGhai, S Kaur, M. Prashar, RK Goel, NS Bains, B Keller, HS Dhaliwal and Kuldeep Singh (2007) Mapping of adult plant stripe rust resistance genes in diploid A genome wheat species and their transfer to bread wheat. Theor Appl Genet (published online) Dhillon N P S, Ranjana, K Singh, Eduardo, I Monforte, A J Pitrat, M Singh, P P 266 and N K Dhillon (2007) Diversity among landraces of Indian snapmelon (Cucumis melo var. momordica). Genetic Resources and Crop Evolution DOI 10.1007/s10722-006-9108-2 Garg M, H S Dhaliwal, P Chhuneja, D Kumar, Quan-Wen Dou, H Elamein, H Tanaka and H Tsujimoto (2007) Negative effect of chromosome 1A on bread making quality shown by modification of 1D addition in durum wheat (Triticum durum). Theor. Appl. Genet. 114:1141-1150. Garg T, K Singh, M Ahuja, J S Sidhu, H S Dhaliwal and P Chhuneja (2007) Validation of the molecular markers linked to a major pre-harvest sprouting tolerance QTL mapped on wheat chromosome 3A. Indian J. Crop Science 2: 223-225. Juneja S, A Das, S Sharma, B Patra, Y Vilkal, S Joshi, T S Bharaj, J S Sidhu and K Singh (2006) Genetic diversity in a set of 127 accessions of wild rice, Oryza nivara Sharma et Shastry as estimated using microsatellite markers. Current Science 91: 1079-85 Kuraparthy V, P Chhuneja, H S Dhaliwal, S Kaur, R L Bowden and B S Gill (2007) Characterization and mapping of cryptic alien introgression from Aegilops geniculata with novel leaf rust and stripe rust resistance genes Lr57 and Yr40 in wheat. Theor. Appl. Genet. 114: 1379-1389. Kuraparthy V, S Sood, P Chhuneja, H S Dhaliwal and B S Gill (2007) Identification and mapping of tiller inhibition gene (tin3) in wheat. Theor. Appl. Genet. 114:285-294. Kuraparthy, V, S Sood, P Chhuneja, H S Dhaliwal, S Kaur, R L Bowden and B S Gill (2007) A cryptic wheat-Aegilops triuncialis translocation with leaf rust resistance gene Lr58. Crop Science (accepted). Singh K, M Ghai, M Garg, P Chhuneja, P Kaur, T Schnurbusch, B Keller and H S Dhaliwal (2007) An integrated molecular linkage map of diploid wheat using a Triticum boeoticum X T. monococcum RIL population. Theor. Appl. Genet. 115: 301-312

13. Initiation of R&D activities in Bioinformatics ¾ Designing primers for mapping of genes for biotic and abiotic stresses ¾ Comparative genomics for searching DNA sequences for heat and drought tolerance in wheat & rice

14. Details of Training/ Workshop organized and total no. of user trained A number of trainings have been conducted by Bioinformatics Centre for making researchers aware of computer technology, genomic and proteomics.

Table – List of trainings conducted by Bioinformatics Centre No. of Title of the Training Date participants 1. Introduction to Computer Basics, October 17 Operating Systems and their 16-18, 2001 Applications in Agriculture/Life-Sciences 2. Bioinformatics for Agricultural Sciences February 21 20-22, 2002 3. Bioinformatics Tools For Nucleic acid January 17

267 and Protein Sequence analysis 29-31, 2003

4. Internet Access For Biotechnology March 17 Information Tools and Sources 25-27, 2003 5. Genomics & Proteomics in October 15 Biotechnology 29-31, 2003 6. Bioinformatics tools in immunology March 15 16-18, 2004 7. Bioinformatics & Molecular Approaches December 14 for Data Mining 13-15, 2004 8. Bioinformatics & Biotechnology December 13 14-16,2005 9. Bioinformatics: Basis & its uses in gene December 30 cloning 11-14, 2007

15. Impact shown by your centre on the growth of biotechnology and allied areas The Bioinformatics center has made possible the availability of 24 h internet connectivity to the faculty and research fellows of the department which has made possible use of Bioinformatics tools for searching and downloading DNA sequences from NCBI and TIGR sites.

16. Future activities ¾ Intervention through Bioinformatics tools for utilizing the information generated in rice and wheat genomics. ¾ Elucidating the structure of putative novel alien genes using rice genome sequence information ¾ Searching for DNA sequences for heat and drought tolerance using comparative genomics ¾ Conducting trainings on the use of Bioinformatics in the field of genomics ¾ Providing computing and networking facilities to the agricultural scientists ¾ Developing a database for wild wheat & rice germplasm

Additional Details: Name of the Coordinator : Dr. S.C. Sharma ( Feb. 2000-Oct. 2006) Dr.(Mrs.) Parveen Chhuneja (Nov. 2006 till date) Postal Address : Bioinformatics Centre, Department of Plant Breeding, Genetics and Biotechnology, Punjab Agricultural University, Ludhiana. PIN 141004

Phone Number Email Website 0161-2411774 [email protected] http://www.bicpau.org

268

Name of Contact Person: Dr. Parveen Chhuneja

Email: [email protected] [email protected]

269 Rajiv Gandhi Centre for Biotechnology, Trivandrum Coordinator : Dr. Sathish Mundayoor

1. Summary of the progress made by the centre from its inception The Distributed Information Sub Centre was awarded to RGCB when the institute was in its infancy. The facility became the lifeline of RGCB and has played a major role in its growth. The initial grant was used to procure Computers, scanner, printers etc along with a server and a net connection. Totally, eighteen computers have been purchased for the DISC, which includes an SGI-Octane Machine, three SUN workstations, a Pentium Dual Core high performance system and a Wipro Net Power Server. These were used to provide networking and Internet facilities for all the RGCB members. All the three personnel, viz. Information Officer, Technical Assistant and Data Entry Operator were appointed. Eleven databases, three web servers and ten softwares have been developed. Few databases are under development. We are maintaining a mail server, which is accessible to all members in RGCB. All students as well as technical staff were given basic level training in linux platform and all routinely used bioinformatics software packages. The bioinformatics software packages are maintained as a central facility for use of internal as well as external students for various databases, sequence and other analysis. Insight II procured by us was used by our students for various molecular modeling predictions as a part of their research activities. Since its establishment the DISC has successfully conducted three National level seminars on Bioinformatics, in which several eminent speakers from various research institutions/ universities have delivered their talk on frontier areas of bioinformatics. We also organize regular training programmes. Internet connectivity to CDAC Terascale Supercomputing Facility (CSTF) was obtained in order to run high–end bioinformatics applications.

2. Major research activities in Biotechnology and its related fields at your institution The core research teams are currently being grouped under (1) Molecular Medicine and Cancer (2) Molecular Reproduction (3) Plant Molecular Biology (4) Molecular Microbiology (5) Neuro and Stem Cell biology (6) Medical Demography

3. Area of Specialization of the centre Medical and Plant Bioinformatics 4. Major activities of the centre during the year 2007-08 Softwares and databases development to support research activities in RGCB Molecular modeling and simulation studies to support various research activities of groups in RGCB. Hands-on training in Molecular Modeling for RGCB research students Project guidance and hands-on training for B.Tech and M.Sc students from various institutions and universities.

5. Infrastructure facilities in the Bioinformatics Centre 270 Computer & Communication facility 9 Ingram Micro MagixTM PC – 12 No 9 Wipro NetPower Server – 1 No 9 SunBlade Workstation- 3 Nos. 9 SGI-Octane Workstation – 1No 9 Pentium Dual Core – 1 No 9 512Kbps internet connection.

Scientific Software packages 9 GCG Package version 11.0 (Commercial) 9 EndNote v 5.0 (Commercial) 9 Free/Open Softwares:- EMBOSS, Autodock.4, WHATIF, MODELLER Clustal W, Phylip, Cn3D, Rasmol, HMMR, Staden Package, R-statistical package, GeneDoc, Phred, Phrap & Consed package, FTDOCK, PATCHDOCK, GROMACS-3.3, PyMol-0.9.

Databases & other information resources 9 Agricola database 9 Biotech Citation Index 9 Current Contents Connect – Life Sciences 9 CD database on Indian Patents 9 GENE D’CFER and SEAPATH databases

6. Details about staff members working in the centre (Name of the staff, Designation, Specialization and period of working. Please indicate their absorption status)

Name Designation Specialization Period of working K.C. Information Officer Computational Biology, 26-08-04 to Sivakumar Molecular Mechanics present (Not date Absorbed) C. Technical Networking, PC 14-11-02 to Durgaprasad Assistant Maintenance present (Not Absorbed) date Amal. V Data Entry Web Site Design, 02-05-05 to (Not Absorbed) Operator Documentation present date 7. Types of services provided 9 Internet facility 9 Mail Server 9 Network establishment and maintenance 9 Biotech Citations Databases and repositories. 9 Impar training to Studentship and Traineeship 9 Project Guidance to MSc/B.tech Bioinformatics students 9 Facilities for Sequence analysis and Molecular modeling 271

8. Educational activities with details of placement: N/A 9. Initiative to validate the outcome of bioinformatics resources Conformation Dynamics of Isoniazid and rifampicin bound to wild and mutant KATG, INHA and RPOB from Multidrug resistant Mycobacterium tuberculosis – evidence by in vitro binding studies. Molecular Simulation and Interaction Studies of HAD like Phosphatase (Rv3813c) - A Conserved Hypothetical Protein from Mycobacterium tuberculosis H37Rv-evidence by in vitro protein interaction studies. Induced fit DNA recognition in a cisplatin binding groove by carbohydrazone: structural fluctuations investigated through molecular dynamics simulations – evidence by Cytotoxicity assay and FACScan In silico docking and dynamics of plumbagin acts through death receptor mediated pathway in brca1 blocked ovarian cancer cells - evidence by suppression subtractive hybridization (ssh) and microarray New dimensions in function of fibulin, a secretory protein at embryo implantation by molecular modeling and protein-protein interaction studies – evidence by immunoprecipitation, immunocytochemistry and western blot. DOCK-180, a importin like molecule-plausible route for nuclear entry for transcription factors by molecular modeling and protein-protein interaction studies – evidence by immunoprecipitation and MALDI-TOF.

10. Collaborative works/ initiatives : Nil 11. Databases/ Software packages developed 1. Neuro-Medicinal plants Database: A database on important neuro active medicinal plants. The database contain information on: the genus and species names, the common English, description of the plants, medicinal use in literature and by the communities, preparation in literature and communities, previous chemical and biological studies carried out etc. 2. Primer Inventory Database: A database to maintain primer inventory information in a typical biotechnology lab. The database contains information on: primer details, provider data, user details, storage information, quantity details and order information etc; with advanced search facility. 3. Psychiatric Patient Management System: This database is being developed to assist doctors/researchers to diagnose patients with psychiatric diseases like schizophrenia using the international diagnosis standards such as BPRS, PANSS, AIMS etc. 4. TBCaseSheet Database: This database is developed as a case sheet pro-forma of patients under going pulmonary tuberculosis treatment. It will assist the research scholars in Mycobacterial research group to conduct a survey on pulmonary tuberculosis in kerala. 5. Chemcomp Tool: A Chemical compound comparison tool to find pattern searching between two chemical compounds in SMILES/SMARTS format. The tool can also be used to screen a chemical dataset. Perl-Tk is used to build the tool. 6. Chemistry 3D-Builder: A Perl-Tk GUI to generate 3D information of a chemical compound given in SMILES/SMARTS format.

272 12. Papers published or presented in the conferences with reference 9 Thasni K.A, Sivakumar K .C and Priya Srinivas A paper entitled "Mechanism of action of plumbagin in brca1 blocked ovarian cancer cells: an analysis by suppression subtractive hybridization (ssh) and micro array" was presented on Proceedings of the 19th Kerala Science Congress 29-31, January 27-29, 2007

9 Anil Kumar A K, Sivakumar K C, Madhavi Latha G K, Ajay Kumar, Sathish Mundayoor, “Prevalence of KatG Ser315Thr Substitution and Conformation Dynamics of Isoniazid binding among Isoniazid resistant Mycobacterium tuberculosis isolates from Kerala, India”, presented at International Conference on New Horizons in Biotechnology, NIIST, Trivandrum, November 26-29, 2007. (submitted to a special issue of APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY)

13. Initiation of R&D activities in Bioinformatics Please refer paragraph no: 9 14. Details of Training/ Workshop organized and total no. of user trained In-house hands-on training in Molecular Modeling was conducted for 3 days on 15th, 16th and 19th of November. 45 Research Scholars have participated in the programe.

15. Impact shown by your centre on the growth of biotechnology and allied areas. In this you may highlight the details like number of paper published/ number of papers published with the help of your centre, how your centre is promoting various activities of your organization and neighboring institutions, manpower trained, tools developed, patents & copyrights acquired and other services offered etc. 9 Number of papers published: 1 9 Number of papers published with the support of centre: 3 9 Centre provides bioinformatics research and application to research scholars in RGCB. It supports students from neighboring institutions by providing hands-on training and allowing them to use bioinformatics infrastructure facility. Around 30 research scholars in RGCB have utilized this facility. 9 Project Guidance and hands-on training in bioinformatics tools and its application was given to a total of 36 MSc/B.tech students from various institutions/ universities. Hands-on training was given to 70 internal and 16 external students. 9 Databases developed: 11 9 Softwares developed: 10 9 Centre undertakes email server maintenance, network support for RGCB.

16. Future activities 9 Development of databases and softwares relevant to RGCB research 9 Research and development in Bioinformatics. 9 Human Resource Development in Bioinformatics 273

Additional Details: Name of the Coordinator: Dr. Sathish Mundayoor Postal Address: Rajiv Gandhi Centre for Biotechnology, Thycaud PO, Poojappura, Thiruvananthapuram - 695 014, Kerala, India. Phone Number: +91-0471-2342315 Mobile: 09249981969 Email: [email protected], [email protected] Website: http://www.rgcb.res.in

Name of Contact Person(s): Sivakumar.K.C Email: [email protected], [email protected]

274 State Council of Science & Technology for Sikkim Coordinator: B.C.Basistha

1. Summary of the progress made by the centre from its inception Sikkim Bioinformatics Centre in the capacity of Distributed Information Sub- Centre (DISC) under Sikkim State Council of Science and Technology, Department of Science and Technology was established in the year 2001. The Centre actively involves in collection of information on various biological resources, retrieval of biological information and creation and management of databases. The centre serves as an Information Centre for providing in formations on biological resources to the researchers and scholars. The centre also aims in keeping the scientific fraternity abreast with the latest biotechnological advancement and also aims in inculcating the scientific temperament amongst the scholars. The infrastructure of the centre is kept on strengthening with the latest equipments. 512 Kbps leased line internet connectivity has also been established in addition to previously used RF Antenna Internet connectivity provided by the State National Informatics Centre. A new building for Science and Technology in addition to the already existing building is also being constructed to provide better infrastructure facility.

2. Major research activities in Biotechnology and its related fields at your institution

Research activities are being carried out in the field of tissue culture, Vermicomposting and Frankial Biotechnology. Micro-propagation of Cymbidium orchid is carried out on regular basis. Research activities on medicinal and aromatic plants like Geranium (Pelarrgonium graviolense), Asparagus racemose (Kurilo), Patchouli (Pogostemom cablin), and Podophyllum are also being carried out. Awareness programs through trainings, workshops and seminars are conducted at from time to time, IPR, Medicinal plants.

3. Area of Specialization of the centre Tissue culture, Bioinformatics, Database Management System, Medicinal plants and IPR: . 4. Major activities of the centre during the year 2006-07 • The XVIIIth Annual BTISnet Coordinators meet sponsored by Department of Biotechnology, GOI was held successfully at Sikkim at Chintan Bhavan on 3rd and 4th of February 2007. More than hundred participants had taken part in the Meet. It was the first Coordinators meet held in the North East.

• From 10th September 2006 to 16th September 2006 Data Entry Operator along with the Assistant Scientific Officer toured West Sikkim (Kyongsla Alpine Sanctuary, Changu lake and vicinity, Gnathang, North Bengal University & Kalimgpong) for photographic documentation of medicinal and aromatic plants. 275 • Two days training program on “Creation and Management of Biological Database” was held on 7/11/2006 and 8/11/2006. Scientists, lecturers and researchers attended the training program. • Three days training program on “Introduction and Scope of Computational Biology” was held from 3/12/2007 to 5/12/2007. Science graduates, post graduates, research scholars, lecturers and unemployed science (graduates and post graduates) youth were the target groups. Twenty five trainees were trained in the training program. • Animation of biological processes (cell division, protein synthesis, DNA replication) are developed using Flash to help the scholars/students to understand the processes in a pragmatic approach. • Timely release of the scientific news letter “Bio Gyan” is also done by the centre to make the students and researchers aware of the latest techniques in Biotechnology and Bioinformatics and to inculcate a scientific temperament amongst the students. • The website of the Centre along with the Departments is maintained by the Bioinformatics centre.

5. Infrastructure facilities in the Bioinformatics Centre Computer & Communication facility: The Centre is equipped with a dual processor server, P-4 PCs, Two Laptops, CD writer, Scanner, 5100C, DeskJet 810 C and a Xerox machine. Procurement of more PCs is under process.The centre has 24 hours internet connectivity provided by the State National Informatics Centre through RF Antenna along with 512 Kbps leased line internet connectivity provided by Bharat Sanchar Nigam Ltd. Scientific Software packages: Norton antivirus 2006, AVG 7.5, trend Micro Neat suite, PC-illin, Micro media Flash 8 professional, Dream weaver 8. Databases & other information resources The centre has developed database on bio resources of Sikkim Database on 450 species of orchids, 36 species of Rhododendron, and 200 species of medicinal plants has been prepared which are available in CD ROM and shall be launched in website.

6. Details about staff members working in the centre Name of the Design Specialization Period of Absorptio Staff ation Working n Status Mrs. Rabina I.O Biotechnology Three Co- Gurung years & six Terminus months Mr. Bikram Rai T.A Computer Two Years Co- Terminus Mr. Laydong D.E.O Zoology Three Co- Lepcha years & Terminus four 276 months Mr. Prakash D.E.O Botany One year Co- Sharma six months Terminus

7. Types of services provided • The centre acts as an information centre for providing information on various bio resources of Sikkim. • The Centre Library with a good collection of references is used by scholars and researchers. • Free internet facility is provided to the users for searching the biological in formations. • Prepares animations on various biological processes like protein synthesis for better understanding the process. • Student ship is provided to the research scholars undertaking project on Biotechnology and Bioinformatics.

8. Educational activities with details of placement The centre supports scholars pursuing courses in Bioinformatics and Biotechnology.

9. Initiative to validate the outcome of bioinformatics resources Trainings are being conducted at regular intervals; number of trainee attending the training programs is increasing every year and positive response is received from the trainees.

10. Collaborative works/ initiatives Collaborative works with Sikkim Government College in terms of providing computer, internet and library facilities. Collaborative works with North Bengal University, G. B. Pant Institute, Botanical survey of India is being carried out.

11. Databases/ Software packages developed Database on Orchids, Rhododendrons, Medicinal Plants of Sikkim Himalayas. Animation on cell division, protein synthesis etc developed using Flash.

12. Initiation of R&D activities in Bioinformatics The centre has been categorized under “Environment and Biodiversity” and hence takes the initiative to prepare database on various bio resources of Sikkim Himalayas and conducts workshops and trainings on Bioinformatics and Biotechnology. Encourages science graduates, post graduate students and research scholars to take up projects in the field of bioinformatics through studentships.

13. Details of Training/ Workshop organized and total no. of user trained

277 Three days training program on “Introduction and Scope of Computational Biology” was held from 3/12/2007 to 5/12/2007. Science graduates, post graduates, research scholars, lecturers and unemployed science (graduates and post graduates) youth were the target groups. Twenty five trainees were trained in the training program.

14. Impact shown by your centre on the growth of biotechnology and allied areas.

The Bioinformatics Centre, Sikkim plays a leading role in introducing the latest Biotechnological advancements and Bioinformatics to the researchers through trainings, workshops and seminars. Patent in Biotechnology is another aspect of key interest. The centre helps the research scholars by providing informations, library and internet facilities. validating the growing activities of the centre and with more and more research scholars pouring in for facilities of the centre, up gradation of the centre from Distributed Information Sub centre to Distributed information Centre has been made by the centre to the DBT, GOI.

15. Future activities • To bridge the communication gap between the scientific fraternity the centre has taken up the task of preparation of database on profile of scientific community of Sikkim. • Preparation of database on indigenous / traditional knowledge and local health systems (Amjis, Vaids, Bumthing, Phedangba, Jhakri, etc) of Sikkim. • Preparation of Annual working calendar of the centre to streamline the activities of the centre. • Preparation of Software on Chemical Inventory Automation and Library automation. • Database on Profile of Women scientists working in various fields of Sikkim. • Further up gradation of already prepared databases, website and creation of databases on various bio resources of Sikkim. Up gradation of library with more reference books and journals. • To conduct more no of workshops and trainings on Bioinformatics and Biotechnology. Training on “Environment Genomic and Biodiversity “shall be conducted in the month of January 2008.

Additional Details: Shri M. L. Arrawatia, IFS Member Secretary Sikkim State council of Science and Technology Department of Science & Technology, Development Area Gangtok, Sikkim-737101 278

Name of the Coordinator: Shri. B.C.Basistha

Postal Address: Sikkim State council of Science and Technology Department of Science & Technology, Development Area Gangtok, Sikkim-737101 Phone Number: 03592-228370 Mobile: 09434109894 Email: [email protected] www.dstsikkim.gov.in/disc.htm Name of Contact Person: Shri B.C.Basistha Email: [email protected]

279 T. M. Bhagalpur University, Bhagalpur Coordinator : Dr. R.P.Upadhayay

1. Summary of the progress made by the Centre from its inspection The Sub-DIC University Centre of Bioinformatics, T.M.Bhagalpur University was established in the Oct.’05. Since its inception the Centre has developed good infrastructure in the form of three Servers (Mail, Database & Firewall), 15 Computers and other communication equipments. The Sub-DIC has procured various scientific softwares like Windows Server 2003, MS-Office 2000, SQL Server 2000, Borland Turbo C++ Suite, Visual Studio, Emboss, EXOME Blast, EXOME & EXOME ED etc. The Centre is providing the facilities for downloading scientific literature and also to access various online biological databases to research scholars and students in the Centre. So far, about 150 users comprising of teachers, staffs and students of T.M. Bhagalpur University have availed the services of the Centre. The centre is having 512 kbps BSNL Broadband connectivity for Internet. The Center has published a book on "Emerging Fields in Bioinformatics" which was released on 9th April'07 by the Hon'ble Chancellor of Bihar. The database of "Katarni" cultivar of rice has been prepared which will be beneficial for the socio-economic empowerment of the farmers and will also help the researchers in improving of this and other cultivars of rice. The Centre is engaged in preparation of one another database on "Paharia" (a primitive tribal community of Dravidian origin) with the objective to identify the genetic reasons for the gradual decrease in the population. The centre has started regular classes on Computer Application and Bioinformatics for the Post and Under Graduate students of Biotechnology. The center is acting as an integrated information resource on all aspects of Biotechnology research, Molecular Biological data such as Gene Bank, Nucleic Acids and Protein Sequences etc., are accessible over the network from worldwide resources in molecular biology.

2. Major research activities in Biotechnology and its related fields at your institution : A. Genomics • Cytogenetic studies of selected plant species. • Genetic improvement in some selected crop and ornamental plant species. • Damage repair of DNA in animal system. • Gene sequencing of some rare plants (DBT Project). B. Dynamics of Genomics & proteomics • General protein finger printing and isozyme polymorphism

3. Area of Specialization of the centre : Dynamics of genes and proteins.

4. Major activities of the centre during the year 2007-08 The major activities of the centre are as follows: • One book on “Emerging Fields in Bioinformatics” was published by the Centre. • The database of "Katarni" cultivar of rice is being prepared and it will be beneficial for the socio-economic empowerment of the farmers and will also help the researchers in improving of this and other cultivar of rice.

280 • Biochemical and cytological study of "Katarni" cultivar of rice is almost complete and results are encouraging enough to continue the research on katarni. • Another database on "Paharia" (a primitive tribal community of Dravidian origin) residing in and around the Rajmahal Hills of Santhal Pargana near to Bhagalpur District is being prepared with the objective to identify the genetic reasons for the gradual decrease in the population which will certainly help in conserving the gene pool as well as the population of this aboriginal tribal community. • Imparted regular theory and practical classes to the M.Sc. Biotechnology students on Computer Applications & Bioinformatics. • A Bioinformatics club has been established where teachers, researchers and students sits once in month and extent maximum utilization of the resources available at Bioinformatics Centre. The club thus provides a platform for collaborative scientific research work. • The Centre is assisting faculties and students from neighboring departments and college/Institutions in updating their knowledge through different databases / software available in the centre and also providing practical training in Computer based applications, software analysis, computational methods etc to Doctoral and Post graduate students.

5. Infrastructure facilities in the Bioinformatics Centre: A. Computer & Communication facility • Server: IBM Server X Series (260, 236, 226) (Tower) with 17” CRT Monitor • 12 clients workstation: IBM Think Centre with 17” TFT monitor(2), 15” TFT monitor(3), 17”CRT Monitor(7) • One Laptop: IBM ThinkPad Intel P-M Processor 1.66 Hz. Networking Equipments: • Modem: One External, • Internet Connection: 512 kbps BSNL Broadband Connectivity Power Supply: • One SAMTEK 5 KVA Online UPS, One ELNOVA 2KVA Online UPS (2 hrs backup), Twelve ELNOVA UPS 600 VA (15 min. backup) Printer: • One Xerox color laser Printer phaser 6100, One Xerox Mono Network Laser Printer 3500DN, One Xerox Photocopier 5821 with star stabilizer

B. Scientific Software Packages • Exome, Exome Blast, Exome – ED, Widows 2003 Server with xp clients, Red Hat Linux 9.0, Oracle 9i, Rasmol 2.6, Embosswin 0.8, Swisspdbviewer, Gram, Autodock, Make2DB

C. Databases and other Information resources 100 books covering various fields of bioinformatics including genomics, proteomics, structural bioinformatics, drug designing and computational biology etc.

281 6. Details about staff members working in the Centre:

Name Designation Area of Specialization Period of working Dr. R.P.Upadhaya Coordinator Molecular Biology since 1-11-2005 Kumari Vandana Information Officer* Bioinformatics since 03-7-2006 Er. Rakesh Ranjan Technical Assistant* Statistics & Comp. Appl. since 22-6-2006 Mr. Saket Vinayak Data Entry Operator* Comp. Appl. & Hardware since 28-6-2006

* The university has approached State Government for permanent absorption of manpower within the University.

7. Types of Services provided: • Use of databases and software packages required by research scholars and Post graduate students. • Internet access and Email facilities are provided to the faculty, staff, scholars and students of University. • Assisted faculties and students from neighboring departments and college/Institutions in updating their knowledge through different databases / software available in the centre. • Provided practical training in Computer based applications, software analysis, computational methods etc to Doctoral and Post graduate students. • Our team can assist any progressive organization / institute in developing, integrating and maintaining valuable biological data so that it can be accessible in a safe and comfortable manner.

8. Education activity with details of placement: P.G. Diploma in Bioinformatics will begin from this academic session.

9. Initiative to validate the outcome of bioinformatics resources: To be taken care of.

10. Collaborative works / initiatives: Collaborative works are primarily in the area of Biotechnology thus a Bioinformatics club has been established where teachers, researchers and students extent maximum utilization of the resources available at Bioinformatics Centre. The club thus provides a platform for collaborative scientific research work. Such collaborative work in Bioinformatics needs to be further promoted at this Centre. We are preparing a database on Euryale Ferox with the collaboration of National Research Centre for Makhana, Darbhanga Bihar.

11. Databases / Sortware packages developed: To cater to the regional and national needs, the centre has developed a database on “Katarni” a local race of Oryza sative which is famous for its aroma and fineness.

12. Papers published or presented in the conferences with referece: 282 • Upadhyay R.P. & Singh Vandana “Bioinforamtics: a pursuit of Environmental Management” International Symposium on Recent advances in contemporary Biology, Environmental issues & sustainable development page-70, S.K.University, Dumka September 2007. • Upadhyay R.P. & Singh Vandana “Biomarkers in Cancer” communicated in Journal Bioinforamtika. • Upadhyay R.P. & Pan T.K. “Database storage of Cyto-taxonomic assessment and genetic improvement and conservation of germplasms of Reiniwardtia Spp. (Linaceae)”National Symposium on Germplasm evaluation : present trends page-136, Punjabi University, Patiala January 2006. • Upadhyay R.P. & Pan T.K. “Collection, conservation, evaluation and preparation of Database of Germplasms of Bamboos from states of Bihar and Jharkhand” National Symposium on Germplasm evaluation : present trends page-137, Punjabi University, Patiala January 2006.

13. Initiation of R & D activities in Bioinformatics: • Bioinformatics related problems are regularly given to M.Sc. Biotechnology students for their work. • Near Bhagalpur, a primitive tribal community of Dravidian origin called “Paharias”. residing in and around the Rajmahal Hills of Santhal Pargana. This isolated patch of human genome has been selected for investigation and with the objective to identify the genetic reasons for the gradual decrease in the population. The centre is collecting relevant informations for future genomic research to be undertaken.

14. Details of Training /workshop organized and the total number of user trained: Four days training course was organized by the centre on “Retrieval and Analysis of Biological Informations in Genomics & Proteomics”. During the training course, 30 participants (teachers, research scholars and students) from the different Universities of State and outside have participated and rigorous training has been imparted to them by highly trained professionals in the field.

15. Impact shown by your centre on the growth of biotechnology and allied areas: • Papers published with the help of Bioinformatics Centre. • The centre has developed as an Information Hub for whole of the University. • Bioinformatics awareness spread through the Institute web-site and by organizing workshop. 16. Future Activities : During ensuing year, the centre proposes to strengthen infrastructures in terms of software tools for biological data analysis for providing better services to the users. Besides this the following activities will also be undertaken. • Web server development and web site hosting at Institute Server. • Starting P.G. Diploma course in Bioinformatics from next academic session.

283 • To cater to the regional and national needs, the work on the specific databases being currently developed by the centre will continue. • Students will be allotted under the studentship-scheme to accomplish the task in bioinformatics. • To train faculty, students and research scholars who can make use of bioinformatics techniques and tools to enhance the efficiency of scientific research.

Additional Details: Name of the Co-ordinator: Dr. R.P.Upadhayay

Postal Address: Coordinator Sub-DIC University Centre of Bioinformatics T.M.Bhagalpur University, Bhagalpur- 812007

Phone No. 0641-2501753 Mobile: +91-(94312)15481 Email: [email protected] Website: www.bioinformatics-tmbu.org.in

Name of Contact Person: Vandana Email: [email protected]

284 Tamilnadu Veterinary and Animal Sciences University, Chennai Coordinator : Dr.P.Dhanapalan

1. Summary of the progress made by the centre since its inception The Bioinformatics centre of this institution with various inhouse facilities is actively engaged in serving the scientific community with current technical and scientific literature in the field of Biotechnology, Veterinary and Animal Sciences and allied areas.

¾ Information Dissemination information retrieval service since 1992. 50447 research scholars have been benefited. Provided research information to 66 universities and 188 colleges. ¾ Education Offering PG Diploma in Bioinformatics course from 2004-2005 M.Sc bioinformatics course propsoed ¾ Software packages Developed An applicaton tool Information Retrieval Package Student Relational Database Management System (SRDBMS) based on VCI syllabus ¾ Databases created a) Database on abstracts of Research findings on Poultry by TANUVAS scientists (upto 2000) b) Database on abstracts of PG theses (1996-2003) and Database on abstracts of completed research schemes of TANUVAS (1998-2003) ¾ Training Programmes Conducted 25 batches on “Information Retrieval System” and 14 batches on “Bioinformatics and Information Technology” ¾ Studentship/Traineeship projects completed 16 studentship/traineeship projects have been completed

2. Major research activities in Biotechnology and its related fields in our institution

2.1 Completed research schemes in Biotechnology -24 2.2 On-going research schemes in Biotechnology - 8

3. Area of Specialization of the centre : Veterinary and Animal Sciences including Fisheries Sciences

4. Major activities of the centre during the year 2006-2007

4.1 Education activities : * Offering PG Diploma in Bioinformatics course * Bioinformatics papers to M.Phil and M.V.Sc scholars

4.2 Training programmes organized: 5 batches on Information Retrieval System and 2 batches on Bioinformatics and Information Technology.

285 4.3 Offline Information Retrieval : During 2006-2007, 708 scientists/research scholars and during 2007-2008 (Upto Dec 2007), 411 scientists/research scholars have benefited.(Total users: 15186)

4.4 Online Information Retrieval : During 2006-2007, 5636 teaching faculties and research scholars of TANUVAS and for the year 2007- 2008 (upto Dec 2007), a total of 1899 have availed the online facilities (Total users: 35261)

4.5 Establishment of Wetlab At Bioinformatics centre, a Wetlab was established at a cost of 2.3 lakhs with 6.5 lakhs worth of equipments

4.6 512 KBPS Leased line Internet connectivity was renewed at a cost of Rs.1.43 lakhs for the year 2007-2008

5. Infrastructure facilities in the Bioinformatics Centre A. Computer & Communication facility : The center is equipped with various hardware such as * 10 nos of IBM Desktop PCs * 10 nos of Lenovo systems * Black and colour Printers & Scanner * LCD Data Projector & OHP Projector etc. to facilitate online and offline information retrieval and training B. Communication Facilities

1. 512 Kbps leased line connectivity 2. Internet facility : • login id [email protected]. • broadband connection @ 128 Kbps with login id [email protected]. • Seminar Hall with state of art computer aided teaching facility C. Scientific Software Packages and application tools z Exome Version 1.1 , Lasergene Tool z MS SQL server 2000 ,Visual studio.net . D. Databases & other information resources 1. Databases on CDROM : ) VETCD,BEASTCD, MEDLINE , ASFA & FSTA ) BIOSIS , Derwent Biotechnology Abstracts ) CDROM Current Contents (CCOD) on Life Sciences & Agricultural ,Biological and Environmental Sciences ) NUCSSI ) Focus on Veterinary Science and Medicine (1994 to Jan’1999) in diskette

Other Information Sources : * Text Books : 33 Nos * Journals : Advanced BioTech, cheiron Indian Journal of Biotechnology , Biospectrum * Online Access to e -journals a) http://www.blackwell-synergy.com 286 b) http://www.bioinformatics.oupjournals.org c) http://www.scientist.com d) www.doaj.org e) www.highwirestandford.edu 6. Details about staff members working in the centre Name and Designation Specialization Period of Remarks Qualification of Staff working Dr.P.Dhanapalan,Ph.D. Professor and Clinical Medicine From TANUVAS Head and Project 30.4.2007 Staff Coordinator Dr.A.Wilson Aruni,Ph.D, Associate. Microbiology From -do- Professor 11.12.2006 Ms.P.L.Sujatha Assistant. Librarian Information From -do- M.Sc., ADCNET Science, IT 3.11.1999 Ms.T.Mohanasundari Information Officer Library Science From DBT staff M.A.,MLIS 17.12.1990

Ms.V.Malarvizhi Technical Assistant Electronics From -do- D.E, D.I.T Engineering and IT 22.3.1991 Ms.M.Seethalakshmi Data Entry Operator Computer Science From -do- B.Sc, MCA, BLIS and applications, 22.7.1993 library information Science 7. Types of services provided : Ö Conduct of PG Diploma in Bioinformatics – One Year duration Ö Conduct of Training programmes on “ Bioinformatics and Information Technology” and “Information Retrieval System” ÖOnline and offline Information Retrieval Services Ö Database Creation Ö PG course on Bioinformatics and its applications Ö Studentship/traineeship projects

8. Educational activities with details of placement Conduct of PG Diploma in Bioinformatics Courses offered for M.Phil and M.V.Sc (Animal Biotech) students.

Students were placed in teaching & research institutes and pharmaceutical & software companies

9. Initiative to validate the outcome of the Bioinformatics resources

Development of software/application tool 9.1 Information Retrieval Package (IRP) 9.2 Student Relational Database Management System (SRDBMS

10. Collaborative works/initiatives : with the line departments and provided research information to 66 universities, 188 colleges

11. Databases/Software packages developed : a. Databases : i. Abstracts of Post-Graduate Research 1996-2003 ii. Abstracts of poultry research findings of TANUVAS up to 2000 iii. Abstracts of completed research Schemes of TANUVAS (98-2003) 287 b. Software : i. Information Retrieval Package ii. Student Relational Database Management System

12. Papers published or presented in the conferences with reference: (i) Dr.A.Wilson Aruni et al, Molecular modeling of …. Cancer, (ii) P.Thenmozhi et al, Study on phylogenetic … small ruminants (iii) A.Poongodi et al, Insilico study on the … proteins, (iv) A.Wilson Aruni et al, Genome microevaluation ……with avian (v) A.Wilson Aruni et al, Insilico analysis …… isolates of Tamilnadu,

13. Initiation of R&D activities in Bioinformatics : ♣ Research projects for a period of 3 months are being carried out by Students of other Universities on payment basis in the areas of Genomics- Comparative and function genomics

14. Details of training/workshop organized and total no. of user trained a. 14 programmes on Bioinformatics & Information Technology conducted and 246 faculties and research scholars have been benefited b. 25 programmes on Information Retrieval System (IRS) conducted and 402 PG scholars and 189 teaching faculties of TANUVAS have been benefited. (Total 591) c. One training on “Computer Appreciation Programme “ have been conducted and 17 technical staff of TANUVAS benefited).

15. Impact shown by centre on the growth of biotechnology and allied areas: Copy right obtained : Copy right has been obtained for “Information Retrieval Package”, a search engine developed by Mrs.M.Seethalakshmi and Dr.G.Thulasi through NRDC, New Delhi from Register of Copyrights

16. Future activities : i. PG Diploma course in Bioinformatics ii. Proposed to start of M.Sc course on Bioinformatics iii. Conduct of training programme on “Bioinformatics and Information Technology” and on “Information Retrieval System” iv. Training to participants of various in-service training programmes , ICAR, summer institute etc v. Literature retrieval service through offline and online vi. Creation and Updation of database . vii. Conduct of studentship projects on Bioinformatics

Additional Details :

Name of the Coordinator : Dr.P.Dhanapalan

Postal Address : Professor and Head & Project Coordinator 288 Bioinformatics Centre & ARIS Cell Madras Veterinary College Vepery, Chennai – 600 007

Phone Number : 044-25360106/25365418/25381506 ext.264 Fax : 044-25360114 Email : [email protected] [email protected] website :www.tanuvas.tn.nic.in

Name of the contact person: Dr. P. Dhanapalan

289 Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu Coordinator : Dr. P. Balasubramanian

1. Summary of the progress made by the centre from its inception The Distributed Information Sub Centre (DISC) has been functioning in Tamil Nadu Agricultural University since 1989. It is housed in the Department of Plant Molecular Biology and Biotechnology at the Centre for Plant Molecular Biology. In the early years of inception, the DISC was primarily involved in providing access to literature and sequence information via online and offline databases. Trainings were organized annually on different bioinformatics titles to the students and scientists of life sciences. This centre is the first major science and technology network in TNAU to establish linkage between scientific communities at national and international levels.

1. The DISC has established an internet browsing facility @ 512 kbps for the benefit of scientists and students 2. A bioinformatics lab has been established with facilities for sequence analysis, molecular modeling and database development 3. The DISC had so far conducted a total of 27 bioinformatics training programs 4. Curriculum development for MSc (Bioinformatics), B. Tech (Bioinformatics) and for the Open and distance learning PG Diploma program in Bioinformatics 5. Three agriculturally important databases have been created 6. External students research projects are being carried out

2. Major research activities in Biotechnology and its related fields at your institution The Department of Plant Molecular Biology and Biotechnology of TNAU conducts research in the following areas for the genetic enhancement of crop species.

1. Development of genetically modified egg plant with cry 1Ac against shoot and fruit borer 2. Genetic engineering of rice cv. IR64 for drought and salinity tolerance using the gene for trehalose biosynthesis 3. Nutritional improvement in rice: Golden rice program and Iron enrichment in rice through transgenic approach 4. Genetic engineering of rice for pest and disease resistance 5. Regeneration and genetic transformation of cotton, banana, tomato, papaya and groundnut 6. Genetic engineering and marker assisted selection for low phytate content maize 7. Marker aided selection for rice yellow stem borer resistance, mapping of genes associated with brown plant hopper (BPH), white backed plant hopper (WBPH) and bacterial leaf blight (BLB) resistance in rice 8. QTL mapping and marker aided selection for drought tolerance in rice and cotton 9. Isolation and characterization of cry genes from native Bt isolates 10. Characterization of root proteome of rice for water stress

290 11. Cloning and characterization of abiotic stress inducible promoters from rice 12. Database on upstream sequence of drought/ salt stress inducible genes in rice 13. Study of the structure function relationships in GUS

3. Area of Specialization of the centre: Agricultural Biotechnology 4. Major activities of the centre during the year 2007-08 Research and training in bioinformatics have been major activities of this centre. Three databases have been successfully developed. They include: Rice Germplasm Database (a database on TNAU released rice varieties), Salinity Stress in Rice (a comprehensive database on salinity stress in rice) and Sprome: A database on abiotic stress inducible promoters in rice. Training to the students on bioinformatics tools have been done. Besides, our faculty members have delivered guest lectures on bioinformatics titles to the BIF centre at the University of Calicut, Kerala. Maintenance of the bioinformatics lab and other infrastructure such as ensuring internet connectivity for the use of students and staff are some of the other activities. Further, the DISC has been instrumental in updating the curriculum of the B. Tech (Bioinformatics) during this academic year. Also, we have taken up to host a web page exclusive for the bioinformatics centre, TNAU.

5. Infrastructure facilities in the Bioinformatics Centre A. Computer and communication facility 1. Ten Intel Core Duo 2.0 computers connected to an IBM server is used for bioinformatics research purpose 2. Another ten Pentium IV machines are connected to an Intel Xeon server and used for bioinformatics teaching and training activities 3. A 512 kbps internet connectivity has been established exclusively for the user centre routed through an IBM proxy server 4. A Sun biocluster with 4+1 nodes have been purchased from the financial support of TNAU for specific bioinformatics applications such as molecular dynamics and docking 5. An Apple workstation caters to molecular modeling studies 6. UPS (5 + 5 Kva) provides uninterrupted power supply to the user centre 7. HP color, mono printers, scanner are available B. Scientific software package Name Purpose Mapmaker/Mapmaker QTL Linkage map construction and QTL analysis IRRISTAT for windows Statistical analysis of experimental data Reference manager Literature reference data base Adobe Photoshop, Adobe Photo editing and documentation Acrobat professional EMBOSS, BioEdit, Exome Analysis of protein and nucleotide sequence Exome BLAST, ClustalX RasMol, AutoDock 4.0 Modeling and Docking Discovery studio (selected modules) 291 MS SQL server For database backend Visual Studio For database front end BioSuite Sequence analysis and molecular modeling Genocluster (server edition with Sequence analysis ten user license) Windows 2003 server + twenty For networking client license

C. Databases and information resources On-line/Off-line information retrieval: The facilities offered in respect of information retrieval are being used extensively by the scientists and students of TNAU and other institutes. Internet based access to various biological databases is being followed.

6. Details about staff members working in the centre (Name of the staff, Designation, Specialization and period of working. Please indicate their absorption status)

Mr. G. Kousikan SRF Dec 26th 2006 Not absorbed (Systems (resigned on April Administration) 2007) Dr. N. Rajinimala SRF April 2007 - Not absorbed (Bioinformatics) resigned Mr. M. Sujit Kumar JRF (Systems June 2007 - till date Not absorbed administration) Ms. Sri Vidya SRF Oct 2007 - till date Not absorbed (Bioinformatics)

7. Types of services provided 1. E mail access and web browsing 2. Literature search and retrieval 3. Annual training programs 4. Students project work in bioinformatics 5. Students thesis work 6. Biological database development 7. Bioinformatics research 8. Statistical analysis

8. Educational activities with details of placement The Department of Plant Molecular Biology and Biotechnology had started an MSc program in Bioinformatics in the year 2004. Students with bachelor degree in agriculture and allied sciences are eligible to join this program. The curriculum encompasses the basics of computer programming, molecular biology and genetics. The core subjects include structural and functional genomics, computational systems biology and database management systems. From the academic year (2006-07) a four year undergraduate program B. Tech 292 (Bioinformatics) had been started in this department. Besides, a one year PG Diploma program in Bioinformatics had been started as an distance learning course. So far two batches of 13 MSc (Bioinformatics) students had passed out, most of them are pursuing further research and some have joined software company.

9. Initiative to validate the outcome of bioinformatics resources-not yet 10. Collaborative works/ initiatives Industry interactions 1. ADVANTA India Ltd., Hyderabad 2. Mahyco Research Foundation, Maharastra 3. RASI seeds, Attur, Salem dt.

Interactions with other institutions 1. IRRI, Philippines 2. National Institute of Agrobiological Sciences, Japan 3. Cornell University, USA 4. IISC, Bangalore 5. Delhi University (South campus) 6. Madurai Kamaraj University, Madurai 7. Sugarcane Breeding Institute, Coimbatore 8. National Research Centre for Banana, Trichy 9. Central Tuber Crops Research Institute, Trivandrum

11. Databases/ Software packages developed Rice Germ plasm database, Salinity Stress in Rice database and Sprome: A database on abiotic stress inducible promoters in rice 12. Papers published or presented in the conferences with reference Raghu et al. 2007. Morphological and simple sequence repeats (SSR) based finger printing of south Indian cassava germplasm. International Journal of Integrative Biology, 1: 141-149. Senthil. 2007. Genomic tools for germplasm characterization. In: Strategies for utilization of plant resources in Asian countries, 1 – 2 Nov 2007, Korea. Elayabalan et al. 2007. Towards engineering resistance against banana bunchy top virus through RNAi approach. In: Two day conference on Biotechnology for human welfare, 20 -21 July 2007, Coimbatore Bharani et al. 2007. Bacterial leaf blight resistance genes pyramiding through molecular marker assisted selection in rice (Oryza sativa L.). In: 2nd International conference on Rice for the future, 5 – 9 Nov 2007, Thailand. Kalaiponmani et al. 2007. Standardization of somatic embryogenesis and regeneration in banana cultivars Rasthali (AAB) and Poovan (AAB). In National conference on banana, 25 - 28 Oct 2007, Tiruchirapalli. Elayabalan et al. 2007. Initiation of embryogenic cell suspension and regeneration in hill banana virupakshi or sirumalai (AAB) through different explants. In: In National conference on banana, 25 - 28 Oct 2007, Tiruchirapalli.

13. Initiation of R&D activities in Bioinformatics-research has been initiated

293

14. Details of Training/ Workshop organized and total no. of user trained - The annual training program in bioinformatics is yet to be conducted for this year

15. Impact shown by your centre on the growth of biotechnology and allied areas The Department of Plant Molecular Biology and Biotechnology has been into teaching and research on Biotechnology for the last two decades. It has been mainly involved in transgenic research and molecular breeding for ultimately improving crop plants against biotic and abiotic stresses. The department currently offers B. Tech programs in Biotechnology and Bioinformatics, Masters programs in Biotechnology and Bioinformatics and a PhD program in Biotechnology. The students of this department mostly make use of the bioinformatics centre. Besides, the facility is also extended to outside researchers for carrying out their research projects. A total of six outside students were admitted this year for carrying out their project work in bioinformatics. Further, this centre has developed three databases which are agriculturally important. Also, a patent has been filed towards patenting an indigenously cloned chimeric Cry2A protein of Bacillus thuringiensis with higher insecticidal activity.

16. Future activities: Development of a transcription factor database, and strengthening research in bioinformatics Additional details : Dr. P. Balasubramanian Director (CPMB) Coordinator (DISC) Centre for Plant Molecular Biology Tamil Nadu Agricultural University Coimbatore – 641 003

Phone (O) : 91 - 422 - 6611262 Fax : 91 - 422- 2431672 Email : [email protected]

294 Tropical Botanic Garden and Research Institute Palode, Kerala Coordinator : Dr. P. N. Krishnan

1. Summary of the progress made by the centre from its inception

The Department of Biotechnology, Govt. of India has sanctioned a Sub-DIC to TBGRI in 1998. Since its inception, the Sub-DIC (Centre) has been focused on biodiversity informatics particularly on plants and its environments. The Centre has developed several globally competent software packages for the organization of biodiversity data, its analysis, modeling and interpretation. The Centre also gathered / generated mammoth quantity of valuable data and organized into databases and made available to the users. Salient contributions of the Centre are (1) Developed five software packages for biodiversity data organization, analysis and interpretation and made available on the web for free access/download. (2) Developed seven databases related to biodiversity; primary data of about 1300 plants and detailed data of 700 plants were incorporated into the database and made available on the web. (3) Bioinformatics publications - three papers in peer reviewed journals, two papers communicated, 18 papers in seminars/symposia/ workshop proceedings and two training manuals; 32 papers were published by the scientists of TBGRI using the facility. (4) Human Resource Development - 45 students from various institutions were carried out their M.Sc./M.C.A/B.Tech. dissertation / project works in the Centre, 12 students were trained for a period of six months with the support of DBT studentship, 7 short-term trainings were conducted and trained 160 personnel, organized 3 National seminars and 2 National workshops, One 21 days training for college teachers, and the scientists of the Centre delivered 26 invited lectures to various institutions. (5) Developed three web sites for TBGRI and a web portal for DBT and periodically up-dating information on these sites. (6) In order to extend the facility to more number of users and interacting with IT industries and initiating collaborative R & D ventures, the centre has established an extension centre near Kerala University and Technopark Thiruvananthapuram, where the R & D programmes are going on. (7) The Centre has also initiated programmes on Barcoding of Life Forms.

2. Major research activities in Biotechnology and its related fields at your institution

The Biotechnology and Bioinformatics division of TBGRI currently focusing on the following R & D areas: (1) Conservation Biotechnology, (2) Bioproduction of plant specific compounds, (3) Bioprospecting and DNA-based technologies, (4) Bioinformatics, (5) Plant tissue culture based commercial propagation, (6) Barcoding of life forms, and (7) Training, extension and conventional Biotechnology

3. Area of Specialization of the centre Bioinformatics and Biodiversity Data Management

4. Major activities of the centre during the year 2007 - 08 • Primary data such as taxonomic details, local name, habit, distribution, phonological details, conservation status, details of useful parts, economic 295 importance, photographs, etc. of 700 plant species conserved at TBGRI campus were collected and organized into a web enabled database. • Field exploration trips to sacred groves of Thiruvananthapuram district were conducted and colleted detailed data and incorporated into the database. www.tbgri.in/sacredgroveonline • Incorporated primary data of 1300 endemic plants of India into the Plant Info database, documentation of photographs is in progress. • Developed a software package for organizing the data of endemic plants of India. The quality testing of the software package is in progress. • Initiated the development of a software package for herbarium database organization. • Reshaped and updated information on the websites www.bioinfotbgri.org and www.tbgri.in • Initiated a project on Barcoding of Plant species. • Maintaining BTISNet publication and library resource web portal. • Provided facility and guidance to 5 M.Sc Bioinformatics students for dissertations.

5. Infrastructure facilities in the Bioinformatics Centre A. Computer & Communication facility SI. Item No. of Total No units No. of Units 1. Web server (IBM) Pentium IV , III 1, 1 2 2. PCs Pentium II, III , IV 3, 2, 9 14 3. Laptop computers 1 1 4. Printers: HP Laser jet 2100, 2840, Inkjet, TVS 345 1, 1, 1, 1 4 dotmatrix 5. 2 KV UPS, 5 KV UPS 2, 1 3 6. LCD projector 1 1 7. LAN connectivity within the Bioinformatics Centre & 1 Leased line internet connection 512 Kbps

B. Scientific Software packages : Nil C. Databases & other information resources: Nil

6. Details about staff members working in the centre SI. Name Designation Specialization Periods of No. Working 1 Dr. S. Sreekumar Information Ph. D. (Botany). Experience Since 2001 Officer / in SQL, MS access, .net, scientist B VB; Macromedia, Photoshop & HTML. 2 Dr. C. K. Biju JSA / Ph. D. (Botany), Experience Since 2001 Technical in SQL, MS access, .net, Assistant VB; Macromedia, HTML & Photoshop 3 Miss. Sawmiya Das D. E. O M.Sc. Botany & PGDCA June 2005 * Absorbed as regular employee of the institute 7. Types of services provided Web server, Internet, guidance for M.Sc. / M.C.A. dissertation, data analysis for research papers, library, training, web portal for BTIS Centres, Web sites maintenance and information updating.

296 8. Educational activities with details of placement Forty five students were completed their M.Sc / M.CA dissertation works, of these, 6 of them working as teachers, 4 of them doing research work and 10 of them got placement in private entrepreneurs. Information about others is not available.

9. Initiative to validate the outcome of bioinformatics resources A committee comprising software expert, subject expert on the area of Taxonomy, Biotechnology and Conservation biology is functioning to evaluate the outcome of the centre.

10. Collaborative works/ initiatives The centre joins with apex centre and developed the web portal system for BTISNet Publications and Library resources.

11. Databases/ Software packages developed

Plant Info version – I: An online database package for organizing a centralized digital database including all information related to plants and its environment. Currently, the database comprises details of about 300 plants and taxonomic categorization of 1300 plants . www.tbgri.in/plantinfo Seed Pack version – I: Software package for the management of Seed Bank data. www.tbgri.in/seedpack LitFriend version – I: Software package for the personalized management of bibliographic data and its citation. www.tbgri.in Fungal Database – Meliolales: Database comprises information about 400 species of Meliolales reported from India. www.tbgri.in/fungi Garden Info version – I: Software package for the management of germplasm collection and monitoring data of botanic gardens & its networking. Using this package TBGRI has digitized the details of 800 live species conserved in the campus. www.tbgri.in/gardeninfo BioLit: Software package for the management of publications of an institution in digital form. Biotechnology publications of TBGRI are made available to the public using this tool. www.tbgri.in/biolit Sacred Groves of Kerala: An online database package for digitizing data of sacred groves of Kerala. Currently the database provides online access to information on more than 150 sacred groves of Kerala and 400 plant species. www.tbgri.in/sacredgrove Wild Ornamental plants of the Western Ghats: Database comprises information on wild ornamental plants of the Western Ghats. This database is created in CD version. BTISNet Publication & Library: A Web portal site connecting all BTIS Centres and providing centralized access to publication and library resources. www.tbgri.in/bioinfopub Endemic plants of Kerala: The database comprises detailed information about 284 endemic plants reported from Kerala. The database can be made available on the web during the month of April 2008 onwards.

12. Papers published or presented in the conferences with reference

297 Sreekumar S., Biju C. K., Hari Sankar G. and Krishnan P. N.( 2007) LitFriend: A Software package for personalized management of bibliographic information and its citation. Current Science 93 (4): 456-458. Sreekumar, S, Biju, C.K. and Krishnan, P.N. (2007) Biological database organization in Microsoft Access. Training manual, published by TBGRI, Thiruvananthapuram. Sreekumar S, Biju Ck and Krishnan P N. (2007) Bio informatics an overview, Rural Agricultural work experience programme organized by Kerala Agricultural University, College of Agriculture, Padanakkad on 6th September 2007. Biju CK, Sreekumar S, and Krishnan P N. (2007) Biodiversity with special reference to agriculture, Rural Agricultural work experience programme organized by Kerala Agricultural University, College of Agriculture, Padanakkad on 6th September, 2007. Sreekumar S, Biju Ck and Krishnan P N. (2007) Biodiversity with special reference to agriculture, Rural Agricultural work experience programme organized by Kerala Agricultural University, College of Agriculture, Padanakkad on 7th September, 2007. 13. Initiation of R&D activities in Bioinformatics The Centre has developed several software tools for biodiversity data documentation, retrieval, analysis and interpretation. Currently, the centre is engaged in the development of protocols for barcoding of plant species and a web portal for its data dissemination and analysis.

14. Details of Training/ Workshop organized and total no. of user trained Organized a 5 days National workshop on ”Biodiversity Database Organization and its Management” from 16th to 20th July 2007. 15 participants including senior scientists, professors and college lectures were participated in the workshop.

15. Impact shown by your centre on the growth of biotechnology and allied areas. The major impacts made by the centre are shown below

Total Number i. Software packages and databases developed : 5, 7 ii. Number of plant species primary data made available : 1300 on the web iii. Number of plants detailed data made available on : 700 the web iv. Web sites developed and maintained : 3 v. Web portal developed and maintained : 1 vi. Papers published in peer reviewed journal and :3, 2 communicated (Bioinformatics papers only) vii. Papers published in seminar/symposia workshop : 18 abstract /proceedings viii. B.Tech., B.E, M.C.A and M.Sc. bioinformatics : 45 dissertation carried out in the Centre ix. Students trained with DBT studentship : 12

298 x. Short term training programme organized to teachers : 7, 160 and research students and no. of personnel trained xi. National seminars / symposia / workshop organized :3 , 2 by the Centre and in collaboration with other institutions xii. Three week training course for college teachers : 1 xiii. Students’ Ph.D. thesis and Biotechnology papers : 8, 32 published with the support of the Centre xiv. Average number of personnel using the facility for : 300/p. m. internet access and other services xv. Invited lectures delivered by the Bioinformatics staff : 26 in various educational institutions

16. Future activities • To establish a centre for barcoding of plant species and a National web enabled barcoding data (sequence data) repository for the identification of plant species. • To develop a National web portal for biodiverisity Informatics and interlink the available information resources, thereby the users can access the biodiversity related information from a single window. • To develop a National database repository for biodiversity informatics comprises the preliminary data of plants such as taxonomic position, distribution, phenological and physiological data, economic importance, images, etc. • To develop necessary computational tools / software packages for database organization, data mining, data analysis and interpretation, and also develop computational models leading to novel discoveries. • To continue the ongoing database organization and complete the organisation of comprehensive database including all information of plants growing in Kerala State. • To establish genetic sequence database of the intraspecific variants of the endemic plants of the Western Ghats. • To develop TBGRI as a Nodal Centre for National Plant diversity information and computational solution provider for Biodiversity data management, data analysis and interpretation.

Additional Details:

Name of the Coordinator: Dr. P. N. Krishnan Postal Address: Biotechnology and Bioinformatics Division, TBGRI, Palode, Thiruvananthapuram Phone Number: 04722869622 Fax No.: Email: [email protected] , [email protected] Website: www.tbgri.in , www.bioinfotbgri.org , www.tbgri.in/stec.htm

299 Name of Contact Person(s): Dr. S. Sreekumar, Scientist B & Information Officer, Saraswathy Thangavelu Extension Centre, TBGRI, Puthenthope, Thiruvananthapuram 695 586. Email: [email protected]

300 University of Calcutta, Kolkata Coordinator : Dr. Subhasis Mukherjee

1. Summary of the progress made by the center from its inception:

This center started functioning as a modest Sub-DIC since 1993 and had been upgraded to a full DIC in 2003. This Centre also coordinates to a great extent the One Year Advanced Diploma Course in Bioinformatics which has been running since 1999-2000 academic session. This center has been made an integral part of the host institute, providing both extra-mural as well as intra-mural support to the appropriate institutions and department. This center is involved in all allied activities of this region.

2. Major research activities in Biotechnology and its related fields at your institution: i. Spinal Chord Regeneration in Zebrafish. ii. Development of Antimicrobial drugs iii. Study of microbial biodiversity iv. RNMV-induced growth promotion in jute v. Plant Somatic embryo genesis

3. Area of specialization of the center: i. Human Resource Development – The center conducts a one year advanced diploma course in bioinformatics and plays a major role in running a two year M.Sc. course on Bioinformatics and Biophysics. ii. Research – Structural Bioinformatics and Systems Biology

4. Major activities of the center during the year 2007-2008

The DIC has provided facility for research for the life science groups of the university. The Bioinformatics group of the department has been able to publish nine papers during this period. One database on transcription regulation by Abscisic acid in plants was developed. The center has already organized some lectures on drug design, biochemical pathway modeling and transcriptomic analysis of zebrafish embryo development. The center is also planning to organize a workshop in March’08 on Systems Biology. Four students had been registered to submit their doctoral work on various aspects of Bioinformatics during the said period from the bioinformatics group, serving as the nucleus of the DIC and the One year Advanced Diploma activities.

5. Infrastructural facilities of the Centre

a. Computer and communication: The center has a dedicated link of 2mbps for exclusive use of the teaching and the research activities of the center. The center is also serving as the nodal hub of the in-campus and trans- campus network backbone of the host institution. The center, through the in-campus web facility, has a 200% redundancy as far as the communication is concerned. 301 b. Scientific software packages: The center uses the GCG packages as gifted by the DBT. A large number of bioinformatics tools like BIOPERL, EMBOSS, PHYLIP,CLUSTALW, MODELLER, AUTODOCK and GROMACS, etc. are available to researchers and students. c. Database and other information resources: ‘TRABAS’,detailing the effect of ABA induction on a plant's transcriptome, developed and maintained in- house. It is also available at www.bioinformatics.org/trabas.

6. Details about the staff members

SL. NAME OF THE DESIGNATION WORKING ABSORPTION NO STAFF SINCE STATUS (Y/N)* 1. Ms LUNA MITRA JUNIOR 2000 NO ASSISTANT 2. Ms BARNALI DO 2000 NO MANNA

7. Types of services provided: Assisting the research and educational activities in the university.

8. Educational activities with details of placement provided: i. The center conducts a one year advanced diploma course in bioinformatics and plays a major role in running a two-year M.Sc. course on Bioinformatics and Biophysics and also organizes seminars on modern areas of biology related to bioinformatics. ii. The students are normally placed in prestigious national and international laboratories (TIFR, SINP, BI, Univ. of Maryland, etc.) and related industries (Dr. Reddy’s laboratory, TCS).

9. Initiative to validate the outcome of the bioinformatics resources. Presently only at the level of research publications.

10. Collaborative work/ initiatives:

i. Karolinska Institute, Sweden ii. Institute of Bio-organic Chemistry, Poland iii. University of California, Davis iv. With Department of Science and Technology, Government of West Bengal, in areas of IPR. v. With Bengal Engineerring and Science University in the area of system methodologies. vi. With Machine Intelligence Unit, India Statistical Institute, Kolkata in the area of System Biology and Bioinformatics.

11. Database/ Software packages developed

302 A fully featured database entitled "Transcriptional Regulation by ABA Signaling (TRABAS)” detailing the effect of ABA induction on a plant's transcriptome was hosted on www.bioinformatics.org/trabas.

12. Papers published /presented : 1. Hydrophobic, hydrophilic and charged amino acids network within protein, Md. Aftabuddin and S. Kundu (2007) Biophysical Journal, 93, 225-231 2. Dynamics of Leucine-rich Repeat Proteins (2007) A. Lahiri and S. Basu. Biophys. Rev. Letts (In press) 3. Interactions of HIPPI, a molecular partner of Huntigntin… (2007) P. Majumdar, A. Choudhury, M. Banerjee, A. Lahiri and N.P. Bhattacharyya. FEBS J. DOI 10.1111/j.1742-4658.2007.05922.x 4. Molecular Dynamics simulation of the preferred conformations of 2- Thiouridine in aqueous solution (2007) A. Lahiri, J. Sarzynska, L. Nilsson and T. Kulinski. Theor. Chem. Acc. 117, 267 5. Physics in Medical Science – appreciating Physics in Everyday Life, Subhasis Mukhopadhyay, NCSTC-NETWORK, Department of Science and Technology, Government of India, New Delhi, 2007 6. Gene Interaction - An Evolutionary Biclustering Approach -- Sushmita Mitra,; Ranajit Das,; Haider Banka,; Subhasis Mukhopadhyay, Information Fusion, ( in Press) 7. Identification of Gene Regulatory Pathways: A Regularisation Method – Mouli Das, Rajat De and Subhasis Mukhopadhyay, PreMI-07, Lecture Notes In Computer Science, pp 425-432, 2007, Springer-Verlag 8. Evolutionary Biclustering with Corelation for Gene Interaction Networks – Ranaji Das, Susmita Mitra, Haider Banka and Subhasis Mukhopadhyay, , PreMI-07, Lecture Notes In Computer Science, pp416-424, Springer- Verlag 9. Jolly Basak, Sudip Kundu and Amita Pal (2007) Phylogenetic Analysis of Divergent Structural Organization of Nucleotide Binding Domain Encoded by Resistance Genes and Gene Homologs in the Family Fabaceae. Indian Journal of Biotechnology 6, 9-17 Conference Presentation: a) Analysis of regulatory element and functional class associations: Comparison in Arabidopsis and other plants –Ananyo Chaudhury and Ansuman Lahiri at European Conference on Computational Biology (2007) b) Domain Combinations in Leucine-rich Repeat Proteins – Anindita Banerjee, Ananyo Chaudhury, Soumalee Basu and Ansuman Lahiri at European protein Society Meeting, Stockhlom (2007)

13. Initiation of the R&D activities in Bioinformatics Structural Bioinformatics and Systems Biology

14. Details of the Training workshop A lecture series on drug design by Prof. Indira Ghosh, Pune University was organized. Total number of users trained was fourteen.

15. Impact shown Number of papers published in the area of bioinformatics and computational biology are nine. Manpower trained: 30 303 Tools developed: TRABAS, a database and AminoNet, a software for network analysis of amino acid residues in protein structures.

16. Future Plan

The TRABAS database and its subsequent modifications will be hosted in one of the servers of the Bioinformatics Centre, University of Calcutta. An initiative is being taken by the center to make Systems Biology a thrust area for teaching and research in this institution.

Additional Details :

Coordinator: Dr. Subhasis Mukherjee Postal Address: Department of Biophysics, Molecular Biology and Genetics University of Calcutta, 92 APC Road, Kol-700009 E-mail: [email protected]

304 University of Kashmir, Hazratbal, Srinagar, J&K Coordinator : Prof. K. I. Andrabi

1. Summary of the progress made by the center from its inception • The Center has developed software packages like INSUSENZ (for computing Peripheral Insulin sensitivity using OGTT data) and an application LIBSOFT (for library automation). • Developed a database on “Medicinal & Aromatic Plants” of J&K State. The database is available on our website www.bioinfoku.org • Successfully conducted seven national level workshops. • Has its own VSAT (SCPC) with 1 Mbps bandwidth for Internet connectivity. • Has been providing services to various Institutes of the valley and Science departments of the University campus. • Has acquired several Software packages related to biosciences and the research scholars from Biosciences field are getting benefited from these packages. • Has started one-year (two semesters) PG diploma in Bioinformatics course.

2. Major research activities in Biotechnology and its related fields at your institution

• Sequence variations in disease related genes and its relationship with ethnicity • Molecular evaluation of oxidative stress as a marker for disease. • Potential of medicinal herbs to harbour signal transduction modulators. 3. Area of Specialization of the Centre: Polymorphism studies in pure ethnic population [Kashmir]. 4. Major activities of the center during the year 2006-07 • One of the faculty member of Department of Biotechnology, has been deputed for six months training in Bioinformatics at IBI Solutions Chandigarh • Successfully organized a National level workshops held on “Introduction to Genomics and Proteomics” in March 2007. • The Centre arranged series of online lectures related to Bioinformatics for P.G. students of Department of Biotechnology, Kashmir University, wherein faculty of Bioinformatics Centre, JNU, New Delhi were roped in. • The center procured Sun Fire X2100 compute server on which BLAST,FASTA,CLUSTALW have been locally installed .This is a step towards building a full BIOX package(Integrated bioinformatics software & hardware solution) • Procured CLC Combined Workbench, a package enabling users to make a large number of advanced proteins, DNA, and RNA sequence analyses, combined with smooth data management, and excellent graphical viewing and output options. 5. Infrastructure facilities in the Bioinformatics Center A. Computer & Communication facility

305 • The Center has its own VSAT (SCPC) with I Mbps bandwidth from Ernet. • Has Pentium D desktop with TFT monitors equipped computer lab. • IBM Xeon Server Core Duo and SUN Fire X2100 compute node B. Scientific Software packages • Properties of Organic Compounds Ver.6.0 • InStat • ChemSW • EnzFitter • Sigma Plot graph library • GraFit Ver. 5.0 • Softwares available online

C. Databases & other information resources • The center recently procured Sun Fire X2100 compute server on which BLAST,FASTA,CLUSTALW have been locally installed. This is a step towards building a full BIOX package(Integrated bioinformatics software & hardware solution) • CLC Combined Workbench. • Current Content Databases a) Agriculture, Environmental Sciences and Biology. b) Life Sciences. 6. Details about staff members working in the center Name Designation Specialization Period of working /Absorption Molecular Coordinator 18 years Prof. K.I. Andrabi Biology Application & Server side Programming 4 + years Information (Java (Yet to be Mr. Mujtaba Shafi Officer technologies), absorbed) Linux, & Networking To be Advertised Technical

Assistant 7 years. Data Entry Ms. Arifat Ara (Yet to be Operator absorbed) 7. Types of services provided • Literature browsing and web data mining for all research scholars of the university. • Computational lab facility for post-graduate students, research scholars and faculty of the science departments in general and biotechnology in particular.

306 • Project training pertaining to Bioinformatics tools, databases, data access and data mining. • Access to BIOX grid package (integrated software/hardware solution from SUN Microsystems) for Molecular Biology.

8. Educational activities with details of placement • The center in addition to “PG Diploma in Bioinformatics” is offering research-based activities to scholars/P.G Students of Science Faculty. Of late research scholars of Department of Biotechnology, University of Kashmir has been provided with the access to BIOX software package (BLAST, FASTA, CLUSTALW AND VARIOUS MOLECULAR MODELLING TOOLS). • The centre annually conducts national workshops and till date about 140- 160 personnel have been trained in various fields viz; computational biology, Proteomics, Genomics and web based Bioinformatics tools

9. Initiative to validate the outcome of Bioinformatics resources 10. Collaborative works/ initiatives • Centre collaborates with the department of biotechnology to provide facility for one of the computational courses in M.Sc Biotech programme. • Centre ha entered into s collaboration with a U.S based software company BQE Inc. to explore the possibility of developing user-friendly data mining software.

11. Databases/ Software packages developed • The Center has developed a database on " Medicinal & Aromatic Plants of J&K". The database has a GUI based Interface with Visual Basic as its front end. Complete information on more than 133 plants has already been collected. The information consists of folklore medicinal uses, chemistry, medicinal uses, botany, geographical distribution etc. A web-enabled Interface of the Database has also been developed and has been made online on the centers website.. • A software program "INSUSENZ" for computing the peripheral insulin sensitivity from oral glucose tolerance test data has been developed. • Web enabled interface of “Medicinal & Aromatic Plants in J&k” has been developed using Java server pages (JSP) technology on Macromedia Jrun4 Server and is available on intranet.

12. Papers published or presented in the conferences with reference Research Papers published in peer reviewed journals by using Bioinformatics Support • Ishfaq Ahmed, Rohina Jan,,Riyaz A Pandit ,Tariq Qureshi & Khurshid Andrabi, (2007), Exon10 Polymorphism in TGF Beta Gene does not Assxcoaite with High Myopia in Pure Ethnic Pedigrees.Biochemical Genetics (In press). • Peerzada Kaiser, Chand Raina, Rajinder Parshad,,Sarojini Johri, Vijeshwer Verma,Khurshid I. Andrabik and Ghulam N. Qazi , Protein Expression and Purification , 45(2), 2006, 262-268.

• Mahrukh Hameed, Basir Ahmad, Khalid Majid Fazili, Khurshid Andrabi and Rizwan Hasan Khan, Journal of Biochemistry, 141(4), 2007,573- 583.

307 Bioinformatics Research Papers Published, in peer Reviewed journal by your centre. Masood & Mujtaba Shafi, Bioinformation 1(2): 56-57 (2005).

13. Initiation of R&D activities in Bioinformatics 14. Details of Training/ Workshop organized

Topic Year No. of participants PC Familiarization & applications 2000 13 Introduction to Bioinformatics & Biostatistics-I 2001 18 Computer fundamentals & Networking 2001 06 Introduction to Bioinformatics & Biostatistics-II 2002 14 Bioinformatics & Internet 2003 17 Internet Resources & Statistics for Biologists 2004 15 Bioinformatics: Computer Methods in Biology 2005 15 Introduction to Genomics and Proteomics 2007 21

15. Imapct by the centre on the growth of biotechnology • The centre has been consistently organizing workshops to create awareness about the potential of biotechnology in the state. • The availability of data analysis facility especially in molecular analysis has prompted many researchers to switch their interests in biotechnology. • Our collaboration with the researchers of Deptt of Biotechnology has been quite productive yielding data of highest quality.

16. Future activities • The centre envisages to increase its software and data analysis resource to cater to requirements in other areas of biotechnology viz Proteomics, Molecular Modeling, Drug Designing etc • The center envisages starting a Postgraduate program in Bioinformatics from next year. Additional Details Name of the Coordinator: Prof. K.I. Andrabi Postal Address. Professor & Head, Department of Biotechnology & Coordinator, Bioinformatics Center, The University of Kashmir, Hazratbal, Srinagar(J&K) -190 006. Phone Number: 194-2428723 Fax No.: 194-2428723 Email: [email protected], [email protected] Website: www.bioinfoku.org Name of Contact Person(s): Prof. K.I. Andrabi Email: [email protected], [email protected] University of Pune, Pune Coordinator : Prof. Indira Ghosh

1. Summary of the progress made by the centre from its inception Since established in 1987 Bioinformatics centre, University of Pune is conducting the research in molecular modeling, prediction of 3D structures and structure based drug design in bio-macromolecules. Since 2003 with the aid of COE grants it has expanded its research area in Genome assembly and Comparative Genomics, Metabolic pathway analysis, organization and interaction of proteins in Virus, epitope mapping, Chemo-informatics and 308 target based drug design. During the academic year 2006-07 the Centre has carried out several activities, viz. training, development of new databases and programs, organization of national and international conferences and workshops. Prof. GNR Teaching Complex along with the main building, covering two floors in each, houses state-of-art three lecture halls (each of 60-70 students capacity), three in- silico laboratories for M.Sc.& CRCDM students and up-to-date library. Since 2002 we have completed 4 batches (22-30 students/year) of M.Sc students (100 Credits, 2 years course) along with 4 batches of ADB students (22 each batch) (52 credits 1 year course). These students have completed a number of projects (30-40/year). The center also supports Bioinformatics related all the curriculum activity of Institute of Bioinformatics & Biotechnology, all the life sciences departments and the MBA- Biotechnology course at University of Pune. Since 2006 the classes for integrated course in IBB has been running at our premises for theory and practical. Experimental research activities of the scientists of IBB are also being shared at the Bioinformatics premises as a full scale laboratory has been established in the same premises. The Center is able to increase the high power computing facilities (one 12 cpu, one 4 cpu & one 8 cpu server) and 60 new IBM/HP PC for research and teaching activities in addition to updating the two Battery backup. In addition to classroom teaching Center is conducting through its own virtual classroom environment telecasting several web-based training programs on MATLAB, e-Chemoinfo, Open source programs, workshops etc. in and out of the department to our students over the whole year using the BIOGRID VPN facility provided by DBT. Centers newly subscribed a 4Mbps(1:1) line with STPN, Pune has been a boon to aid this activity. A novel certificate course in Clinical research and clinical data management has been flagged off since Nov 2005 as a part of the training activities in the center and has created more than 300 well trained personal to help the clinical research area in the country and abroad. This course has been conducted as a joint venture with public –private partnership and are franchised as UoP in 5 cities including Bangalore, New Delhi, Hyderabad, Chennai& Bhubaneswar. Though In research fellow position presently we have two DBT-SRF, two DBT JRF, 4 COE, 2 BINC, 1 Seascape & one IBM JRF at the center and last year we were able to fill up only the JRF, teaching associate under COE positions (3) but could not retain the RA/faculties for 2007-08. The scientists do not appreciate temporary positions at this level. Till now 6 JRF has been registered for Ph.D and 2 of them are almost at the last stage of completion. Since 2005 Bioinformatics center has been successfully coordinating the BINC examination at the national level under the guidance of DBT. This project will be running for three years and served the purpose of providing an accepted standard of Bioinformatics teaching & learning to find high quality Bioinformaticians. In February 2008 this year’s BINC will be held at six centers including one at NEHU, Shillong to ease the difficulty of the students from North East region of the country. In addition to existing DBT-COE project, this year the center has been able to attract one grant of COE from Ministry of Information technology and a research project.

2. Major research activities in Biotechnology and its related fields at your institution 309 More application oriented research activities have been added to the existing portfolio of development of programs and databases research. • Comparative analysis of Metabolic Pathway in Microbial systems • Epitope mapping • Genome annotation and identification of SSR & VNTR for diagnostic tool. • Development of Interaction force field profile at the active site of protein to map the selectivity of enzymes . • vHTS of target protein and developing a Scoring system for analysis • Searching active site using the pharmacophore: a chemo-proteome approach to identify the receptor. • Developing physical measurement criteria to map protein interior.

3. Areas of Specialization of the centre • Development of databases and data mining tools in the areas of Biotechnology with stress on Virology, protein and nucleic acid sequences and structures & other related areas. • Molecular modeling and prediction of 3D structures and interactions of bio- macromolecules. • Genome assembly and Comparative Genomics • Metabolic pathway analysis & application to drug targets • Chemo-informatics and target based drug design

4. Major activities of the Centre during the year 2007-08 Courses were conducted with an introduction of online method (ICMS) for the students to acquire knowledge. The course syllabus was updated during 2007 to accommodate flexibility and removing the redundancy. In addition to the existing Databases and programming resources, new algorithms have been developed for prediction of active sites, designing of pharmacophore, tools to comparing metabolic pathway, scripts for conducting metabolic pathway and flux balance analysis. Application oriented works have been initiated using the VirGen & CEP resources. Several High Throughput docking of relevant active sites are completed and new scoring algorithms are in progress to identify the probable chemical hits, this is to search for inhibitors from the known chemical databases

a. Metabolic alphabets in bacterial system The amount of genomic data is increasing at an overwhelming rate. As on January 3, 2008 there are 702 published complete genomes and 3405 ongoing genome projects. One of the processes that differs living organisms from non-living objects is metabolism. Comparative metabolomics has become very important to understand the function; evolution and creation of organisms by ab initio approach in laboratory. Very few Bioinformatics tools are available to carry out comparative metabolomics. A very efficient Bioinformatics tool has been developed to compare genome wide metabolic pathways from KEGG database 310 using KEGG API. Using this technique and identifying a set of 34 pathways, which are essential for survival of bacteria, a set of common metabolic alphabets have been developed for characterization of bacterial pathway systems. b. Epitope mapping & vaccinology AgAbDb: Immunoinformatics provides tools for reverse vaccinology and encompasses development of knowledge bases and algorithms for prediction of epitopes. AgAbDb, a database archiving molecular interactions of antigen-antibody co-crystal structures, has been developed (http://202.41.70.51:8080/agabdb2/). The interactions are compiled at two levels, viz. residue level and atomic level. The compilation pertaining to the interacting residues provides insight into the geometrical and stereochemical features of the epitope. In addition VirGen and CEP servers have online access for accomplishing the objectives.

CEP: Conformational epitope Prediction server (http://bioinfo.ernet.in/cep.htm) has been developed and is running on the Bioinformatics server since September 2005. This server is used extensively and the paper has received 22 citations. The server pages have been updated recently and the data pertaining to the accuracy of the algorithm is made available on the site. The work is also being carried out to improve the accuracy of epitope prediction. c. Genome sequencing, annotation and analysis Genome annotation of an Indian isolate of Shigella flexneri was a project carried out jointly by Institute of Bioinformatics & Biotechnology, at University of Pune. The reads obtained by sequencing of the Indian isolate 1a of Shigella flexneri were assembled using the Gap4 program. The partial genomic sequences in terms of assembled contigs were annotated using programs such BLAST, IS finder, GeneMark and ShiBASE. Addition to this Bioinformatics approaches have been applied to identify the simple sequence repeats in the genome for developing PCR based sero typing /diagonosis tools in the virulent strains of Shigella Using the relevant outcome of this project SSR & VNTR were designed and 40 strains of Shigella flexneri were screened under a joint project with NICED, Kolkata..This result experimentally validate the novel concept of using VNTR as diagnostic tools to discriminate the strains of pathogenic bacteria. d. Mapping of selectivity and specificity profiles A novel method has been developed to compare the GRID potentials for different chemical probes to build the selectivity profile for plasmepsins, protease in Plasmodium species. Using discrimination analysis our result shows the selectivity between Plasmepsins and human aspartic proteases. The study illustrates the potential in analyzing the selectivity and specificity of aspartic protease family towards receptor-ligand recognition using main discriminating features like hydrogen bonding and electrostatics interactions. Hence the selectivity profile will be helpful in designing novel candidate for drug, which discriminates human aspartic protease with other pathogens. 311

e. Development of analysis tools for scoring and filtering from vHTS Two series of high throughput in silico docking using heterologous computing facility has been completed on 1.4 million compound set in search of novel compound as hit in acid protease, Plasmepsin II and in Ftase in Cancer using in-house developed script for parallel processing of Open-eye docking SW called FRED. Development of analysis tools are in progress for handling the appropriate clustering of the hits.

f. Pharmacophore: in search of active site to identify new target

Functional sites determine the activity and interactions of proteins and as such constitute the targets of most drugs. However, the exponential growth of sequence and structure data far exceeds the ability of experimental techniques to identify their locations and key amino acids. An attempt to device a novel in-silico protocol for active site determination of protein has been developed using pharmacophore approach as a search protocol. A database of orphan targets of Mycobacterium tuberculosis H37Rv proteins, which contains the sequence, structure and function information, has been developed in house. A pharmacophore was built using a combinatorial library generated from the anti-TB scaffolds identified from the previous work. The in house program for pharmacophore docking into protein structure is developed in C and Perl languages and successfully identified a novel target for anti-Tb.

g. Novel measurement criteria to characterize proteins inhomogenity Construction of an algorithmic framework to describe inhomogeneities in mass, hydrophobicity and polarization content within protein interior assuming radial symmetry has been developed and applied to proteins from extremophilic and mesophilic organisms. This radial partitioning scheme of protein interior could successfully differentiate the mass distribution pattern in extremophilic proteins from mesophilic proteins.

5. Infrastructure facilities in the Bioinformatics Centre A. Hardware and Network : The center has purchased/ updated several of the servers which were supporting the mirror database, email services, BINC server , Intranet and IBIN project from DBT server. We have also updated our Bandwidth to higher Mbps lines from STPN. B. Databases & other information resources Mirror sites at Bioinformatics Centre ¾ EBI databases: 27 databases and EMBOSS sequence analysis tools (Sun Solaris) ¾ PDB database: Protein structure databank (Sun Solaris) ¾ S-star: Bioinformatics online education (Linux) 312 C. Scientific Software packages (Acquired last year)

Software Purpose Open Eye Sw for designing Small and large molecular designing and Chemicals docking, mapping etc are provided.

The Cambridge Structural Database The world repository of small molecule crystal (CSD), Conquest etc..(Windows & structures & the Interface for the CSD Linux ) Systems. AMBER Ver. 9 Package of programs for molecular dynam simulations of proteins and nucleic acids CHARMM ver. Molecular dynamics and mechanics ADF QM/MM SW DS -Medchem Explorer A package to design pharmacophore.

6. Details about staff members working in the centre (Name of the staff, Designation, Specialization and period of working. Please indicate their absorption status) ¾ Prof. Indira Ghosh, Director, Professor, IBB (Bioinformatics, Biotechnology& Drug Design) 01.09.03 ¾ Dr. Urmila Kulkarni-Kale, Reader (Bioinformatics) 01.09.05 ¾ Mrs. Sangeeta Sawant, (IBB) Lecturer (Bioinformatics) 01.05.03 ¾ Sanjay Londhe, Jr. Information Scientist (Information Technology) 20.04.94 ¾ Dr. Shah Vaishali, J. (IBB) Lecturer (Computational Physics) 17.12.03 ¾ Dr. A. Deshpande, Adjunct Professor ( Statistics, Environmental science & Fuzzy Logic ) 01.02.05 ¾ Prof. A. S. Kolaskar, Advisor, NKC. During 2007-08 total number of JRF/SRF/project assistance were 15. 6 TA/JRF from COE, one SRF & 3 JRF from DBT, 2 from BINC and 1 each from MCIT project, from Seascape Learning & IBM have been granted to the center. Seven Research Fellows have already been registered for Ph.D under Prof. A. S. Kolaskar & Indira Ghosh.

7. Types of services provided • Sequence analysis user queries Researchers / experts in life sciences who wish to analyze sequence and structure data of genes or proteins send their queries to the center. The experts in the center carry out the required analysis and it is sent along with the interpretations. ƒ Library facilities Library has 2000 books, 5000 bound volumes and online full text access to more than 2000 journals. This facility is made available to all academic institutions from India. Digital Library (DL) having 400 pdf, word and image files has been created using Greenstone Digital Library software. DL is accessible on intranet. Center has established access to more than 2000 full text journals and 8 bibliographic databases under the UGC-INFONET University consortia network in November 2004.

313 ƒ Knowledge management Recently, the library has established an intranet portal called “InfoPath” This portal has been created using open sources content management software called “Plone”. Infopath indexes electronic text image as well as audio files. InfoPath organizes the information under different organizational processes like administration, services, teaching, library, reports, digital library, etc. Users can upload and download files on this portal and also submit their reviews. • Courses are ONLINE (ICMS) A set of tools for providing online course materials and teaching utilities have been developed . This also have been extended by developing ONLINE Registration form for BINC , for Workshop and for admission .

8. Educational activities with details of placement M.Sc in Bioinformatics ://bioinfo.ernet.in/courses/IndexMSC.html Under the dynamic leadership of Prof. A. S. Kolaskar, the founder Director of the Centre the Bioinformatics Centre has highly competent faculty, both in-house and contributory, dedicated administrative support, state-of-the-art computer systems with full internet connectivity and modern library facilities. The Centre have started the 2 year M.Sc. Program in Bioinformatics from the academic year 2002-03. Given the excellent infrastructural facilities and academic programs like active research, interactive teaching and industry collaboration, the Centre has gained in reputation both nationally and internationally. It is hoped that the M.Sc. program throws open highly promising career opportunities to aspiring students. Present input for M.Sc is 30 students/year. 50% of them are employed in Industry and the rest opt for Ph.D or academic jobs. Clinical Research and Clinical Data Management"(CRCDM) http://www.clinicpune.org/ a post graduate certification 6months(weekend course)

New Pharmaceutical Drugs, biological, herbal and natural remedies, nutraceuticals and probiotic food products, and select cosmetics require drug safety and efficacy testing before they are introduced in the market. This testing for drugs on humans comprises Clinical Trials referred as Phase I, II, III trials prior to market launch of the product & Phase IV after market introduction. India has one of the largest patient populations for most of the diseases with genetic diversity. Availability of highly qualified medical practitioners is attracting conduct of global clinical trials in Indian hospitals and clinical sites since India has implemented GCP as per ICH global standards. It is now possible that the data from conduct of trials in India as per GCP guidelines maybe submitted for approval of the drug in USA, Europe, Japan, etc along with submission to authorities in India. The clinical trial industry is doubling in revenue every 2years and as per Mckinsey estimate India has the potential to become one billion dollar revenue industry. This high growth has created the mandatory need for more clinical research professionals in GCP for conduct Management of the trials.

314 Since 2005, 300 students have passed out of this certificate course and tit has been franchised to 5 other cities in India. 90% of the students are now working in the Clinical research industry. A novel approach has been taken using Public-Private partnership to support this course

9. Initiative to validate the outcome of bioinformatics resources

The Centre is collaborating with the experimentalists to validate the hypothesis/predictions based on bioinformatics analyses. Collaboration with the scientists from NICAD in Kolkata, NCCS, NIV in Pune, NIPER, Chandigarh & IRRH, Mumbai has helped in validating several predictions done by the researchers in the wet lab.

10. Collaborative works/ initiatives • Collaborations with national and international organizations

Functional and structural annotation and prediction of structures.

Several activities are going on to annotate unknown proteins and predict it’s three-dimensional structures. One of the success story is the collaboration work with National Institute for Research in Reproductive Health, Mumbai by identifying a novel progesterone binding protein ER60, which has low sequence similarity (18%) and revealed to have a Protein disulphide isomerase (PDI) classical fold. The experimental work is in progress to validate the hypothesis.

ƒ Collaborative activities with industries and other agencies

Synergy Networks: Collaboration for Clinical research and data management Serum Institute, Pune : Contract R&D IBM Life sciences : Research scholarships and IBM-CAS academy fellowships. Seascape Learning : OpenEye SW country wide support.

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11. Databases/ Software packages developed Databases Name of database Mode of Access (online/offline) Size of Completion Status DB Indian Bioresource Web based: Completed and Information Network http://bioinfo.ernet.in/ibin/ updated periodically (IBIN) portal : Web portal for searching any information regarding bio organisms. Antituberculosis Web based: Completed and Compounds http://203.129.231.23/indira/ updated periodically Database : A novel data mining procedure to look for new antitubercular agents and targets as well as to find a minimum common bioactive substructure (MCBS). Pathophyl: Database Web based: Ongoing of phylogenetic http://203.129.231.23/indira/ profiles for each protein of Mycobacterium tuberculosis, Pseudomonas aeruginosa, Staphylococcus aureus. Virgen ver2.0 Web-based: 200MB Completed and Contains genomic updated periodically data of 25 viral http://bioinfo.ernet.in/virgen/virgen.html families that include 2895 genomes and 23121 annotated proteins CEP server: Web based: >GB Completed & Conformational http://bioinfo.ernet.in/cep.htm Updated epitope Prediction server Metabolic pathways Web-based : 1GB Ongoing in http://202.41.70.51/mpe/ collaboration with Jalja tech.pvt.

PepConfDb Web-based (Proposed) 50MB Ongoing AVIS Web-based 1GB Completed

Software/Databases with search engine developed :

• Name: IBIN: Indian Bioresource Information Network (IBIN) portal : Web portal for searching any information regarding bio organisms. Mode of access : Online • Name: Pathophyl : Profile prediction of pathogenic bacteria. Mode of access: Online ƒ Name: CEP: conformational epitope prediction Mode of access: Online 316 ƒ Name: Protein Conformational state prediction Mode of access: On request ƒ Name: Antigen Mode of access :Online as well as through EMBOSS and UWGCG ƒ Name: Virus identification matrices Mode of access: Online

12. Papers published or presented in the conferences with reference

Papers published:

1. Rahim F*, Deshpande A, Hosseini A*. Fuzzy Expert System For Fluid Management In General Anaesthesia. Journal of Clinical and Diagnostic Research [Serial Online] August 2007, 1:256-267. 2. Hosseini Ashraf , Ranade Suvidya H. , Ghosh Indira, Khandekar Pramod (2007). Simple sequence repeats in different genome sequences of Shigella and comparison with high GC and AT- rich genomes. DNA Sequence. 3. Chaitanya N. Hiremath (2007) Abbreviated Profile of Drugs (A-POD): A unique numerical and graphical representation for compound properties and its use in ADMET prediction, IJIB, 1(1), 44-50.

4. Greenbaum, J. A., Andersen, P. H., Blythe, M., Bui, H. H., Cachau, R. E., Crowe, J., Davies, M., Kolaskar, A. S., Lund, O., Morrison, S., Mumey, B., Ofran, Y., Pellequer, J. L., Pinilla, C., Ponomarenko, J. V., Raghava, G. P., Van Regenmortel, M. H., Roggen, E. L. , Sette, A., Schlessinger, A., Sollner, J., Zand, M., Peters, B.(2007). Towards a consensus on datasets and evaluation metrics for developing B-cell epitope prediction tools. J. Mol. Recognit. 20(2), 75-82.

5. Kulkarni-Kale, U., Ojha, J., Manjari, S., Deobagkar, D. D., Mallya, A.D., Dhere, R. M. & Kapre, S. V. (2007). Mapping antigenic diversity & strain-specificity of mumps virus: a bioinformatics approach. Virology. 359, 436-446.

6. A. Kumar and I. Ghosh (2007). Mapping Selectivity and Specificity of Active Site of Plasmepsins from Plasmodium falciparum Using Molecular Interaction Field Approach. Protein & Peptide Letters , 14(6), 569-574.

7. A.D. Ghate, B.U. Bhagwat, S.G. Bhosle, S.M. Gadepalli and U. Kulkarni-Kale(2007). Characterization of Antibody-Binding Sites on Proteins: Development of a Knowledgebase and Its Applications in Improving Epitope Prediction. Protein & Peptide Letters, 14(6), 531-535.

Proceeding, Posters and awaiting for publications : Poster presented by Sweta Kohli at “The 18th International Conference on Genome Informatics” held in Singapore from 3rd to 5th December 2007 titled “Metabolic alphabets in bacterial system”

13. Initiation of R&D activities in Bioinformatics

a. Our center is co-ordinating the BioInformatics National Certification (BINC) Examination. BINC Examination, the first one was conducted on November 12-13, 2005. This examination has been instituted by the Department of Biotechnology (DBT), Government of India with an objective to certify Bioinformatics professionals and to facilitate industries 317 and potential employers for recruitment. University of Pune has been identified to continue this events for three years as a nodal agency by the Department of Biotechnology, Govt. of India to coordinate this examination along with four centers namely, Jawaharlal Nehru University, New Delhi; Anna University, Chennai; West Bengal University of Technology, Kolkata and Institute of Bioinformatics and Applied Biotechnology, Bangalore. b. International interactions are also been strengthen by processing a collaborative research and teaching activities with University of Utah , USA , under the guidance of Prof. A. S. Kolaskar. More such activities are underway. c. Center has received a Grant in 2007 August from Ministry of Information technology as “Center of Excellence” .

14. Details of Training/ Workshop organized and total no. of user trained The following workshop were arranged by the center (number of attendee):

1. 23.07.2007: Felicitation Day on `BioInformatics National Certification (BINC) Examination’ in the hands of Prof. A.S. Kolaskar, Advisor, National Knowledge commission and Dr. T. Madhan Mohan, Advisor, Department of Biotechnology, Govt. of India, New Delhi (30) 2. 23.07.2007: `Bioinformatics Day’, to commemorate the invaluable scientific contributions of late Prof. G.N. Ramachandran, the department has celebrated by arranging an oration by the eminent scientist having substantially contributed in the areas of Bioinformatics, Genomics, Proteomics, Structural Biology and Application of Bioinformatics. This year’s oration has delivered by Prof. A.S. Kolaskar on title – Bioinformatics – hotter than hottest. This function was chaired by Dr. Swaminathan Sivram, Director, National Chemical Laboratory, Pune. (100) 3. 01.08.2007: Bioinformatics Day celebration: Prof S.K. Brahmachari, Director, IGIB, New Delhi has delivered GNR Oration lecture on ‘Hope and reality’, Prof. A.S. Kolaskar, Chairman, National Knowledge Commission and M.D. of DSK Global Education and Research Pvt. Ltd., was the chairman of this occasion. GNR-IGIB and DBT Prize distribution function was also held during this time. (100). 4. December 11 -17, 2007: WORKSHOP on "Knowledge Discovery In Life Sciences:, Modeling of Small Molecules to Macromolecules” website: http://bioinfo.ernet.in/workshop07/ (50)

15. Impact shown by your centre on the growth of biotechnology and allied areas. In this you may highlight the details like number of paper published/ number of papers published with the help of your centre, how your centre is promoting various activities of your organization and neighboring institutions, manpower trained, tools developed, patents & copyrights acquired and other services offered etc. • Prof. Kolaskar is deeply involved in the planning activities in human resource generation in technology in our country being the advisor of the Knowledge management Council led by Prime Minister. He has been member of several national and international level committees. Prof. Indira Ghosh in collaboration with Dr. Devapriya Choudhury, JNU has organized a workshop to train the SAARC manpower at Thailand during July 2007. Prof. Indira Ghosh has been influencing the national level of teaching and research in Bioinformatics by being active member in the group on

318 developing Bioinformatics & Medical Informatics in the Ministry of Information technology and ICMR respectively.

• Every Year our faculties attended & deliver lectures for at least 2-4 other BIF/BIC workshops and 1-2 Colleges running Bioinformatics programs to train the manpower .

• International/Indian Conferences & Teaching

Presented papers by Indira Ghosh :

2008 Jan2-4 with Kalyani University , BIF Workshop :Macromolecule- ligand interaction & drug design” in West Bengal. 2007 Dec 16-19 “Instructional workshop in Bioinformatics” Jointly by the University of Hyderabad and the C. R. Rao Advanced Institute of mathematics, Statistics and Computer Science at the University of Hyderabad Campus, Hyderabad, India 2007 Dec 20-22 at the"International Conference on Bioinformatics" http://www.uohyd.ernet.in/sls/cbt/bif/Training/conf2007.htm. 2007 Nov21-23 workshop on ‘Functional genomics and evolutionary Biology” at the Institute of Life Sciences, Bhubaneswar . 2007 Nov 29-30th. At Sophia College , Mumbai on “Frontiers in BioSciences” 2007July2-6th with Biotec, Thailand and JNU, India jointly organized and taught the workshop on “Molecular Dynamics: Theory & practice” in Bangkok Thailand, 2007, May 10th. Symbiosis Institute of Health Sciences, Pune, ”Clinical Data Management” 2007, May 2nd., Workshop lecture at Bangalore ,”Functional annotation”. At Tata Auditorium. 2007, April 6th. , Workshop lecture & Demo on “in Silico Toxicity prediction” at NIRRH, Mumbai. 2007 , Feb 26-28th, CUP07 at SantaFe , USA 2007, Feb 9-12th. : Mumbai University , Bioinformatics – Application in Life Sciences, workshop inauguration lecture : “Hypothesis based Biology : a new era” 2007 , Jan 22-24th : ”International Conference on Chemoinformatics” at NCL Pune 2007, Jan 12-14 : Kolkata “Chromosomes to Neurons”

Presented papers by Urmila Kulkarni-Kale:

2007, Aug23-12Sep. Teacher’s training program organised by Goa University. 2007 Dec 1st. Proteomics & genomics seminar organised by College of Pharmacy, University of Pune .

• Teaching to students of other departments at the University and institutes

319 All life sciences departments (students~50), Institute of Bioinformatics & Biotechnology (students~60) and MBA biotechnology dept.(students~ 70) have Bioinformatics as a part of their syllabus. The faculty of the center teaches these courses. A special module based exchange program in teaching was done for the first time with our students doing 2 credit experimental course at WBTU, Kolkata and their students crediting the 2 credit course on structure prediction, modeling and simulation of Proteins at out center during 3 weeks in the summer of 2007.

• Specialized on site training programs

Short-term training in Bioinformatics is provided to scientists / researchers of various institutes and industries as per their demand.

• Summer training / short term projects

Students from University departments (M.Sc 30 & 5 students from IBB) and neighboring institutions are accepted for short-term projects / summer training in Bioinformatics. In addition to this, in 2007 we have trained 2 project student from IIT Roorky ,1 from IIT Kharagpur and IBB, Noida.

• Consultancy to industry

a. Bioinnovat(Synergy Networks) : Collaboration for Clinical research and data management courses has been expanded to five more centers including one at H.V. Desai Hospital, Pune , 1 at New Delhi and one at Sankar Netralaya, Chennai, 1 at Bangalore, T. John College and 1 at Hyderabad, LVPrasad Hospital. b. Seascape Learning, LLC (Seascape): Advisory collaboration with the organization has supported a JRF scholarship and provide on-line support to international and Indian customer for the Open-eye Software suits developed by the OE .

16. Future activities As a part of Center of Excellence research projects in the field of identification of gene target and pharmacophore in the disease specific area like infectious & parasite disease and diabetes are in progress. A few extended works are cited as follows: • Genome annotation and comparative genomics :

Diagnostic tools using Genome annotation and comparative genomics of Shigella flexnary 1a, an Indian isolate will be another major activity in the future in collaboration with NICED,Kolkata.

• Identification of correlated pathway using upstream comparison of genes and operons of pathogenic bacteria :

320 A novel idea of clustering the genes belong to the same pathway has been initiated using the upstream sequence profile of the genes in pathogenic bacteria.

ƒ Target Identification using Metabolic pathway control analysis in pathogenic bacteria case study with M.Tb:

MCA & Flux balance analysis are the system biology related methods applied to understand the mechanism of persistence of bacteria and hence to identify the appropriate way of inhibition of the vulnerable and unique enzyme in the metabolic pathway. Flux balance analysis of whole genome of M.Tb is the method applied to identify the target under dormant bacteria.

Additional Details:

Name of the Coordinator : Prof. Indira Ghosh

Postal Address : Director, Bioinformatics Centre, University of Pune, Pune 411 007. Phone Number : 020 2569 0195, 2569 2978 Fax No. : 020 2569 0087 Email : [email protected] [email protected]

Assam Agricultural University, Khanapara, Guwahati Coordinator : Dr. Probodh Borah

6. Summary of the progress made by the centre from its inception: Adequate infrastructure with required hardware and software has been developed at the centre and the facilities are being used by the faculty members and students of the institute as well as some other neighbouring institutions of higher education. So far two training programmes have been conducted on different aspects of bioinformatics tools and their application in biological research and a total of 32 biology teachers/researchers of various institutes within and outside state participated in these programmes. Another training programme is scheduled for February 18-21, 2008. Additionally, so far 85 faculty members/subordinate staffs of the host institute have been trained in eight batches under a computer literacy programme conducted by the centre.

7. Major research activities in Biotechnology and its related fields at your institution: Some noteworthy contributions made by the institute in biotechnology related research are: molecular characterization of Salmonella enterotoxin, standardization and application of PCR for virulence screening of Escherichia coli and Salmonella, production of cell culture adapted duck plague vaccine, molecular characterization of swine fever virus, development of potassium

321 thiocyanate extract vaccine of Pasteurella, cryo-preservation of ova and application of embryo transfer technology in goat, cow and yak etc.

8. Area of Specialization of the centre: Animal Biotechnology

9. Major activities of the centre during the year 2007-08: i. Necessary infrastructure of the centre was developed and required hardware, software etc. were procured. ii. Two training programmes were conducted and 32 teachers/researchers were trained on bioinformatics tools and their application in biology teaching and research. Another training programme is scheduled for February 18-21, 2008. iii. Altogether 85 faculty members and subordinate staff in eight batches of the host institute have been offered training on computer applications.

10. Infrastructure facilities in the Bioinformatics Centre i. Computer & Communication facility: 10 computers, 2 servers, one Laserjet and one Inkjet printer, one Photostat machine. The computers are connected to the faculty LAN with 24-hour 512 kpbs Internet connectivity with adequate power backup. ii. Scientific Software packages: Visual Studio, My SQL, Exome, Bioedit, Phylip, ClustalW etc. iii. Databases & other information resources: VETCD (1989-1999).

11. Details about staff members working in the centre (Name of the staff, Designation, Specialization and period of working. Please indicate their absorption status): Name of the Period of Absorption Designation Specialization staff working status Assoc. Professor Ph.D. Veterinary Since Dr. P. Borah Permanent and Coordinator Microbiology inception Assoc. Professor Ph.D. in Dr. B.K. and Member, Since Veterinary Permanent Sarmah Executive inception Physiology Committee M.Sc. Sri Arunav Research Since (Computer Temporary Gupta Associate 18.12.2007 Science) Sri Pradip Since Nov., Typist B.A. Permanent Sarmah 2007

12. Types of services provided: Internet surfing, training and assistance on use of online databases and bioinformatics tools, statistical analysis of biological research data, guidance in genomic research etc.

13. Educational activities with details of placement: None so far except conduction of training programmes. However, a proposal for opening of PG courses in Animal Biotechnology has been submitted to DBT for approval.

322 14. Initiative to validate the outcome of bioinformatics resources: Through publication of research articles in reputed journals.

15. Collaborative works/ initiatives: Teachers/researchers of neighbouring institutions like Guwahati Medical College, Gauhati University, Cotton College, B. Barooah College etc. have been trained and offered facilities for use in their research works.

16. Databases/ Software packages developed: None so far. 17. Papers published or presented in the conferences with reference: None so far.

18. Initiation of R&D activities in Bioinformatics: Work has been initiated.

19. Details of Training/ Workshop organized and total no. of user trained: i. Short-term hands-on training on “Bioinformatics Tools and Their Application in Teaching Biological Sciences” from March 20-22, 2007, in which 12 participants were trained. ii. Short-term hands-on training on “Bioinformatics Tools and Their Application in Biological Research” from December 03-06, 2007, in which 20 participants were trained. 20. Impact shown by your centre on the growth of biotechnology and allied areas: The centre is encouraging faculty members and students for optimal use of the facilities available at the centre for promoting their teaching and research activities. An e-learning module is in the process of development which has been available in the faculty LAN. The Internet facility is being used extensively by the faculty members and PG students. Two papers published with the help of the centre so far.

21. Future activities: The future activities envisaged include development of a database of indigenous livestock and wildlife of the north-east India, development of tools for identification of pathogenic microorganisms on the basis of standard criteria, etc.

Additional Details: Name of the Coordinator: Dr. Probodh Borah Postal Address: Department of Microbiology, College of Veterinary Science, Assam Agricultural University, Khanapara, Guwahati-22 Ph: 0361-2307329 (R), 0361-2331501 (O), Mobile: 094351-16191 Email:[email protected] Website: www.aau.ac.in Name of Contact Person(s): Dr. Probodh Borah Email: [email protected]

323 Alagappa University, Karaikudi, Tamil Nadu Coordinator: Prof. S. Karutha Pandian

1. Summary of the progress made by the Centre from its inception Bioinformatics Infrastructure Facility (BIF) was established at Alagappa University during November 2006 and it was formally inaugurated by the Hon’ble Union Finance Minister on 24.11.2007. It serves to the student and teaching community of the Alagappa University and its affiliated colleges. M.Sc., Biotechnology students use this facility for their Bioinformatics Practical and hence they are placed well immediately after finishing their PG programme. One PhD was produced using this facility and 10 more research students are using this facility. A 2 MBPS broadband internet connectivity from BSNL is being utilized for bioinformatic purposes by the PG students, Research Scholars and Faculty members of the host and neighbouring Departments/Institutes. Journals with online and printed versions are being subscribed in the area of Biotechnology, Microbial Technology and Bioinformatics. Seven Research Papers have already been published in International Journals with decent impact factors using the computational facility of the Centre. Database is being generated for the 16S rRNA sequences of marine bacteria form the Gulf of Mannar for biotechnological prospects. This facility was also utilized to identify the bacteria associated with goat skin which are involved in the deterioration of skin as part of the CSIR’s New Millennium Indian Technology Leadership Initiative (NMITLI) Scheme. 2. Major research activities in Biotechnology and its related fields at your institution i) Biotechnology for Leather: Towards Cleaner Processing. This work is being carried out with the collaboration of 11 other National Institutes/Universities under the New Millennium Indian Technology Leadership Initiative (NMITLI) scheme of CSIR. The culturable bacteria associated with goat skin were identified through 16S rRNA based typing and that in turn paved the way for coming out with suitable technologies for bio and ambient preservation of skin without common salt. Marine bacterial enzymes have successfully been employed for dehairing of goat skin. ii) Study on Gene Expression technologies using C. elegans. C. elegans is being used as a model organism for studying the host pathogen interaction through RNAi technology through DBT funded Project “RNA-interference mediated silencing of antimicrobial genes on the pathogenic effect of Salmonella typhi on vitamin transport of Caenorhabditis elegans” under Rapid Grant for Young Investigator. Marine natural products are also being screened for novel antibiotics and anticancer compounds using C. elegans as live infection model. iii) Marine Microbial Diversity/Genomics The microbial diversity associated with the predominant coral of Gulf of Mannar viz Acropora digitifera is assessed/catalogued through culture dependent and culture independent methods with an objective of coming out with novel antiviral compounds from the coral associated bacteria against the aquaculture pathogen blotched snakehead virus (BSNV). This project is funded by the DBT, Government of India. iv) Bioactive Compounds from Marine Microbes

324 Screening of antibacterial, antifungal and AHL (quorum sensing signal) degrading molecules from marine actinomycetes are underway. Screening of marine bacteria as a probiotics against aquaculture pathogens is also carried out. v) Plant Biotechnology: Agrobacterium mediated gene transfer and ex-situ conservation of medicinally and commercially important plants are being carried out for increasing the tolerance to salinity and drought in commercially important crops such as Rice. Ex-situ conservation of medicinally important plants through synthetic seed preparation, micro and macro-propagation is also under progress. vi) Pharmacology of marine natural products and Antioxidant properties of Olive Oil (DST funded Project) 3. Area of Specialization of the Centre Marine Microbial Biotechnology, Microbial Genomics and Proteomics and Environmental Biotechnology 4. Major activities of the Centre during the year 2007-08 Research Projects funded by National agencies such as CSIR, DST, DBT have been carried out. The microflora associated with the goat skin have been identified and 16S rRNA sequences of marine bacteria associated with coral reef ecosystem of Gulf of Mannar Marine Biosphere Reserve and bacteria associated with the deterioration of animal (goat) skin submitted to ribosomal data base. Marine alkaline protease from Bacillus pumilus has been successfully applied for dehairing of goat skin. Antibacterial and Quorum sensing signal degrading compounds have been isolated from marine Actinomycetes. Basillus sp. has been used successfully as a probiotic bacterial organism against Aquaculture pathogen Vibrio sp. Standardized the protocols for ex-situ conservation of medicinally and commercially important crops. The antioxdant properties of olive oil have been established using cell lines. Theoretical and practical training have been given to the PG and PhD students in bioinformatics. A National Workshop on Genome and Proteome Analysis was conducted during January 7-9, 2008 and twenty five candidates have got hands on training through this Workshop. 5. Infrastructure facilities in the Bioinformatics Centre i. Computer & Communication facility: High End Server (HP ML 350 G4/G5) with Windows Server 2003R2 Medium End Server (HP ML 110 G3) each with Windows Server 2003 R2 P4 PCs (10), High Speed Network Laser Printer (HP LaserJet P3005d) Deskjet Printer (HP Business Inkjet 1000) Scanner (HP Scanjet 2400) Photocopier (Konica Minolta Bizhub 210) 2MBPS Broadband internet connectivity from BSNL with dedicated IP address and wireless modem (WA1003A) for Wi-Fi access. Firewall from Syntensia (White Knight). ii. Scientific Software packages: Windows 2003 Server with License Red Hat Linux Enterprise Edition 4 Microsoft Visual Studio, .NET MS SQL Server (Std.) MS Office 2003 and Anti Virus Packages.

325 Action is being initiated for getting application software such as GCG Wisconsin Package, Biosuite (from TCS) and Sigma Plot, DTMM, Reference Manager and Coral Draw iii. Databases & other information resources: The centre currently uses the databases and resources that are freely (open access) available over the internet like NCBI, EBI, ExPASy, etc., The BIF has been subscribing Nature, Nature Biotechnology, Nature Reviews of Microbiology, Science and NISCAIR Journals. 6. Details about staff members working in the Centre Dr. R.A.L. Sathiyanathan RA Biochem/ Nov 19- to date Bioinformatics Mr. K. Syed Musthafa Tech Asst Biotech Nov 15- to date Mr. S. R. Senthilkumar Tech Asst Biotech Nov 15- to date 7. Types of services provided (a) Training in Bioinformatics: Theoretical and practical training on Bioinformatics is provided to the M. Sc., Biotechnology students through a 3 credit course under Choice Based Credit System. Doctoral students are utilizing the facility for solving their research problems using bioinformatic tools. (b) E-Mail and Internet Facility: The BIF is regularly providing INTERNET facility to all the interested users working in the area of biotechnology and related areas through BSNL (2 MBPS broadband) and University server. The scientists and researchers are regularly using this facility for literature search and as well as for net surfing. Presently 50 M.Sc. students, 12 research scholars and 5 faculty members are regularly using this facility apart from students and teachers/scientists from neighbouring Institutions. (c) Access to Printed Journals and Online access to E- Journals 8. Educational activities with details of placement 1. M.Sc., Biotechnology Programme- offered since 2002 in which there is a 3 credit course on Bioinformatics. All the candidates who have passes this Programme have got placement in Research Institutes, Biotech Industries and Academic Institutions in India and abroad. 2. Doctoral Programme in Biotechnology- offered since 2002. 3. M.E. Environmental Engineering Students of Alagappa Chettiar College of Engineering and Technology (TN Govt. College affiliated to Anna University) are taught on Environmental Microbilogy and recombinant DNA Technology since 2004. 9. Initiative to validate the outcome of bioinformatics resources Marine bacteria which have been identified through 16S rRNA and known (by in silico analysis) for production of antiviral compounds are being subjected to screening for antiviral compounds against aquaculture pathogens. 10. Collaborative works/ initiatives 1. A collaborative Project “Biotechnology for Leather: Towards Cleaner Processing” is being carried out with the collaboration of 11 other National Institutes/Universities under the New Millennium Indian Technology Leadership Initiative (NMITLI) scheme of CSIR. 2. A DBT sponsored Project “Evaluation of bacterial diversity associated with the coral Acropora digitifera by 16S rRNA gene sequences and screening for antiviral activity against the aquaculture pathogen blotched snakehead 326 virus (BSNV) “ is being carried out in collaboration with the Fisheries College & Research Institute (Tamil Nadu Veterinary and Animal sciences University), Tuticorin. 11. Databases/ Software packages developed Ribosomal data base for the marine bacteria associated with coral reefs, sponges, marine sediment and sea water are being established which will pave the way for sustainable tapping of marine microbial wealth for biotechnological prospects and protection of marine environment. 12. Papers published or presented in the conferences with reference 1. Ravi AV, Musthafa KS, Jegathammbal G, Kathiresan K and Pandian SK (2007) Screening and evaluation of probiotics as a biocontrol agent against pathogenic Vibrios in marine aquaculture. Letters in Applied Microbiology 45: 219-223. 2. Rajesekar A, Ganesh Babu T, Maruthamuthu S, Karutha Pandian S, Mohan S, and Palaniswamy N (2007). Biodegradation and corrosion behaviour of Serratia marcescens ACE2 isolated from diesel-transporting pipeline. World Journal of Microbiology and Biotechnology 23:1065-1074. 3. Rajasekar A, Ganesh Babu T, Karutha Pandian S, Maruthamuthu S, Palaniswamy N and Rajendran A (2007). Role of Serratia marcescens ACE2 on diesel degradation and its influence on corrosion. Journal of Industrial Microbiology & Biotechnology 34:589-598. 4. Rajesekar A, Ganesh Babu T, Karutha Pandian S, Maruthamuthu S, Palaniswamy N and Rajendran A (2007). Biodegradation and corrosion behaviour of manganese oxidizer Bacillus cereus ACE4 in diesel transporting pipeline. Corrosion Science 49: 2694-2710. 5. Kiruthiga PV, Beema Shafreen R, Karutha Pandian S and Pandima Devi K (2007). Silymarin protection against major reactive oxygen species released in environmental toxins: Exogenous H2O2 exposure in erythrocytes. Basic & Clinical Pharmacology & Toxicology 100: 414- 419. 6. Kiruthiga PV, Beema Shafreen R, Karutha Pandian S, Arun S, Govindu and Pandima Devi K (2007). Protective effect of silymarin on erythrocyte haemolysate against benzo(a)pyrene and exogenous reactive oxygen species (H2O2) induced oxidative stress. Chemosphere 68:1511-1518. 7. Ramseh M, Marx R, Mathan G and Karutha Pandian S. (2007). Effect of fungicide bavistin on in vitro plant conversion from sodium alginate encapsulated uninodal microcuttings of micropropagated Bacopa monnieri (L.) –A Pharmaceutically valuable ayurvedic herb. Journal of Environmental Biology (In Press).

13. Initiation of R&D activities in Bioinformatics Bacterial genomic sequences associated with virulence will be analysed with special emphasis on pathogenecity islands and M genes. 14. Details of Training/ Workshop organized and total no. of user trained Workshop Title Duration No. of Participants 1. National Workshop on Mar 14-16, 2007 75 Genomics, Proteomics and Bioinformatics 2. National Workshop on Jan 07-09, 2008 25 Genome and Proteome Analysis 15. Impact shown by your centre on the growth of biotechnology and allied areas. In this you may highlight the details like number of paper published/ number of papers published with the help of your centre, how your centre is promoting various activities of your organization and neighboring institutions, manpower trained, tools developed, patents & copyrights acquired and other services offered etc. No. of M.Sc., Biotech Students trained 50 No. of Ph.D. Scholars Passed out 01 No. of Ph.D. Scholars currently availing the facility 10 No. of Papers Published 07 Workshop Manual Released 01 327 No. of candidates trained through Workshops 100 16. Future activities • Generation of comprehensive genomic and proteomic database for the microbes from Gulf of Mannar. • Organization of one-week training workshop for the teachers from Government and Government aided colleges from the affiliated colleges of Alagappa University and from other parts of the country during Nov 2008. • Undertaking research in the area of Marine Microbial Genomics for biotechnological prospects and for protecting the environment. • Development of ribosomal database for the marine bacteria associated with coral reefs, sponges, marine sediment and sea water for sustainable tapping of marine microbial wealth for biotechnological prospects and protection of marine environment. Additional Details: Name of the Coordinator: Prof. S. Karutha Pandian Postal Address : Coordinator Bioinformatics Infrastructure Facility Department of Biotechnology Alagappa University Karaikudi 630 003, Tamil Nadu Phone Number: 04565 225215 Fax No.: 04565 225202 Email: [email protected] Website: www.alagappabiotech.org; www.alagappauniversity.ac.in

Name of Contact Person(s): Prof. S. Karutha Pandian Email: [email protected]

328 Bharathiar University, Coimbatore Coordinator : Dr. P. Shanmughavel

1. Summary of the progress made by the centre from its inception The post graduate course in bioinformatics was commenced in Bharathiar University during 2001 for the first time in India. In endorsement of the massive research activities performed by the Bioinformatics Division, it has become an independent department of the university during the academic year 2006. It fosters research and developmental activities in major thrust areas like Nano Science and Drug delivery, Molecular modeling and Drug Design, Comparative Genomics, Computational Biology, Biodiversity Informatics and Phytomatics. The department is engaged in various innovative projects in the disciplines mentioned, supported by National and International agencies like DBT, UGC & ITTO, Japan. The department also conducts M.Phil and Ph.D courses.

2. Major research activities in Biotechnology and its related fields at your institution. Nano Science and Drug delivery, Molecular modeling and Drug Design, Comparative Genomics, Computational Biology, Biodiversity Informatics and Phytomatics.

3. Area of Specialization of the centre: Computational Biology and Bioinformatics

4. Major activities of the centre during the year 2007-08 Three Research Schemes Awarded and three conferences/Workshops conducted.

5. Infrastructure facilities in the Bioinformatics Centre Computer & Communication facility 11 nos of Intel Pentium, 5KVA online UPS with 10 Nos of batteries, ISDN Router, Sun Netraj Server, Unix based student workstation,LCD Projector and Scientific Software packages Bio- Suite are available. Databases & other information resources A database on “The Digitized Inventory of Tropical Timber Resources of India” is completed.

6. Details about staff members working in the centre (Name of the staff, Designation, Specialization and period of working. Please indicate their absorption status) Three Teaching staffs, two office staffs are permanent. Nearly 15 scholars pursuing Ph.D and 8 scholars doing M.Phil in Bioinformatics. 7. Types of services provided. Teaching and Research Development of Database and Software

8. Educational activities with details of placement. 329 All the post graduate and diploma students were easily absorbed by the Bioinformatics company and research institutions.

9. Initiative to validate the outcome of bioinformatics resources . Awarded three M.Phil’s in the field of Bioinformatics. 10. Collaborative works/ initiatives with the following institutes. 1.Global Forest Information Service (GFIS), Vienna, Austria. 2. Global Biodiversity Information Facility (GBIF), New Zealand. 3. Indian Institute of Technology, New Delhi 4. Indian Agricultural Research Institute, New Delhi 5. University of Delhi, New Delhi.

11. Databases/ Software packages developed: ¾ Database Model for Industrial Plantations. ¾ Digitization and Automation of Tropical Forest Biomass, 3. Nucleotide and Protein Manipulation tool.

12. Papers published or presented in the conferences with reference Ten papers and two Conference Proceedings. 13. Initiation of R&D activities in Bioinformatics .M.Phil and Ph.D. 14. Details of Training/ Workshop organized and total no. of user trained Three seminars and workshops are conducted and more ten 800 participants benefited.

15. Impact shown by your centre on the growth of biotechnology and allied areas. Two Faculty development programmes (Orientation) conducted by current academic year. (More than 40 University/college teachers trained).

16. Future activities. Our future activities include development of Software and databases. Additional Details: Name of the Coordinator: Dr. P. Shanmughavel, Postal Address: Dr. P. Shanmughavel, Coordinator, Bharathiar University, Coimbatore - 641046 Phone Number : +919486446101 Fax No. : +91-422-2422387 Email : [email protected] Website : http://www.b-u.ac.in Name of Contact Person(s): Dr. P. Shanmughavel, Email: [email protected]

330 CCS Haryana Agricultural University, Hisar Coordinator : Dr. Sudhir Kumar

1. Summary of the progress made by the centre from its inception: The Bioinformatics Section, CCS HAU, Hisar was granted a fund of Rs. 20.0 lacs for the establishment of BIF. The Section has added hardware and software and has a leased line Internet connectivity of 512 Kbps in place.

The Section started M. Sc. Programme in Bioinformatics in 2004. A separate infrastructure with latest hardware and other infrastructural facilities is in place in the College of Basic Sciences & Humanities.

2. Major research activities in Biotechnology and its related fields at your institution: • Micro-propagation of crop plants • Development of transgenics • Molecular mapping, gene tagging and Marker assisted selection • DNA Fingerprinting • Value addition to plants and microbes 3. Area of Specialization of the centre: Teaching Bioinformatics Bioinformatics in Agricultural Sciences (rice crop of interest)

4. Major activities of the centre during the year 2006-07: Teaching Consultancy to researchers 5. Infrastructure facilities in the Bioinformatics Centre Computer & Communication facility PCs – 50 Servers – 2 8-Node Cluster – 1 Internet connectivity – 512 KBPS Telephone and Fax – 01662-289114, 234003; 284310 (Fax) Scientific Software packages GPL software, MOE, ChemOffice, PAUP Databases & other information resources PDB (local mirror) 6. Details about staff members working in the centre (Name of the staff, Designation, Specialization and period of working. Please indicate their absorption status) NIL

331 7. Types of services provided Teaching, Internet access, consultancy

8. Educational activities with details of placement M.Sc. Bioinformatics – started in 2004 Placement – 2004-06 batch - 16/17 2005-07 batch - 9/13 9. Initiative to validate the outcome of bioinformatics resources NONE as the BIF is one year old only 10. Collaborative works/ initiatives Creation of Multimedia database of crop plant diseases (with the Department of Plant Pathology, CCS HAU, Hisar)

11. Databases/ Software packages developed Database –NIL Software – One (Statistical analysis for agricultural Scientists) 12. Papers published or presented in the conferences with reference 1. G. Bala and Sudhir Kumar. QSAR studies on HIV-1 Reverse Transcriptase Inhibitors. Proceedings of National Conference on Advances in Chemical Engineering and technology. March 26-27, 2007, 101-108. 2. Jyotika and Sudhir Kumar. Virtual Screening on HIV-1 Reverse Transcriptase Inhibitors. International Conference on Molecular Cellular Biology and Therapeutics of HIV and Associated Viral Infection(CoMBaT HIV), 12-14th January,2007

13. Initiation of R&D activities in Bioinformatics • Parallelization of bioinformatics algorithms • Tools for sequence analysis and gene finding 14. Details of Training/ Workshop organized and total no. of user trained Nil, One proposed March 3-12, 2008 15. Impact shown by your centre on the growth of biotechnology and allied areas • Imparting education to PG students of Bioinformatics • Teaching basic bioinformatics course to Biotechnology students • Assisting in data analysis to researchers 16. Future activities To start Ph.D. in Bioinformatics

332 Plant genome annotations and analysis

Additional Details: Name of the Coordinator: Dr. Sudhir Kumar Postal Address: Bioinformatics Section, College of Basic Sciences & Humanities, CCS Haryana Agricultural University, Hisar – 125 004 Phone Number: 01662-289114, 234003; Mobile: 9354320276; Email: [email protected]; Website: http://hau.ernet.in/bioinfo Name of Contact Person(s): Dr. Sudhir Kumar Email: [email protected]

333 Dr. B. R. Ambedkar Center for Biomedical Research, Delhi Coordinator : Dr. Madhu Chopra

1. Summary of the progress made by the centre from its inception ACBR is running courses M.Sc. and M. Sc.-Ph.D. in biomedical sciences covering almost all subjects of biotechnology and related fields. Students at ACBR study courses like Biochemistry, Genetics, Medicinal Chemistry. The Bioinformatics facility thus developed over years has been strengthened by purchasing 3 more workstations to existing 3 nos. Software licenses have been increased from one to three on various modules of INSIGHT II. A workshop has been organized on 28-20 January 2008 for 15 participants to give hand on training to them on available software modules. A list of publication in the year 2006 has been provided to show scientific progress during this period.

2. Major research activities in Biotechnology and its related fields at your institution Following are the fields of research in biotechnology. The mandate is to perform and promote high quality research in Biomedical Sciences, in areas that touch human health, such as: Medicinal Chemistry; Bio-organic Chemistry; Protein Chemistry; Proteomics; Natural Product Chemistry; Bio-Inorganic Chemistry; Drug Metabolism and Toxicology; Pharmacology; Medical Biotechnology; Molecular Genetics; Developmental Biology

3. Area of Specialization of the centre ¾ Medicinal Chemistry and Natural Products ¾ Molecular Genetics and Medical Biotechnology ¾ Clinical Biochemistry and Immunology ¾ New drug discovery and commercialization

4. Major activities of the centre during the year 2007-08 1. 6th Annual Symposium on Frontiers in Biomedical Research November 30-December 2 2006 2. Summer undergraduate Research Training Programme (Annual)

5. Infrastructure facilities in the Bioinformatics Centre iv. Computer & Communication facility Computer Labs with A Cs 2 Capacity of Computer Labs 12 X 2= 24 Lease Line connection provided by the University. No. Of Configuration Used as Computers 1 SGI Silicon graphics, Workstation Research Facility, Insight II and Catalyst 6 HP 4300 workstation Research Facility, Insight II and Calalyst 17 P-4, RAM 512, HDD 80 GB Other softwares : Accelrys GCG , TSAR, Statistical Analysis Tool, DEEP VIEW etc. 40 P-3, RAM 256, HDD 20 GB 11 P-2, RAM 256 + 32 MB, -Do- 334 v. Scientific Software packages S. Software Year USEFUL TOOL No. (Purchase) 1. Insight II 2003 Protein structure prediction and modeling Drug design. Docking 2. CATALYST 3D QSAR, pharmacophore modeling 3. Accelrys Package 2003 Protein and nucleic acid seq analysis -GCG tool 4. TSAR 2003 2 D QSAR 5. Statistical analysis 2006 Statistical data & Analysis tool Tool 6. Dragon 2003 Descriptor calculator for QSAR 7. DEEP VIEW -- Basic visualiser 8. Graph Pad Statistical Analysis 9. AMBER 2005 DNA-Protein interaction and modeling 6. Details about staff members working in the centre (Name of the staff, Designation, Specialization and period of working. Please indicate their absorption status) Professor= 1; Reader= 2; Lecturer = 5

7. Types of services provided: Teaching and Research

8. Educational activities with details of placement Ph.D. Students : Completed : 65, Ongoing : 60 Students Qualified CSIR-UGC-NET Examination (1999-2006): 140 Career options by students: Research 97 % ; Other Jobs 3 %

9. Collaborative works/ initiatives: Various projects are under progress with national and international Institues such as with INMAS, DEPAS (DRDO), IGIB (Mall Road, VPCI (DU), ICPO (Noida), ST In Corporation, Italy; SIDA Sweden

10. Papers published or presented in the conferences with reference • Ganapathi M, Singh G.P, Sandhu K.S., Brahmachari S.K., Brahmachari V. 2007. A whole genome analysis of 5 Œ regulatory regions of human genes for putative cis-acting modulators of nucleosome positioning. Gene, 391, 242-251. • Bengani H, Ganapathi M, Singh G.P. and Brahmachari V. 2007. Mining of Putative cis-acting Elements for Chromatin Mediated Regulation of Hox Genes in Mammals by in-silico Analysis. J. of Experimental Zoology (Mol Devel & Evolution), 308:1-12. • Bakshi R., Mehta A.K., Sharma R., Maiti S., Pasha S., Brahmachari V. 2006. Characterization of a human SWI2/SNF2 like protein hINO80: Demonstration of catalytic and DNA binding activity. Biochemical and Biophysical Research Communications 339, 313–320. • Madhu Chopra and Anil K. Mishra, Ligand-Based Molecular Modeling Study on Chemically Diverse Series of Cholecystokinin-B/Gastrin Receptor Antagonists: Generation of Predictive Model Journal of Chemical Information and Modeling, 45, 1934-1942, 2005. 335 • Invited lecture “Three dimesional pahrmacophore modeling and database searching for drug design and development of target specific pharmaceuticals” by Dr. Madhu Chopra, December 2006, Frontiers in Biomedical Research, December University of Delhi • Workshop on Pharmacoinformatics: Tools for Drug Target Identification at NIPER March 14th-16th,2007, “Computer aided drug design of novel NSAIDs as selective cyclooxygenase –2 inhibitors as anti cancer agents” Ruby Gupta and Madhu Chopra Poster presentation by RG

11. R &D activities in Bioinformatics i. Design, Synthesis and Evaluation of Non Peptidic CCK-B/Gastrin Receptor Specific Antagonists for Targeting CCK-B receptor Expressing Tumors. ii. Computer-Aided Design of Novel NSAIDs as Selective Cyclooxygenase-2 (COX-2) inhibitors to target tumors: Mechanistic study of anticarcinogenic role of NSAIDs iii. In Silico Prediction : mechanism of transacetylation activity of Calreticulin. iv. Mining the Human Genome for Global regulatory Genes: Characterization and Functional analysis v. Role of Epigenetics in Genome Function and Transactions. vi. Cloning and functional characterisation of ETO-binding protein in normal and acute myeloid Leukemia.

12. Details of Training/ Workshop organized and total no. of user trained : Being organized in January 2008 as detailed below:

• 7th Annual Symposium On Frontiers In Biomedical Research (Fbr- 2008):Workshop on Bioinformatics and Molecular Modeling in Drug Design 28th-30th January, 2008 • Total no. of participant to be trained: 15

13. Impact shown by your centre on the growth of biotechnology and allied areas. In this you may highlight the details like number of paper published/ number of papers published with the help of your centre, how your centre is promoting various activities of your organization and neighboring institutions, manpower trained, tools developed, patents & copyrights acquired and other services offered etc.

• Year of Course Commencement : 1998 (M.Sc.-Ph.D. Combined Programme in Biomedical Sciences) • Visiting/Guest Faculty: 20 • Research Publications (Last 6 years) : 75 • Patents & Technologies Transferred : 5 • Number of Projects: (i) Industrial : 3 (ii) Government Agencies : 48

14. Additional Details: Name of the Coordinator: Dr. Madhu Chopra Postal Address: Dr. B. R. Ambedkar Center for Biomedical Research, University of delhi, Delhi 110007

336 Phone Number 011-27666272 Mobile:09810488199 Website:www.acbrdu.edu Name of Contact Person(s): Dr. Madhu Chopra Email: [email protected]; [email protected]

337 Fakir Mohan University, Balasore, Coordinator : Prof. Amarendra Narayan Misra

1. Summary of the progress made by the centre from its inception:

The Bioinformatics Centre of Fakir Mohan University, Vyasa Vihar, Balsore- 756017, Orissa is now established after procuring all the necessary hardware suggested by Department of Biotechnology (Govt. of Inida, vide DBT order No. BT/BI/04/055/2001 dt. 22 September 2006). Due to prohibitive cost and other limitations, the softwares could not be obtained so far. Once the BIF is shifted to the new campus of the University during February-March 2008, the Centre will be fully functional.

2. Major research activities in Biotechnology and its related fields at your institution:

Stress signaling and adaptive strategies in living systems, Marine Biotechnology, Biosensors, Nano-biology, Blood related problems.

3. Area of Specialization of the centre:

Teaching in Biotechnology and Biosciences.

4. Major activities of the centre during the year 2007-08

Establishing the infrastructural facility.

5. Infrastructure facilities in the Bioinformatics Centre A. Computer & Communication facility: Only computers are procured as per DBT specifications. Steps are being taken by the University for the procurement of communication facilities will be installed. B. Scientific Software packages: Nil C. Databases & other information resources: Nil

6. Details about staff members working in the centre (Name of the staff, Designation, Specialization and period of working. Please indicate their absorption status): Nil

7. Types of services provided: Services will start only when the Centre is established.

8. Educational activities with details of placement: Not applicable.

9. Initiative to validate the outcome of bioinformatics resources: Not applicable.

10. Collaborative works/ initiatives: Collaborative works are initiated with the Department of information and Communication Technology.

338 An initiative is made to establish long term collaborative work with CIFA, OUAT and other University Institutes having Bioinformatics and Biosciences research and teaching programs.

11. Databases/ Software packages developed: Nil

12. Papers published or presented in the conferences with reference: Nil

13.Initiation of R&D activities in Bioinformatics: Two students are enrolled for Ph.D. degree related to Bioinformatics.

14.Details of Training/ Workshop organized and total no. of user trained: March 24-25, 2007. Users trained 50.

15. Impact shown by your centre on the growth of biotechnology and allied areas. In this you may highlight the details like number of paper published/ number of papers published with the help of your centre, how your centre is promoting various activities of your organization and neighboring institutions, manpower trained, tools developed, patents & copyrights acquired and other services offered etc. Once the facility is fully functional at a permanent floor in the School of Biotechnology building, which the University projects to be ready by February 2008, various activities of the Bioinformatics Centre will be started. This includes starting of M.Sc. Bioinformatics course initially, before moving to other Bioinformatics activities. At present the students and faculties of the Department are trained in various aspects of Bioinformatics.

16. Future activities: Teaching and research programs in Bioinformatics.

Additional Details: Name of the Coordinator: Prof. Dr. Amarendra Narayan Misra Postal Address: School of Biotechnology, Fakir Mohan University, Vyasa Vihar, Balasore-756019, Orissa State Phone Number: 06782-261580 Mobile: 9437295915 Email: [email protected]

Name of Contact Person(s): (i) Prof. Dr. Sukadev Nanda, ii) Dr. A.C. Kar, Vice-Chancellor, Registrar, Fakir Mohan University, Fakir Mohan University, Vyasa Vihar, Balsore-756019, Vyasa Vihar, Balsore- Orissa State. 756019, iii) Mr. S. Marandi, Orissa State. Controller of Finance, Fakir Mohan University, Vyasa Vihar, Balsore-756019, Orissa State.

339 Forest Research Institute - Dehradun Coordinator: Er. Neelesh Yadav

1. Summary of the progress made by the centre from its inception: Forest Research Institute –Dehradun is received the grant for BIF on November, 2007. A core group has been created in the institute for the special research initiative for Bioinformatics. FRI is the premier institute of forestry research in the country. The Institute also administered training of forest officers and forest rangers in the country and after Independence it was aptly renamed as Forest Research Institute and Colleges. The separate Bioinformatics lab is under progress, hardware/ software is available but procurement of new tools is under process.

2. Major research activities in Biotechnology and its related fields at your institution: The FRI has a well established infrastructure of laboratory, library, herbarium, arboreta and experimental field areas for providing scientific and training services. The genetics & tree propagation , Forest pathology (Molecular biology lab) , tissue culture discipline , Nanotechnology research in forest products, Statistical modeling of trees , of are the main research domain those are working biotechnology aspect of forestry.

3. Area of Specialization of the centre : Forestry Biodiversity Informatics ,Bioinformatics Education & Human Resource Development , Database of DNA fingerprinting of important tress species like Sal, Deodar, Shisham, Eucalypts etc. ,Medicinal plants of forests, Forest Products, Forest Soil and Land Reclamation, Genetics and Tree Propagation, Non-wood Forest Products, Pathology, Silviculture

4. Major activities of the centre during the year 2006-07 : NA 5. Infrastructure facilities in the Bioinformatics Centre

Computer & Communication facility : The BIF centre has order to procure the 10 Desktop computers (Core 2 duo based processor) , Web server, database server, Internet connection is available through LAN in whole campus, but process for separate leased line is under progress.

Scientific Software packages: SPSS, Windows server Standard 2003, Visual studio .NET (1 User), MS-Office 2007 , SQL Server 2000, MySQL server 5.0 , PHP 5, Apache server, (Open source soft wares),

Databases & other information resources: vii. Web based interactive database for Botany Herbarium (Approx 3,30,000) has been develop by the centre and the data entry work is going on. viii. The database of Forest insects is developed. ix. The Development of Medicinal pants of northern India in under progress. 6. Details about staff members working in the centre (Name of the staff, Designation, Specialization and period of working. Please indicate their absorption status) 340

Sl.No. Name Designation Specialization Period of Absorption Working Status 1 Er. Neelesh Coordinator Bioinformatics, Since Year Permanent Yadav data mining, 2003 as IT Communication Scientist ,

7. Types of services provided : E-mailing ,Internet access, LAN management ,System management, Web designing & hosting, Software development, Database development on forestry reserach,Hardware maintenance of FRI, Digitization of old collections of forestry, Human Resource Development in Bioinformatics at FRI University-Dehradun, R&D and S&T Publications, Computational services, Information support to whole FRI.

8. Educational activities with details of placement: FRI was conferred the status of Deemed University in 1991 with the objective of imparting education in different branches of forestry and environment. Courses being run by the FRI University are:

Two year Degree Courses: • M.Sc.Forestry (Economics and Management) • M.Sc. (Wood Science and Technology) • M.Sc. (Environment Management) One Year Diploma Courses: • Post Graduate Diploma in Management of Non-Wood Forest Product Resources • Post Graduate Diploma in Biodiversity Conservation Six Month Certificate Course: • Certificate course in Pulp & Paper Technology Doctoral Programme: • Under its Doctoral Programme the University also confers Ph.D. Degree in various fields related to forestry and environment.

9. Initiative to validate the outcome of bioinformatics resources : The activities of the center has helped in popularizing the concept, utilities and tools of Bioinformatics among the similar organizations and individuals. Center has successfully meet their information requirements. New databases in the areas of forestry research have been generated. The network and services created is playing instrumental role in communication, database research, patent searches and market search. Centre is also very useful for biology teaching for FRI University-Dehradun.

10. Collaborative works/ initiatives : IARI, IIT Roorkee, Forest Survey of India, IGNAF-Dehradun, ENVIS center of FRI,

11. Databases/ Software packages developed : 1.Digital Herbarium System of FRI. 2.Insects Information System.

12. Papers published or presented in the conferences with reference:

341 Forestry Bioinformatics, Neelesh Yadav, a paper presented in Scientific Data and Knowledge within the Information Society ,20th CODATA International conference, Beijing, China.

Role of Bioinformatics in Forestry Research, invited lecture delivered at national Biotechnology conference -2006: CurrentTrends & Future Perspectives at IIT-Roorkee, by Neelesh Yadav and published in proceedings.

13. Initiation of R&D activities in Bioinformatics: Since its inception the Centre has focused on R & D activities particularly in the area of biodiversity database development of computational tools for its storage, retrieval, analysis, interpretation and computer graphic modelling. The centre has also focused on the development of appropriate tools for integrating the information resources of BTIS Centres. The centre is tryng to become CoE for Bioinformatics forestry Research.

14. Details of Training/ Workshop organized and total no. of user trained : NA

15. Impact shown by your centre on the growth of biotechnology and allied areas. In this you may highlight the details like number of paper published/ number of papers published with the help of your centre, how your centre is promoting various activities of your organization and neighboring institutions, manpower trained, tools developed, patents & copyrights acquired and other services offered etc.

- NA (Because BIF FRI-dehradun recently established) 16. Future activities : • To establish a national database repository for forestry biodiversity informatics and provides biodiversity data analytic tools and techniques. • To develop a web portal on forestry Bioinformatics and integrate the information and all other resources of ICFRE institutes with BTISnet. • To establish a comprehensive database including all information of plants growing in India particularly and genetical data bank of imp. Plants species. • To establish a web portal for establishing collaborative ventures with the institutions / researchers working on biodiversity matters and integrating the information resources. • To establish genetic sequence database of the intraspecific variants of the endemic plants of the Himalayan region. • The centre would link with other R & D / Educational institutions for establishing regional sub-centres throughout Uttarakhand state for biodiversity data documentation. • The data acquisition related with the plants of Uttarkhand, UP, Himachal Pradesh, J&K will be carried out in these regional centres. Data management, data analysis and interpretation, formulation of novel strategies and R & D initiatives for sustainable utilization of the genetic 342 resources will also be carried out through cooperative functioning of the main centre and the sub-centres. • To develop FRI-Dehradun as a Nodal Centre for “National Forestry Bioinformatics Research & Development” which will be an information and computational solution provider for forestry Biodiversity data management, data analysis and interpretation

Additional Details: Name of the Coordinator: Er. Neelesh Yadav Postal Address: 1, Hill Road, FRI Campus, P.O. New Forest-Dehradun (248006) Phone Number:0135 2754023 ext 4234 Mobile: 9411385495 Email: [email protected] Website: www.fri.res.in

Name of Contact Person(s): Er. Neelesh Yadav, Scientist Incharge, IT Cell, FRI Email: [email protected]

343 Guru Jambheshwar University of Science & Technology, Hisar Coordinator : Prof. J. S. Rana

1. Summary of the progress made by the centre from its inception: i. The Executive Committee as per DBT guidelines has been approved. ii. Three bays air-conditioned laboratory has been established from BIF. iii. Independent Telephone line along with broad band internet by BSNL installed from BIF. iv. 13 HCL Computers purchase through this grant. v. Introductory Bioinformatics course introduced in M. Sc. Biotechnology and M.Tech. Nano Sc. & Tech

2. Major research activities in Biotechnology and its related fields at your institution Sl. Name of Student Name of the Ph. D. Research title Name of the No Supervisor Already Completed 1. Dr. Purkayastha “Race identification of Prof. Ashok Chaudhury Sharmishtha Macrophomina phaseolina causal agent of root rot of cluster bean using molecular markers.” 2. Dr. Anita Punia “Studies on DNA fingerprinting of Prof. Ashok Chaudhury Some Superior Guar Genotypes by RAPD.” 3. Dr. Pal Minakshi In Vitro Culture and induction of Prof. Ashok Chaudhury Shikonin Production in Arnebia.” 4. Dr. B. Kaur “Identification of races of Xanth Prof. Ashok Chaudhury Axonopodis pv. Cyamopsidis using molecular markers.” Ph. Ds under Progress 5. Ms. Gaurva Priyanka Genetic Transformation of Rice for Prof. Ashok Chaudhury Enhancement of Salinity Tolerance. 6. Ms. Bansal Monika Genetic Transformation of Tomato Prof. Ashok Chaudhury (Lycopersicon esculentum) for Enhancement of Salinity Tolerance. 7. Ms. Praveen Dahiya Isolation, Screening Purification & Dr. Neeraj Dilbaghi Characterization of Microbial Lipases. 8. Mr. Umesh Gautam Biochemical and Molecular Marker Prof. Ashok Chaudhury Studies for Bread Quality Improvement in Wheat. 9. Ms. Pooja Arora Molecular approaches for the development of SCAR assay as a diagnostic tool for the detection and distribution of dsRNA among isolates of Macrophomina phaseolina. 10. Mr. Rakesh Yadav Studies on Genetic Modification of Prof. Ashok Chaudhury Lignin Biosynthesis Pathway in Poplars for Low Lignin Content. 11. Mr. S. T. Bharani Characterization of myostatin gene Dr. Neeraj Dilbaghi Kumar in indigenous chicken breeds. 12. Mr. Raman Kumar Bioremediation of waste water for Dr. Namita Singh heavy metals through microbes. 13. Ms. Sarika Poonia Low temperature acclimatization and Dr. Namita Singh its regulation in the Cyanobacterium Spirulina. 344 14. Ms. Meenu Rani Studies on genetic diversity in (Aloe Dr. Vinod Chhokar bardabensis) genotypes using molecular markers. 15. Mr. Yogesh Kumar Marker assisted gene pyramiding to Dr. Vinod Chhokar enhance rust resistance in wheat. 16. Mr. Sandeep Jaglan DNA fingerprinting of some Dr. Priyanka Siwach important lines of Isabgol. 17. Ms. Priyamvada Molecular mapping of leaf rust Dr. Priyanka Siwach resistance gene LR34 in wheat. 18. Ms. Uma Gaur Genetic characterization of Indian Prof. Ashok Chaudhury duck populations (Anas platyrhynchos) using molecular markers. 19. Ms. Suman Bangar In vitro culture and genetic diversity Prof. Ashok Chaudhury studies of Fenugreek using molecular markers. 20. Ms. Geetu Identification of SNP markers for Prof. J.S.Rana wool genes indigenous sheep breeds. 21. Ms. Manju Rani Characterization of Helicoverpa Prof. J.S.Rana armigera for their insecticidal resistance in semi and cotton eco system. 22. Ms. Manju Yadav Molecular characterization of Prof. J.S.Rana mustard (Brassica juncea) genotypes for their resistance against mustard aphid. 23. Ms. Seema Genetic characterization of cotton Prof. J.S.Rana varieties for their resistance against sucking pests. 24. Mr. Alok Pandey Study on gene expression in buffalo Dr. Namita Singh in vitro matured oocytes and SCNT produced cloned embryos. 25. Ms. Sonia Kohar Production purification & Dr. Namita Singh characterization of microbial Phytase enzyme & its application in animal feed. 26. Mr. Anil Kumar Molecular characterization of major Dr. Vinod Chhokar candidate genes associated with milk fat % in Indian buffaloes. 27. Mr. Vikas Beniwal Purification, characterization Dr. Vinod Chhokar molecular gene cloning, sequencing of tannases form bacteria. 28. Ms. Mukta Agarwal Identification of molecular Markers Dr. Vinod Chhokar Related to Chapati Quality traits in Wheat. 3. Area of Specialization of the centre We specialize in the areas of food, industrial, plant and animal biotechnology 4. Major activities of the centre during the year 2007-08 ¾ The Executive Committee as per DBT guidelines has been approved. ¾ Three bays air-conditioned laboratory has been established from BIF. ¾ Independent Telephone line along with broad band internet by BSNL installed from BIF. ¾ 13 HCL Computers purchase through this grant. ¾ Introductory Bioinformatics course introduced in M. Sc. Biotechnology and M.Tech. Nano Sc. & Tech. 5. Infrastructure facilities in the Bioinformatics Centre 345 Computer & Communication facility: We have developed a full fledged alboratory with internet facilities for about 35 students. The work on further improvements in the database management across the department is underway and would be completed very soon. Scientific Software packages In addition to the entire Window package we have procured the educational tool of the basic software package for biology teaching in this laboratory Databases & other information resources: We plan to procure more databases of use in this laboratory on receipt of funds for the purpose 6. Details about staff members working in the centre (Name of the staff, Designation, Specialization and period of working. Please indicate their absorption status)

Sl. NAME OF THE DESIGNATION WORKING ABSORPTION NO. STAFF SINCE STATUS (YES/NO)* 1. Dr. J.S. Rana Professor& 2006 YES Chairman 2. Dr. Ashok Chaudhury Professor 2001 YES 3. Dr. Neeraj Dilbaghi Reader 1998 YES 4. Dr. Namita Singh Sr Lecturer 2001 YES 5. Dr. Vinod Chhokar Sr Lecturer 2001 YES 6. Dr. Priyanka Siwach* Sr Lecturer 2001 YES 7. Anil Kumar Lecturer 2005 YES 8. Dr. Rajesh Thakur Lecturer 2006 YES 9. Santosh Kaushik Lecturer 2006 YES 10 Sandeep Kumar Lecturer 2006 YES 11. Dr. Alka Rao Lecturer 2006 YES 7. Types of services provided: At the moment this laboratory is open for access by all the students 8. Initiative to validate the outcome of bioinformatics resources We are in the process of developing our facility for this purpose and would update it further in the coming year for the purpose of validating the outcome qualitatively 9. Collaborative works/ initiatives: We collaborate with the department of Biotechnology and molecular Biology, CCS Haryana Agricultural University Hisar, Central Institute of Research on Buffaloes, National research centre for equines and Centre of Plant Biotechnology Hisar on various aspects of research and teaching 10. Databases/ Software packages developed : None 11. Papers published or presented in the conferences with reference 12. Initiation of R&D activities in Bioinformatics We are still developing our facility for this purpose and would initiate the research activity in the coming academic session. 13. Details of Training/ Workshop organized and total no. of user trained We propose to organize the training in the month of February, 2008 346 14. Impact shown by your centre on the growth of biotechnology and allied areas. In this you may highlight the details like number of paper published/ number of papers published with the help of your centre, how your centre is promoting various activities of your organization and neighboring institutions, manpower trained, tools developed, patents & copyrights acquired and other services offered etc. The Department of Biotechnology is an upcoming Department of the region and is competing well in the research areas like food biotechnology, industrial Biotechnology, plant biotechnology, Nano science & Technology. Within seven years of its establishment the department has earned a reputation of a progressive department in the academic circles. This can be judged by the fact that the department has earned several research projects from various funding agencies like DBT, DST, Govt. of India, UGC, State level Science and Technology department. The department is continuously working towards developing and strengthening the existing faculties and creating the new facilities in the innovative programme of research like Bioinformatics. Therefore it is imminent to have the facilities like Bioinformatics for biology teaching to meet the increasing demand o the qualified technocrats in this specialized field. 15. Future activities ¾ To strengthen the research facilities for Bioinformatics ¾ To start M.Sc. Bioinformatics course specialized in the areas of Food and industrial Biotechnology ¾ Gene expression data analysis (using dimensionality reduction and supervised/unsupervised classification methods, gene–marker recognition and mining, and analysis of gene-expressional time series) ¾ Protein structure alignment methods, including computational discovery of embedded sequence-structure- functional relationships ¾ We plan to develop our full fledged facility of Bioinformatics in the coming year alongwith the development of

Additional Details: Name of the Coordinator: Prof. J.S.Rana Postal Address: Department of Biotechnology, Guru Jambheshwar University of Sc. & Tech. Hisar-125001 Phone Number:01662-263165 Mobile: 09896300256 Email: [email protected] Website: www.gju.ernet.in Name of Contact Person(s): Prof. J.S. Rana Email: [email protected]

347 HNB Garhwal University, Garhwal Coordinator : Prof. Asha Cahndola-Saklani

1. Summary of the progress made by the centre from its inception We have been experimenting, at a miniscule level, with innovative methods like computer-aided teaching (CAT), inquiry based projects, Learn-while- Serve Biology outreach programs with a view to improve Biology & allied teaching in rural Himalaya for several years. Since 2006 these have been brought under the frame-work of DBT-BIF Centre catering to various levels. Thus: • Career counseling & research orientation- 10+, UG students • Training in analytical & Biological techniques including molecular, research methodologies, internet access, search & retrieval, data base development & mining, application of statistical and Bioinformatics tools – PG & research • Sensitization of local students through innovative student - community interactive research projects towards Biology based programs with special reference to biodiversity, bio-resource technology (including entrepreneurship) and community health care, simultaneously generating data base amenable to application of Bioinformatics tools. • Preparation of course material –CD ROMs, Web based etc. • Introduction of Bioinformatics PG courses (already approved by BOS, HNBGU) 2. Major research activities in Biotechnology and its related fields at your institution. Genome diversity of Himalayan human, bird & fish fauna (39 Acc Nos from NCBI with CCMB); Database generation on IDD and thyroid hormone profiles, Genetic/molecular basis of neuro-dev disorders, phyto-chemistry, natural dyes, microbiology 3. Area of Specialization of the centre Environmental Endocrinology, Immunoassay technology, Conservation Biology, Molecular Physiology, Mol Phylogeny 4. Major activities of the centre during the year 2007-08 ¾ BIF serves as a viable student participatory platform in a warm ambience with inquiry based learning as an enjoyable experience motivating critical thinking thru interactive brainstorms, audiovisual seminars, computer sessions, GDs, hands-on demos, nature trails & bird-watching. UG PG students visit the centre daily in spare time. ¾ Introduced m-education (mobile technology) in biology & allied subjects for e- learning and information retrieval at SRT (rural) Campus of HNBGU (UG/PG/Research) ¾ Set up a network for Biology & allied teaching- support & counseling for 10+ students via media seven schools in rural Himalaya (within 10 km radius of the BIF Centre) Trained about 40 UG students in computer applications who in turn trained 5 students each from six neighboring schools ¾ Organised 04 Workshops and 03 Learn-while Serve Biology outreach camps in villages ¾ Two Bioinformatics student projects (Elective MSc Biotech course) Research: Molecular phylogeny of Himalayan fish Schizothorax (D Phil thesis- with CCMB); generated data base on Iodine deficiency disorders, thyroid hormone profiles, health & nutritional status in rural Himalaya; database on genome diversity Him. populations; Commenced work on Mol phylogeny of Him finches & genetic basis of neuro-dev disorders. 5. Infrastructure facilities in the Bioinformatics Centre

348 A. Computer & Communication facility : SRT Campus 02 Servers,10 computers, 02 Telephone connections. 04 Mobile modems; Chauras campus: 05 computers 02 servers Scientific Software packages: GraphPad Prism, Costat, Instat, SPSS, MEGA, PHYLIP Databases & other information resources

6. Details about staff members working in the centre Sl. NAME OF THE STAFF DESIGNATION WORKING ABSORPTION STATUS NO. SINCE (YES/NO)* 1. Asha Chandola-Saklani Coordinator Nov 2006 YES Regular 2. Atul Kathait Bioinformatics Jan 2007 No, Ad hoc Assistant 3. Pratap S Bisht Field Attendant Jun 2007 No, Ad hoc

4. - RA Yet to be appointed

▪ Some Faculty members including Drs PC Lakhera, DK Sharma, N Agarwal, JS Rana regularly visit the centre for internet and also offer help ▪ Several past trainees are giving their services on Learn while Serve basis.

7. Types of services provided Teaching support thru CD ROMs, Internet, AV seminars, computer sessions, WS, Sensitization to biodiversity/bioresources/health care etc thru Bio-outreach camps. Aid student projects/research in data analysis. 8. Educational activities with details of placement: Bioinformatics offered as 01 compulsory credit and 09 credit Elective course in MSc Biotech/Zoo. 10 students placed in Univs /instts (including JNU,NC ,CCMB, NII, IIT Powai etc)& MNC eg. BIOCON, AVENTIS 9. Initiative to validate the outcome of bioinformatics resources Trained 10+, UG, PG students in basic computer education, web based tools (data mining & data compilation) & motivated them towards careers in Bioinformatics/BT. A network for CAT was established for neighboring schools within 10 km radius of Centre. BIF services were brought through Biology outreach camps in interior rural villages of Tehri and Chamoli (15 km from roadhead). 10. Collaborative works/ initiatives : Following projects/PhD programs undertaken with- CCMB Hyderabad: Mol phylogeny of Himalayan finches, Genetic basis of strabismus NBRI Lucknow: Mol Systematics Sapindus, NDRI Karnal: Probiotic culture, IVRI Bareilly PCR based detection of Zoonotic Salmonella IARI Delhi Mol studies maize. 11. Databases/ Software packages developed Database for Iodine deficiency disorders developed from Himalayan villages & about 5,000 thyroid hormone profiles generated. 12. Papers published or presented in the conferences with reference i.A Farswan, Kiran Negi, ACS . XXIII Int Cong Ornithology, Hamburg Germany Aug 2006 ii.Application of Biotechnology and Bioinformatic tools to the science of biodiversity SC Diyundi et al International symp Biogeography & biodiversity, HNBGU 0rganized by Int Geography Union May 2007 iii.Adaptation to high altitude: do genes play any role? Diyundi SC et al Int Symp Human Genetics, JNU 2006 13. Initiation of R&D activities in Bioinformatics Bioinformatics tools are used in on going researches mentioned above. 14. Details of Training/ Workshop organized and total no. of user trained

349 • Student Interactive Brainstorm viz. HRD in Science & Technology: for WHAT & HOW - a Road Map (Higher Edu in UA). Affil College Teachers, students. Lead discussants from JNU, BHU, IIT Kanpur, RTI, Sci & Tech Councils of UA 1-2 Dec 2006 300 participants • lecture-cum-demo Workshop Diagnostic Tools (PCR/immonobased) & Med Instru mentation for UG/PG science students. Lead speakers from NIH Bethesda USA, AIIMS Delhi, PGIMR Chandigarh, HIMS Dehradun 14-15 January 2007. No of users : 300 • workshop on Career orientation in Biotechnology & Bioinformatics for 10+2 Students. SRT Campus, Tehri. 1-5 November 2007 No of users trained: 75 • 03 Learn-while-Serve student participatory Biology Outreach camps in Tehri & Chamoli Garhwal, 7-8 days each; covered 13 villages gathering information on bio- resources, nutrition, health & economic status for database development. No. of users trained 10 PG, 40 UG, 30 10+2 students. 15. Impact shown by your centre on the growth of biotechnology and allied areas. See column 04 16. Future activities • Set up a MobEd lab (Genomic Mobile lab equipped with VSAT) for support of Biology & allied subject teaching in rural Himalaya to cater to schools & colleges within 30 km radius • Set up a network for Biology & allied teaching- support & counseling for 10+, UG students and faculty through Biology outreach camps in NW Himalaya (entirely rural) • Develop e-learning course material on CD ROMs, eventually to be available on web. • Commence Advance Diploma or MSc Bioinformatics from July 2008 • Organisation of workshops to cater to different levels viz. 10+, UG, PG, Research • Organisation of symposia in the fields of Biological diversity & Health care with a molecules to ecosystem approach to provide a multidisciplinary platform • Following shall be the thrusts of research (funds from other agencies shall also be generated) ° Data base compilation on avifauna / ichthyofauna ° Data base generation avifauna, avian song repertoire, incidence of diseases, diagnostic facilities, mountain bio resources ° Phylogeography & Genetic diversity of finches, rudraksh ° Molecular basis of diseases ° Vocalization analysis in birds with a view to render syllable sequence amenable for use of algorithms e.g. UPGMA, to understand evolutionary patterns • Set up Centre of Excellence in Bioinformatics in the heart of the Himalaya and reach out to the entire Stateand eventually to the country and the world Additional Details: Name of the Coordinator: Prof. Asha Cahndola-Saklani FASc Postal Address: Post Box. 45, Srinagar Garhwal Uttarakhand-246174 Phone Number: Mobile 09412018010 Email [email protected] [email protected] Website: under preparation Name of Contact Person(s): Atul Kathait 9997809655 Email: [email protected] [email protected]

350 Holy Cross College, Tiruchirappalli, Tamil Nadu Coordinator : Dr. Daisy. P

1. Summary of the progress made by the centre from its inception:

The Bioinformatics Infrastructure Facility at the Dept. of Biotechnology & Bioinformatics, Holy Cross College was set up in October 2006. BIF, HCC procures has developed a database in the field of medicinal plants in treatment of diabetes and a server for the prediction of CpG islands in genomic sequences. The Facility conducts training programmes in introductory & advanced level of Bioinformatics for college staff, researchers and students of neighboring colleges. The Centre also aids in coursework of the M.Sc Bioinformatics program offered by the Department, besides this two interdisciplinary courses are offered to the postgraduate students of other disciplines. The communication facilities at the facility is been upgraded to 1 Mbps leased line internet connectivity from BSNL from the 512 kbps broadband connectivity.

2. Major research activities in Biotechnology and its related fields at your institution:

The major research activities include isolation and characterization of active compounds in some indigenous medicinal plants responsible for the antidiabetic, antioxidant and antimicrobial activity. Four novel compounds have been isolated and filed for patenting. Docking studies and Insilico analysis of these compounds are being done

3. Area of specialization of the centre:

The main area of specialization is Medicinal Plant studies. Apart from supporting Biotechnology research, the Centre is involved in creating specialized databases of medicinal plants. Other research works include: 1. In Silico Ligand efficacy testing of a purified antidiabetic compounds 2. In Silico analysis of enzymes of functional importance in medicinal plants. This includes the study of the whole metabolic pathway, the enzymes interacting and its products from the annotated entries in biological databases.

4. Major activities of the centre during the year 2007 - 08: • The DBT sponsored BIF was established in the Department of Biotechnology, Holy Cross College in October 2006. • Established a leased line connectivity of 1 Mbps speed at the Bioinformatics centre, from BSNL. • Maintenance and updation of the Facility’s website www.hccbif.org • A database on medicinal plants and a server for prediction of CpG islands were created. • 112 personnel benefited form the advanced & basic level training programmes in bioinformatics.

5. Infrastructure facilities in Bioinformatics Centre:

351 A. Computer & Communication facility Pentium IV HT Servers – 2GB RAM: HP Proliant ML 110G3 - 1 Pentium IV HT Servers – 2GB RAM: HP Compaq dx 7200 - 2 Pentium IV Computers – IntelR PentiumR D Processor 820 with EM64T 512 MB Scanner HP 2400c Printer HP Laserjet 1600 Printer HP Laserjet 1005 Photo Copier: Panasonic 1520P Printer cum Copier LCD Projector VPL ES3WT/2000 Sony 1Mbps Internet Line B. Scientific software packages GENOCLUSTERS (Developed by IGIB, CSIR & Jalaja Technologies) GeneD’cfer, Proteome Calculator, Seapath, PI Host, Proteome Calculator GENES TO DRUGS (Accelrys Package) GCG Wisconsin Package, Insight – II, Discovery Studio, TSAR, Accord and all other online tools

6. Details about staff members working in the centre: Sl. No. Name of the staff Designation Working since Absorption status 1. Dr.Daisy.P Co-ordinator 2006 yes 2. Ms.Nirmala.A Research Assistant 2007 yes

7. Types of services provided: • Training programmes for students, staff and researchers • Project Training for M.Sc & B.Sc students of the host institution as well as of other institutions. • Offering courses in Bioinformatics to PG students. • Support to R&D activities of the Department

8. Educational activities with details of placement:

The Facility conducts two 4 credit course in Bioinformatics to the M.Sc. Biotechnology and Bioinformatics students of the Department. The facility is made use of for the practical coursework of the Bioinformatics students. The passed out students are placed in Biotech companies and R&D institutes.

9. Initiative to validate the outcome of bioinformatics resources:

The research activities and regular training programmes validate the outcome of bioinformatics resources.

10. Collaborative works / Initiatives : nil

11. Databases/Software packages developed: Database for specific Medicinal Plants : DIAB Created a database for Medicinal plants showing positive control on the secondary complications of Diabetes besides checking glycemic levels. Available at: http://www.holycrossindia.ac.in/BIO-TECH-DB/home.html

12. Papers published or presented in the conference with Reference: 352 1. Hypoglycemic and other related effects of Elephantopus scaber extracts on alloxan induced diabetic rats’. Journal of Biological Sciences 7 (2): 433-437, 2007 2. A database for medicinal plants used in treatment of diabetes and its secondary complications. Bioinformation 2(1): 22 -23 (2007) 3. ‘Antidiabetic effect of a novel compound from Gymnema sylvestre R.Br leaves’ presented at the 28th Conference of Indian Association of Biomedical Scientists, Bharathidasan University,Trichy-24.

13. Initiation of R&D activities in Bioinformatics: Research efforts initiated are in the lines of: ƒ Insilico Comparative analysis of the apoptotic proteins of Mice and Humans

14. Details of Training / Workshops organized and total no: of users trained: • National Level workshop on “Bioinformatics: Tools & applications” Jan 8th -10th ’07. • Workshop on ‘Genome and Proteome analysis’ for College Staff, Research scholars, P.G students: Aug 20th - 21st, 2007. • Workshop on Discovery Studio, by Accelrys for Researchers and Scientist: Aug 23-24th 2007 • One day training to the M.Sc., Biochemistry students of Seethalakshmi Ramamswami College, Trichy: October 9, 2007. • An introductory class on Bioinformatics for the students of Srimad Andavan College, Trichy. Total number of persons trained till date is 112.

15. Impact shown by the centre on the growth of biotechnology and allied areas: Besides the Research and academic initiatives, the facility promotes human resource development of the students, staff and researchers.

16. Future activities: • Technical Training & Exposure in premier Commercial Drug designing softwares for scientists. • Open source journal accessibility for M.Sc students, and procurement of books and Journals in Bioinformatics. • To introduce a course on Bioinformatics for Ph.D (Biotechnology) students. • Hands-on Bioinformatics training for the students and staff of rural schools.

Additional details: Name of the Coordinator: Dr. Daisy. P Postal Address: Coordinator, Bioinformatics Infrastructure Facility Dept of Biotechnology & Bioinformatics Holy Cross College Tiruchirapalli – 620 002

353 Tamil Nadu Phone Number: 0431-2700637 Fax No.:0431-2713312 Email: [email protected] Website: www.hccbif.org Name of Contact Person(s): Dr.Daisy.P Email: [email protected]

354 Indira Gandhi Krishi Vishwavidyalaya, Raipur Coordinator : Dr. D. K. Sharma

1. Summary of the progress made by the center from its inception The Department has the credit to have run several national and International funded projects. Till date more than 35 Msc. and and 6 Ph. D. have been awarded degree. The Department of Biotechnology well developed infrastructure and laboratories to carry out scientific research of international standards. The Department has contributed towards HRD in the field of Biotechnology by organizing regular training program. Bioinformatics center is in the process of establishment. International Conference on “ Plant Genomics and Biotechnolgy: Challenges and Opportunities” October 26-28th, 2005.

2. Major research activities in Biotechnology and its related fields at your institution 1. Identification and characterization of biotic and abiotic responsive transcripts in rice using cDNA microarray, gene expression changes of selected genes and identification of the cis–acting elements and their target transcription factors 2. Tagging and mapping of gall midge resistance genes, Gene expression studies and fine mapping of gall midge and the use of in silico data base. In silico anchoring rice cloan contigs with putative candidate genes to QTLs associated with biotic and abiotic stress tolerance in rice 3. Use of different DNA marker to characterize germplas of different crop species, insect and pathogen population and beneficial microorganisms. 4. Standardization of high efficiency regeneration protocol for different crop plants 5. Assessment of rice accessions for nutritional quality traits (protein, lysine and micronutrient content).

3. Area of Specialization of the center :- 1) Mapping and Tagging of genes 2) Collection, isolation and characterization of microorganisms and rice accessions 3) Standardization of high efficiency in-vitro regeneration protocols 4) Transgenic research 5) In silico mapping 6) Screening of elite rice line for nutritional quality traits (protein, lysine and micronutrient content 7) Mushroom breeding

4. Major activities of the center during the year 2007- 08 ™ In silico construction of a new map for major abiotic stresses responsive ESTs. and putative candidate genes, Gene expression studies for gall midge resistance, Mushroom breeding and development of mapping population, Collection and characteization of Trichoderma and Pseudomonas fluorescence and Andrographis paniculata (kalmegh), Assessment of rice accessions for nutritional quality traits (protein, lysine and micronutrient content

355 5. Infrastructure facilities in the Bioinformatics Center b. Computer & Communication facility:- • Purchased Computers and Servers • Software as prescribed by the Govt. of India, Ministry of Science and Tchnology, DBT, (Bioinformatics Division) will be purchased during the current financial year. c. Scientific Software packages :- NIL d. Databases & other information resources NIL

6. Details about staff members working in the center (Name of the staff, Designation, Specialization and period of working. Please indicate their absorption status) 1) Dr. D. K. Sharma (Professor & Head, Department of Biotechnology 20 Years) 2) Dr. A. S. Kotasthane (Associate Professor, Plant Pathology, Microbiology, Microbial genetics Molecular Host Microbe Interaction 18 years) 3) Dr. Girish Chandel (Associate Professor Plant Breeding, Nutritional Fortification, Transgenics 15 years) 4) Dr. (Smt.) Zenu Jha Medicinal Plant Biotechnology 2 Years)

7. Types of services provided

8. Educational activities with details of placement

9. Initiative to validate the outcome of bioinformatics resources : High resolution physical map for all the 12 chromosomes of rice constructed with the use of available molecular marker databse on net is currently being used for fine mapping and functional genomics studies for biotic stresses and tagging of QTLs associated with biotic stresses.

10. Collaborative works / initiatives : NIL

11. Databases/ Software packages developed : NIL

12. Papers published or presented in the conferences with reference ( As In point No 15)

13. Initiation of R&D activities in Bioinformatics

14. Details of Training/ Workshop organized and total no. of user trained : Provided 5 (five trainings) on DNA marker technology since September 2000 to 2004 to 40 participants every year

15. Impact shown by your center on the growth of biotechnology and allied areas. In this you may highlight the details like number of paper published/ number of papers published with the help of your center, how your center is promoting various activities of your organization and neighboring institutions, manpower trained, tools developed, patents & copyrights acquired and other services offered etc. 356 • Fifteen Thesis research related activities were carried out using biinformatics tools • Thirty different papers were presented which are related to tagging mapping, gene expression anlysis and in-silico mapping of genes related to abiotic and biotic stresses

16.Future activities: Discovery of Biotic and abiotic stress tolerance gene(s), Comparative analysis of chromosome structure among the cereals, marker assisted breeding ,Identification and analysis of QTLs for biotic and abiotic tolerance in rice, molecular understanding of 1) Minor gene specificity 2) Resistance mechanism at molecular level 3)signal transduction

Name of the Coordinator: Dr. D. K. Sharma, Professor and Head, Department of Biotechnology, College of Agriculture, IGKV Raipur 492006

Postal Address: Department of Biotechnology, College of Agriculture, IGKV Raipur 492006 India Phone Number: 91-771-2442069 / 2444133 Mobile: 98261-39382; Email: [email protected]

Name of Contact Person(s): Dr. D. K. Sharma, Professor and Head, Department of Biotechnology, College of Agriculture, IGKV Raipur 492006 India Email: [email protected]

357 Indian Institute of Technology, Madras Coordinator : Dr. N. Manoj

1. Summary of the progress made by the centre from its inception: The Bioinformatics Infrastructure Facility (BIF) was established in November 2006 at IIT Madras with grants from the DBT and IIT Madras. The facility is housed at the Department of Biotechnology. The facility primarily provides educational and training facilities by supporting the bioinformatics and computational needs of the various academic programs conducted in the areas of biotechnology.

2. Major research activities in Biotechnology and its related fields Various research areas of biotechnology include: Structure function relationship of ion channels; Biocatalysis and enzyme mechanisms; Mechanisms of signal transduction pathways; Protein engineering; Molecular bioremediation; Optimal bioreactor strategies; Design and synthesis of siRNAs; Protein structure-function relationships; QSAR/QSPR and Drug design and; Bioreactor design; Computational Neuroscience; Biomechanics and Rehabilitation engineering; Molecular dynamics of proteins for drug discovery; Cancer biology; Virology; Human genetics

3. Area of Specialization of the centre: None at present

4. Major activities of the centre during the year 2007-08 The BIF has provided support for the academic programs during this period particularly for teaching courses. The department conducts courses in Bioinformatics, Biomechanics, Structural Biology, Computer Applications in Biology, Biostatistics, Computational Neuroscience, Bioprocess Modeling etc that utilize the computational facilities of the BIF. The facility also provides research students with support for retrieval of material for seminar presentations, online literature survey and data analysis, bioinformatics analysis, use of specialized molecular modeling and drug design software.

5. Infrastructure facilities in the Bioinformatics Centre A. Computer & Communication facility: We have 12 Apple Dual core iMacs running Mac OSX; 1 High end multi processor Mac PRO; 4 HP Pentium IV Graphics workstations; 2 HP Xeon 3D- Graphics workstations; 7 SUN Linux workstations; 12 Pentium IV Desktop PCs; 2 SGI Octane systems; 1 HP printer/scanner/copier; Accessories like external DVD writer, Hard disks, network switches etc. All the computers are connected to the internet on a 33 mbps LAN.

B. Scientific Software packages: InsightII, Cerius2, Autodock, Molecular visualization software, Bioinformatics programs

C. Databases & other information resources: The BIF is extensively used for online literature access through the IIT Madras library e-Gateway.

6. Details about staff members working in the centre: 1. Ms.Bhuvaneshwari Technical Assistant Information Jan’ 07 358 (Temporary position) Technology

7. Types of services provided: The internet facility of BIF is extensively used to download and browse online literature. All major web resources like sequence and structure databases are accessed for data retrieval and bioinformatics web servers. Additionally the BIF is used by students who come for short term projects at IIT Madras from colleges and universities around the country.

8. Educational activities: The educational activities of the biotechnology department that the BIF supports include the B.Tech and M.Tech degree students Additionally, the facility also provides support to research activities by supporting the MS (by research) and the PhD students for their research projects and course work.

9. Initiative to validate the outcome of bioinformatics resources: None

10. Databases/ Software packages developed: None at present

11. Some recent relevant papers published: The SGNH Hydrolase Superfamily: Structural Aspects. Kiranmayee B & Manoj N. 11th ADNAT Convention on Structural Biology Hyderabad. Feb 2007. The repertoire of GPCRs of the Ciona Intestinalis genome. Kamesh N, Aradhyam GK & Manoj N. International Conference on Bioinformatics & drug Discovery, Hyderabad. Dec 2007. Interpreting voltage-sensitivity of Gap Junctions as a mechanism of Cardiac Memory. Krishnan J, Sachdeva G & Chakravarthy VS. Mathematical Biosciences, 2007 (in press). Quantitative Structure Activity Relationships for Commercially available Inhibitors of COX-2. Sivakumar PM & Mukesh Doble. Medicinal Chemistry, 2008, (in press)

12. Initiation of R&D activities in Bioinformatics: Presently bioinformatics R&D activities here are limited to bioinformatics analysis in several BTech, MTech and Summer projects and those of PhD projects of research scholars of the Biotechnology dept at IIT Madras.

13. Details of workshop & total no. of user trained: None till date.

14. Impact shown by your centre on the growth of biotechnology: The primary impact of this centre is in manpower training in Biotechnology at levels that includes undergraduates, postgraduates and research scholars numbering about 300, of the Biotech dept, IITM. In 2007, 11 papers that utilized the BIF number were published in journals and conferences 15. Future activities: The BIF grant will be used for purchase of additional software to support teaching activities and for additional 3D-graphics workstations for Accelrys molecular modeling package. A training program in bioinformatics involving research scholars of the dept is being planned.

Additional Details: Name of the Coordinator: Dr. N.Manoj Postal Address: Department of Biotechnology IIT Madras, Chennai - 600036 Phone Number: 044-22574113 Mobile:9940149208

359 Email: [email protected] Website: http://biotech.iitm.ac.in/ Name of Contact Person(s): Dr. N.Manoj Email: [email protected]

Jamia Millia Islamia, New Delhi Coordinator : Prof. S.I.Ahson

1. Summary of the progress made by the centre from its inception in the year 2007:The Department of Computer Science has produced two Ph.D Thesis in the area of BioinformaticsTopics are : Microarray Gene expression Data Analysis – clustering and classification using statistical methods and machine learning techniques , and Gene regulatory networks. The JAMIA BIF would like to strengthen in these two areas. • The Self-finanincing M.Sc.(Bioinformatics) course (not supported by DBT), uniquely located in the Department of Computer Science of Computer Science of Jamia , started in 2003 is a unique blend of Computing , Maths, Statistics and Biology. • The Department has an MoU with CDFD, Hyderabad where 3 students every are trained for six months. The placement record is 100 % with several students gone abroad for Ph.D and several employed in Pharmaceutical industry, government organizations and several as teaching in various central/state universities. • The Department of Computer Science has established a BIF Lab consisting of SUN High-end, Medium-end servers and Workstations where students and research scholars can excel themselves in the field of Bioinformatics.

2. Major research activities in Biotechnology and related fields at your institution: The JAMIA-BIF focuses on research in AI, machine learning data mining techniques applied to bioinformatics. The Department has publications in data analysis of microarray data, supervised learning and data mining and analysis of gene expression data.

3. Area of Specialization of the centre: Microarray Gene expression Data Analysis – clustering and classification using statistical methods and machine learning techniques , and Gene regulatory networks. Application of Semantic Web and Ontologies.

4. Major activities of the centre during the year 2007-08: The Department organized two 3 days national level training Programs under BIF from 14-16 November 2007 on ‘Databases and Data Mining in Bioinformatics’ and from 9-11 January 2008 on ‘Semantic Web and Ontologies in Bioinformatics’. 360

5. Infrastructure facilities in the Bioinformatics Centre: A. Computer and Communication facility: Sun Server Systems(Multi- platform)- Networked Lab ,High-End X4200 SUN Server, Medium-end X2100 SUN Server, SUN V240 Server, SUN workstations, Pentium4 Compaq PCs, Internet Connectivity through CIT, JMI.

B. Scientific Software packages: Sun Studio 12,Sun HPC ClusterTools, Sun Grid Engine Software, Solaris 10 or Red Hat AS 4.x, Red Hat Workstation 3.0. Sun N1 Grid Engine 6.x.

6. Details of Staff members working in the Centre: No staff member has been allocated for BIF. Some faculty members of Department of Computer Science, JMI and some guest teachers are associated.

*If no, the reason for the Non Absorption to be given. Likely time of Absorption also to be given

7. Types of services provided: • BIF lab set up is being used for the Project work by the internal and external students of M.Sc.(Bioinformatics) ,M.Sc(Biotechnology) and research scholars. • Organizing two National level Training programs in a year for promoting Bioinformatics teaching. 8. Educational activities with details of placement: The Department has an MoU with CDFD, Hyderabad where 3 students every are trained for six months. The placement record is 100 % with several students gone abroad for Ph.D and several employed in Pharmaceutical industry, government organizations and several as teaching in various central/state universities.

9. Initiative to validate the outcome of bioinformatics resources:

10. Collaborative works/initiatives: NIL

11. Databases/Software packages developed: Ontology of Avian Flu Virus H5 N1, Database of medicinal plant.

12. Papers published or presented in the conferences with references: Following is the list of publications of research papers in the areas related to Bioinformatics in the Department of Computer Science: 1. Jayanthi Ranjan, Goyal.D.P, Ahson.S.I. Data Mining Techniques in Human Resource Management Systems for Better Decisions. International Journal of Business Information systems. InderScience Publishers. IJBIS 173. Vol 3 2007 2. Jayanthi Ranjan, Saani Khalil S.I Ahson. Developing and Implementing successful Data Warehouses for Competitive advantage: Issues and Challenges, International journal of information technology , Vol 2 2008 361 3. Jayanthi Ranjan. S.I Ahson. Hierarchical Cluster Analysis for Large Data Sets. Varahamihir Journal of Mathematical Sciences” Vol -1, No 1, (2006), pp 1-16, ISSN 0973-3639. 4. Jayanthi Ranjan. S.I. Ahson. Statistical Agglomerative Clustering Methods for Gene Expression Data – A Comparison. Bioinformatics India Journal (Peer Reviewed). Vol 6, no.3. (2006), pp. 70-80. 5. Jayanthi Ranjan. S.I. Ahson. An Overview of Data Mining Techniques. Proceedings of the National conference on Innovations in Indian Science, Engineering and Technology. IARI-New Delhi. (2006). Vigyan Bharathi Proceedings. pp.62-69. 6. Jayanthi Ranjan. Abhishek Maheswari , S.I.Ahson. A study of Real Time Scientific Data being stored by Indian Scientific Community. Journal of Management Development and Information Technology (JMDIT- Mathura, India). (2006) pp 34-45. 7. Jayanthi Ranjan, S.I. Ahson. ‘A review of Statistical Clustering Techniques’ Bioinformatics journal. 2006. Vol2. Abstract can be found at http://www.bii.in/journal/BIIJOURNAL/FinalPaperAbstract.aspx?ArticleID= 238 8. Jayanthi Ranjan. S.I. Ahson. Clustering in Data Mining: Techniques and Issues. Journal of IT-Techgenesis India, Vol 2 No 2 April 2005, pp. 17-25. 9. Jayanthi Ranjan. S.I. Ahson. Statistical Data Mining Techniques: Issues and Challenges. Proceedings of FACM-2005, March 04-05, 2005, Allied Publishers Pvt Ltd., pp. 429-440. 10. Jayanthi Ranjan. S.I. Ahson. Agglomerative Statistical Clustering Techniques for Genome Databases. Proceedings of FACM-2005, March 04-05, 2005, Allied Publishers Pvt. Ltd., pp.119-131. 11. Jayanthi Ranjan. Tushar Gupta. S.I. Ahson. Information Systems: Security Issues Threats and Challenge.” Proceedings of International conference Ludhiana (2005), pages 55-65. 12. Jayanthi Ranjan. S.I. Ahson. Tushar Gupta. Emerging Trends and Techniques in Business Data Mining. Proceedings of International Conference. INMANTEC (2005), Allied Publishers. pages 55-70. 13. Jayanthi Ranjan. S.I. Ahson. Nearest Neighborhood Method to Cluster Micro Array Data. Proceedings of National Symposium in Bioinformatics. Dept of Mathematics, IIT Roorkey, March 14, 2005, pp. 10-12. 14. S.I.Ahson, Genorobotics,AROB Conference Beppu,Japan,Jan 24-26,2003 15. T.V.Prasad and S.I.Ahson. “Labeling Gene Expression Data using LVQ”,Third Annual RECOMB Sattellite Meeting on DNA Sequencing Technologies and Computations,May 17-18,2003,Stanford University,USA 16. T.V.Prasad and S.I.Ahson, ‘Analysis of Microarray Gene Expression Data’, Proc. Of Second International Conference on Artificial Intelligence in Engineering and Technology, August 3-5, 2004, Kota Kinabalu,Malayasia,Proc. Pp 588-595 17. T.V.Prasad,R.P.Babu and S.I.Ahson, ‘GEDAS—Gene Expression Data Analysis Suite’, Bioinformation (Online Bioinformatics Journal),vol 1,no 3,2005,pp 83-85 18. T.V.Prasad and S.I.Ahson, ‘Visualization of Microarray Gene Expression Data,Bioinformation,Biomedical Informatics Publishing Group,vol1,no 4,2006,pp 141-145.

13. Initiation of R & D activities in Bioinformatics: 362

14. Details of Training/Workshop organized and total no. of user trained: The Department organized two 3 days national level training Programs under BIF from 14-16 November 2007 on ‘Databases and Data Mining in Bioinformatics’ and from 9-11 January 2008 on ‘Semantic Web and Ontologies in Bioinformatics’ in which more than 60 participants from all over the country participated.

15. Impact shown by your centre on the growth of biotechnology and allied areas: The M.Sc.(Bioinformatics) course has attracted a number of students throughout the country. A sizable number of students from different universities/institutions are coming to the centre for the Project/training programs.

16. Future activities: • Development of patents and software tools and databases related to Bioinformatics. • Employing highly technical people for the BIF in the Department. • Extension in the existing SUN lab facility by hiring advanced Bio-cluster Grid components.

Additional Details: Name of the Coordinator: Professor S.I.Ahson Postal address: DEPARTMENT OF COMPUTER SCIENCE, JAMIA MILLIA ISLAMIA (A CENTRAL UNIVERSITY), JAMIA NAGAR, NEW DELHI-110025 Phone Number: 011-26980014 Mobile: 9810581072 Email: [email protected]

363 Jiwaji University, Gwalior Coordinator : Dr. Ishan Patro

1. Summary of the progress made by the centre from its inception: The one-time grant for establishing the Centre was sanctioned in September 2006. The Facility has been established. A Users’ Meet was held on 15.5.07 and most faculty members from all the Science Departments attended. After a short introduction on the purpose and facilities available, a proposed list of the areas where this facility could be used was drawn. The important areas for database development are: Aquatic resource of MP; endangered species and wild-life resource of MP; Microbial wealth of MP; Medicinal plants of MP; Genomic profiles of tribes in MP; Aging population and prevalent age-related problems in MP; Neurological disorders and disabilities in Indian population; and Preparation of teaching aids in Biotechnology for colleges affiliated to this University. These shall be in addition to the normal computational and information technology facilities those could be extended to the faculty and researchers in the University.

2. Major research activities in Biotechnology and its related fields: The ongoing research of interests are: a) Role of microglia and inflammatory changes in neuronal apoptosis, neurodegeneration and neurodegeneration. b) Studies on effects of presence of resting and reactive microglia on endogenous neurogenesis and gliogenesis from neural stem cells. c) Aging changes in microglia per se. Does age related deterioration of microglia and microglial cellular senescence cause increasing disability of microglia to provide neuroprotection following injury? d) Studies on immunophilin ligands as novel modulators of glial activity and mediators of neuroprotection. e) Role of glia in neurogenesis and histogenesis of neurons following exposure to the toxicity of deltamethrin in postnatal rats. f) Gram-negative Bacterial Endotoxin-induced Infertility. g) Genetic Polymorphism in the Tribal Populations of North Madhya Pradesh In Relation To Genomic Diversity and Susceptibility to Tuberculosis. h) Genetics of susceptibility to gall stone and gall cancer i) Genetic diagnosis and counseling for (pre-natal) abnormalities in spontaneous abortions j) Genetics of thalassemia and population screening k) Conservation genetics of Gharial and turtles.

3. Major activities of the centre during the year 2007-08: The Centre provided support to a DBT sponsored Hands-on Workshop on “Methods in Clinical Diagnosis: Cytogenetics, Biochemical, Molecular and Bioinformatics Approaches” during July 23-August 11, 2007. (Conducted by the Centre for Genomics). Centr’s facilities were availed by the School of Studies in Neuroscience in conducting the National Symposium on “Glial Neurobiology” held on October 23, 2007. The Centre supported the teaching of Bioinformatics to the students of M.Sc. Neuroscience (a DBT sponsored programme). Many researchers have been using the facility for their research activity 364 leading to publications.

4. Infrastructure facilities in the Bioinformatics Centre: As sanctioned

5. Details about staff members working in the centre: The position of RA has been advertised.

6. Types of services provided: Information, Computation and internet

7. Educational activities with details of placement: Not applicable

8. Initiative to validate the outcome of bioinformatics resources: Nil

9. Collaborative works/ initiatives: Collaborative work with several Institutes including AIIMS, DRDO, Manipal Institute, NIMHANS, ITRC, CDRI, etc are under progress and several others are being planned.

10. Databases/ Software packages developed: Nil

11. Papers published or presented in the conferences with reference The researchers at this University have contributed towards publications in the following manner: Sequences submitted for GenBank: By PVJ Reddy and. P.K. Tiwari HSP genes GenBank Citations: DQ062119 – Lucilia cuprina heat shock protein 60 gene, complete CDS. EF445946 – Lucilia cuprina heat shock protein 70 (hsp70) gene, complete CDS. EF584332 – Lucilia cuprina HSP90 gene, complete CDS.

By M.S. Rohilla and P.K. Tiwari Cytochrome-b (mitochondrial) genes GenBank Citations: EF558361 - Aspideretes gangeticus cytochrome b-like (cytb) gene, partial sequence. EF558362 - Kachuga kachuga cytochrome b-like (cytb) gene, partial sequence. EF558363 - Lissemys punctata punctata cytochrome b-like (cytb) gene, partial sequence. EF558364 - Kachuga dhongoka cytochrome b-like (cytb) gene, partial sequence. EF558365 - Geoclemys hamiltonii cytochrome b-like (cytb) gene, partial sequence.

Papers published: Saxena Kapil, Patro, Nisha & Patro, Ishan (2007) FK506 protects neurons following peripheral nerve injury via immunosuppression. Cell Mol. Neurobiol., 2007. DOI 10.1007/s10571-007-9221-6

12. Initiation of R&D activities in Bioinformatics: See ‘2’ above. 13. Details of Training/ Workshop: A Workshop on “Bioinformatics: From genome search to phylogeny” shall be held during 1-3 march 2008. We are also planning trainings for M.Sc. Students. 14. Impact shown by your centre on the growth of biotechnology and allied areas: The Centre is helping in research and publication in various areas of biology.

365 15. Future activities: We are planning to extend training to all biology students in the Campus on Bioinformatics. And develop databases on aspects listed above.

Name of the Coordinator: Dr. Ishan Patro Postal Address: Head, School of Studies in Neuroscience & Coordinator, Bioinformatics Centre, Jiwaji University, Gwalior 474011. Phone Number: 0751-4016789, 2231816, 2231616 Fax No.:4016789 Email: [email protected], Website: www.jiwaji.edu, www.neuroscienceju.com

366 Kannur University, Kannur Coordinator : Dr. M. Haridas

1. Summary of the progress made by the centre from its inception

In October 2006 we got the sanction for the establishment of Bioinformatics Infrastructure Facility (BIF) for the promotion of Biology Teaching through Bioinformatics (BTBI) at the Department of Biotechnology and Microbiology, Kannur University. Rs 20 lacs was received from the DBT as initial grant and Rs 6.82 lacs for 2007-08. The infrastructure facility has been established with sufficient number of computers, softwares and leased line Internet connectivity. Also steps had been taken to complete the constitution of an executive committee has already been constituted. Now the centre is ready for facilitating the researchers/other patrons from the outside as well. Dr. C. Sadasivan, Reader, Department of Biotechnology and Microbiology attended the International Conference on Bioinformatics (InCoB-2006) held at New Delhi during December 18-20, 2006. He also attended the INSA-CAS workshop on structural biology, IISc, Bangalore, Dec 21-23, 2007. A two days national workshop was organized during the Jan 10-11, 2008. The theme of the workshop was introductory structural bioinformatics.

2. Major Research activities in Biotechnology and its related fields at the department

a. Modeling and Molecular Dynamic Study of Xeno Estrogen Targets and Phospholipase Inhibitors b. Anti tumor property of Butea monosperma lectin and goat milk lactoperoxidase c. Peptide modeling/synthesis and study of their functionally important secondary structures/critical role of individual residues d. Utilization of coffee treated effluent for the production of various organic chemicals and industrially important enzymes. e. Identification, Characterization and pharmacokinetic studies of anti inflammatory phytochemicals/marine cyanobacterial chemical and their derivatives biotransformed by fermentation. f. Development of inhibitor to β-lactamase from phytochemicals. g. Sequence and structural analysis of bacterial enzymes associated with drug resistance and designing of novel drugs to combat the problem of antibiotic resistances using molecular modeling and other Bioinformatics tools. h. Modeling of inhibitors to enzymes associated with blood coagulation such as thrombin using molecular modeling tools.

367 3. Area of specialization of the Bioinformatics Centre

Structural Bioinformatics

4. Major activities of the centre during the year 2007-08:

The infrastructure facility has been established with sufficient number of computers, softwares and leased line Internet connectivity. Also steps had been taken to complete the constitution of an executive committee has already been constituted. Now the centre is ready for facilitating the researchers/other patrons from the outside as well. A two-day national workshop organized during the Jan 10-11, 2008. The theme of the workshop was introductory structural bioinformatics.

5. Infrastructure facilities in the Bioinformatics centre:

a). Computer and communication facilities available in the department 1 IBM P.C. workstations with Linux and Windows OS (8 nos),IBM Servers 2 2 PC s (14 nos.), 1 laptop computer, printers 3 Leased line internet facility (512 Kbps) 4 Photocopying machine, LCD Projector, Telephone and FAX

b). Scientific Software packages

Insight II, Discover, Affinity, SPDBV, AMBER 9, VMD, ArgusLab and Bio-Suit (purchase order placed) for molecular modeling and computational biology and CCP4 and many free soft wares. a. Databases and other information resources Fungal Database: Provided by Bioinformatics Centre, Tropical Botanical Garden and Research Institute, Thiruvananthapuram, Kerala, India.

6. Details about staff members working in the centre: One RA post sanctioned was notified for appointment. But, could not get a proper candidate in the first instance.

7. Types of services provided: So far, the centre is not in a position to provide any service on demand.

8. Educational activities with details of placement Sponsorship application to start M Sc Bioinformatics is pending with UGC/BDT.

9. Initiative to validate the outcome of bioinformatics resources: Yet to initiate

10. Collaborative works/initiatives: nil

11. Databases/software packages developed: nil

368 12. Papers published or presented in the conferences with references

a). Modeling of Factor XIII Activation Peptide (28-41) V34 L Mutant Bound to Thrombin (JBSD). Divya G Nair, P N Sunilkumar and C Sadasivan. (under revision). b). Disruption Mechanism in the Helix of SPF Peptide by Interchanging Glu5 and Lys10 residues: Inference from Molecular Dynamics Study (JBSD). P N Sunilkumar, Divya G Nair, C Sadasivan and M Haridas. (under revision). c). Role of K10 Residue in Maintaining the Helical Structure of SPF Peptide: A Molecular Dynamics Study. ). P N Sunilkumar, C Sadasivan and M Haridas. (accepted for the Young Scientist Award Contest, Kerala Science Congress, Jan 2008) d). Detoxification of Bisphenol A by Laccase: A Modeling Study. (JMM). Divya L M, Ganesh K Prasanth and C Sadasivan (communicated) e). Conformation of a residue substituted fragment (349-364) of human 1 lactoferrin protein in DMSO-d6 by H NMR and restrained molecular dynamics.). P N Sunilkumar, C Sadasivan and M Haridas. (IJBB in press).

13. Initiation of R&D activities in bioinformatics

a). Strengthen the ongoing research works in molecular modeling of various drug targets and development of novel putative drug molecules b). Sequence and structural analysis of bacterial enzymes associated with drug resistance and design of inhibitors to these enzymes with the goal of developing novel antibiotics against resistant strains of bacteria using molecular modeling and other Bioinformatics tools.

Research Projects Submitted for funding

a). Synthesis, Characterization and Structure-function Correlation of a 21 Residue Peptide Misgurin, Its Analogs and Its Hibrid Sequences.(to DBT, Rs 5,174,500) b). Identification and Modeling of Targets of an Endocrine Disruptor: Bisphenol A (to DBT< Rs 1,720,000)

14. Details of training/workshop organized and total no. of user trained A two-day national workshop organized during the Jan 10-11, 2008. The theme of the workshop was introductory structural bioinformatics.

15. Nil

16. A series of five tutorials/workshops, from introduction to higher levels, in structural bioinformatics has been conceived and being developed to cater the postgraduate students.

369 Name of the Coordinator: Dr. M. Haridas, Professor and Head

Postal Address: Department of Biotechnology and Microbiology Kannur University, Thalassery Campus, Palayad P.O. Kannur-670661, Kerala E.mail: [email protected] Phone: 04902347394, Fax: 04902345317

Name of Contact Person: Dr. C. Sadasivan, Reader E.mail: [email protected]

370 Karnatak University, Dharwad Coordinator: Prof. B. B. Kaliwal

1. Summary of the progress made by the centre from its inception: The grant has been received recently and arrangements are being made to set up laboratory, purchases of computers and other facilities. 2. Major research activities in Biotechnology and its related fields at your institution :Toxicology ,stress induced effects, epidemiology of staphylococcus in northern districts of Karnataka, effect of pesticides on microbes.

3. Area of Specialization of the centre: Reproductive Toxicology, Fermentation Technology, Medical microbiology and Seribiotechnology 4. Major activities of the centre during the year 2006-07 : Nil (As it is granted recently)

5. Infrastructure facilities in the Bioinformatics Centre ¾ Computer & Communication facility : Being established ¾ Scientific Software packages : Yet to be purchased ¾ Databases & other information resources : Need to be done

6. Details about staff members working in the centre (Name of the staff, Designation, Specialization and period of working. Please indicate their absorption status) :Dr.R.D.Sanakal, Teaching Assistant, Ph.D in life science with Computer Diploma and handled bioinformatics theory and Practicals.

7. Types of services provided : -- 8. Educational activities with details of placement : -- 9. Initiative to validate the outcome of bioinformatics resources - 10. Collaborative works/ initiatives : In touch with nearby BTIs centers and education Institutions

11. Databases/ Software packages developed : Nil 12. Papers published or presented in the conferences with reference : See separate page appended 13. Initiation of R&D activities in Bioinformatics : Yet to be initiated 371 14. Details of Training/ Workshop organized and total no. of user trained : Nil

15. Impact shown by your centre on the growth of biotechnology and allied areas. In this you may highlight the details like number of paper published/ number of papers published with the help of your centre, how your centre is promoting various activities of your organization and neighboring institutions, manpower trained, tools developed, patents & copyrights acquired and other services offered etc. : Need to be developed.

16. Future activities: Planning to have workshop for the life science graduates and postgraduates in Bioinformatics.

Additional Details: Nil Name of the Coordinator: Prof.B.B.Kaliwal Postal Address:Post graduate, Department of Biotechnology, Karnatak University, Dharwad Phone Number:91-0836-2779533(O) Mobile: 9449278648 Email:[email protected] Website:www.kud.ernet.in Name of Contact Person(s): Prof.B.B.Kaliwal

372 Kumaun University, Nainital Coordinator : Dr. Veena Pande

1. Summary of the progress made by the centre from its inception

Programme has been sanctioned on 22nd September 2006. Infrastructure and other facilities have been established comprising of 10 desktops, two high end servers and printing and photostat facility. The center has 24 hours internet facility by BSNL broadband. We are exploring different available Proteomics and Genomics softwares for purchase. A three day training was organized from 30 Aug – 1 Sep 2007 for faculty and research scholars of our and different Universities. The facility is used exhaustively by all M.Sc. and PhD Life Sciences students & faculty of the University for carrying out their research smoothly. We have also subscribed print and online versions of few journals.

2. Major research activities in Biotechnology and its related fields at your institution

i. A systematic characterization of local flora and fauna at molecular level and to develop strategy for its conservation. ii. To develop methods for sustainable exploitation of the aromatic and medicinal plants. iii. To study the microbial biodiversity of the region with special emphasis on cold tolerant microbes. iv. Biodiversity and Biotechnological applications of mycorrhizal fungi of Uttarakhand. v. To study the Genetic diversity of casts and tribes of Uttarakhand. vi. To develop protocols for in vitro micropropagation of rare, endangered and important forest species of this central Himalayan region.

3. Major activities of the center during the year 2007-08

A Seminar was organized by the department entitled: and “Biotechnology Innovation systems of India: Policy Measures and Support Mechanisms” Sponsored by APCTT, DBT Govt. of India, New Delhi. Besides that a three days training on ‘Applications of Bioinformatics’ was organized from 30 Aug – 1 Sep 2007 for faculty and research scholars of our and different Universities. Department is also engaged in organizing inter school science competitions, popular lectures by eminent scientist and educational tours to develop scientific out look among youth.

4. Infrastructure facilities in the Bioinformatics Centre a. Computer & Communication facility High end server – 1 Proxy Server – 1 Desktop Computers – 10 Laptops – 3 Multi media projector – 2 Scanner – 2 373 Printers (high end) – 2 (Laserjet), 1 (inkjet) UPS – 5 KV (1), 2 KV (1) Xerox Machine – 1 The computers are connected through LAN and 24 hrs very high speed Broadband internet facility is available. Scientific Software packages- Windows Office 2007, Windows XP, Red Hat Linux, Accelrys Gene etc. b. Databases & other information resources- Yes

5. Details about staff members working in the center (Name of the staff, Designation, Specialization and period of working. Please indicate their absorption status)

Advertisement for the post of 1 Research Associate has been advertised and interview is awaited.

6. Types of services provided The center provides the following services to the students, research fellows and faculty members of the university: (a) E-mail & internet access (b) Training in bioinformatics (c) Online access to public domain databases (d) The center offers a good collection of various journals (online and print version) to all researchers of the university 7. Future activities

Presently department is engaged in research related with medicinal and aromatic plants, Microbial diversity, Genetic diversity and Biotechnological applications of Mycorrhizal fungi of Uttarakhand. After establishment of Bioinformatics facility in the center, it will be easy to access the related database and to proceed the research work in the oriented direction. Department will also organize short term training programmes in Bioinformatics for students and faculty members of nearby institutes/organizations to enrich their knowledge in this area. It will also work in the directions of development of new data bases.

Additional Details: Name of the Coordinator: Dr. Veena Pande Postal Address: Department of Biotechnology Kumaun University, Nainital Uttrakhand-263 001 Phone No: (05942) 235521 Fax No.:(05942) 235576 Email: [email protected] [email protected] Website: www.kumaununiversity.org

374 Lady Doak College, Madurai Coordinator : Dr.R.Shenbagarathai

1. Summary of the progress made by the centre from its inception

Established Bioinformatics Lab facility and organized one workshop.

2. Major research activities in Biotechnology and its related fields at your institution

Microbial Biotechnology ƒ Biopesticide – Searching of new indigenous Bacillus thuringiensis strain to control Spodoptera litura, Culex quinquefasciatus and Anopheles to be used as effective ecofriendly biocontrol agent. ƒ Biopolymer screening and characterization of indigenous mcl- phac producer. ƒ Identification, mapping and characterizing genes associated with phaC1. ƒ TB with HIV coinfection. Molecular characterization of pathogens, new targets and novel drug delivery systems relating to viral, bacterial and parasitic infections.

Ethnomedicine • Antimicrobial activity, biochemical properties and immunomodulatory effects of medicinal plants used by tribes in and around Madurai.

3. Area of Specialization of the centre Microbial Biotechnology

4. Major activities of the centre during the year 2007-08

Organised “Hands on Training in Bioinformatics tools and Applications.” From May 2nd to May 12th 2007.

5. Infrastructure facilities in the Bioinformatics Centre

Computer & Communication facility: 10 from DBT-BIF and 26 from UGC Innovative and CPE grant with internet facility at a speed of 512KB/sec Scientific Software packages : Process of converting InsightII software pacjage into Discovery Studio. Databases & other information resources: Process of building database on rural women’s traditional knowledge on indigenous medicinal herbal plant’s use for common ailments.

6.Details about staff members working in the centre

Name of the Staff: Ms. J.Ida Chrislyn,Designation: Research Assistant,Specilaisation : Bioinfomatics,Period of working ::From Dec1st, 2007 onwards,Absorption status :Based on merit and interview performance.

375 7. Types of services provided Internet usage and Insilico analysis for Lab and Project

8. Educational activities with details of placement Not applicable

9. Initiative to validate the outcome of bioinformatics resources Consolidated feedback from the participants of the workshop after seven months

It was a meaningful practical experience we had during our training course on Bioinformatics training. Really the training was very useful. We have been applying the techniques in our research work which was taught during course work. In fact the training was the base for our future research work in the field of Bioinformatics. The tutorials were very good.

10. Collaborative works/ initiatives Under process.

11. Databases/ Software packages developed Under process

12. Papers published or presented in the conferences with reference

Publications

• Sujatha. K, Mahalakshmi, A. and R. Shenbagarathai (2007),Archives of Microbiology. 188: 451-462. • Ramakrishnan. K, Shenbagarathai. R, Uma. A, Kavitha. K, Rajendarn. R, Thirumalaikolundusubramanian. P. (2007). Japanese journal of infectious diseases. 60 (4): 209-10. • Mahalakshmi, A. and Shenbagarathai, R. (2007). Accepted for publication in JBSD as color processing of US $5,000. Hence, this manuscript was resubmitted in insilico biology.

Presentations • K.Sujatha, M.S.Dhivya Vadhana, K.Ramalakshmi, A.Mahalakshmi, K.Anburani and R.Shenbagarathai (2007). International conference on new horizons in biotechnology (NHBT-2007), NIST, Trivandrum, India Nov 26-29, 2007. • A.Mahalakshmi, K.Sujatha, Poornima Kkani, M.Tamilarasi, G.Geetha, K.Anburani and R.Shenbagarathai (2007). International conference on new horizons in biotechnology (NHBT-2007), NIST, Trivandrum, India Nov 26-29, 2007. • A.Mahalakshmi, K.Sujatha and R.Shenbagarathai (2007) 5th International symposium on Biocontrol and Biotechnology (BCBT-2007). Khon Kaen University, Nongkhai Campus, Nongkhai Province, Thailand (November 1-3, 2007).

13. Initiation of R&D activities in Bioinformatics

• Docking of drug for reverse transcriptase using natural products • Docking of drug for HIV 1-Protease using natural products 376 • Drug designing for schizophrenia by Virtual Screening. • Drug designing for hyperthyroidism by Virtual Screening. • In silico structure based drug designing for type II diabetes.

14. Details of Training/ Workshop organized and total no. of user trained 20

15. Impact shown by your centre on the growth of biotechnology and allied areas. In this you may highlight the details like number of paper published/ number of papers published with the help of your centre, how your centre is promoting various activities of your organization and neighboring institutions, manpower trained, tools developed, patents & copyrights acquired and other services offered etc. Paper published-2, accepted-1.

16. Future activities Process of developing tools

Additional Details:

Name of the Coordinator : Dr.R.Shenbagarathai Postal Address Department of Biotechnology, Lady Doak College, Madurai.-625002 Phone Number:0452-2530527,2524575; Fax No.:091-452-2523585 Email:[email protected] Website:www.ladydoak.org Name of Contact Person(s):Dr.R.Shenbagarathai Email: [email protected].

377 Lucknow University, Lucknow Coordinator: Prof. U.N. Dwivedi

1. Summary of the progress made by the centre from its inception BIF centre is only one year old. During this period the effort was to establish the center with all the facilities. All the purchases were made and the center was made functional. One training program is scheduled to be organized during Feb. 12-16, 2008. The post of RA was advertised however, no appointment has yet been made.

2. Major research activities in Biotechnology and its related fields at your institution The major research activities of the department are summarized as follows:

¾ Biotechnological modification of lignin biosynthesis for improved application of biomass in paper manufacturing and fodder production. ¾ Structure - function relationship in nitrate reductase; ¾ Biochemical role of salicylic acid in plants; ¾ Molecular characterization of mimosine degradation enzymes and genes in bacteria. ¾ Regulatory aspects of Plasma membrane linked redox mediated signal transduction and transfer activities in eukaryotes. ¾ Antioxidants in cardiovascular disorders. ¾ Biochemistry of cataract development during diabetes.

The Department is collaborating in research activities with the other departments of the University as well as with national organizations, such as Central Drug Research Institute, Industrial Toxicology Research Centre, National Botanical Research Institute, Central Institute of Medicinal and Aromatic Plants, Lucknow.

The Department has earned recognition in the form of financial support from Rockefeller Foundation, UNESCO, PL 480, UGC under special Assistance and COSIST Programs and DST – FIST, DBT etc.

3. Area of Specialization of the centre: Plant Biotechnology and Biochemistry

The thrust research areas of the department include:

1. Transgenics. 2. Enzyme Engineering. 3. Metabolism under stress and disease.

4. Major activities of the centre during the year 2007-08 :

378 i. Purchase and installation of computers, servers, printer, scanner, photocopier, softwares etc. ii. Internal members of the department got training in the bioinformatics. iii. One training program is scheduled to be organized during Feb. 12-16, 2008. iv. The post of RA was advertised however, no appointment has yet been made.

5. Infrastructure facilities in the Bioinformatics Centre Computer & Communication facility Scientific Software packages Databases & other information resources 6. Details about staff members working in the centre (Name of the staff, Designation, Specialization and period of working. Please indicate their absorption status)

The post of RA was advertised however, no appointment has yet been made.

7. Types of services provided: Bioinformatics tools being currently used in our research is mentioned below: • Nucleotide and protein search at NCBI and SWISS-PROT, respectively • BLAST to check homology at nucleotide and amino acid level with the biomolecules (DNA / RNA and protein) • EST searches at NCBI • Protein modeling :3D domain and structure of enzymes and protein at NCBI • CLUSTAL to check homology in selected sequences at nucleotide and amino acid level. • Entrez, Pubmed and PubMed Central to search the research articles • Molecular Beacon and Primer 3 to design gene specific primers • CUTTER, TRANSLATOR, AND ALIGNER tools at www.justbio.com • Gene runner (oligo analyzer and oligo explorer) to design and check the suitability of oligos for conventional PCR and Real Time PCR.

8. Educational activities with details of placement Not applicable 9. Initiative to validate the outcome of bioinformatics resources N.A. 10. Collaborative works/ initiatives : N.A. 11. Databases/ Software packages developed - 12. Papers published or presented in the conferences with reference - 13. Initiation of R&D activities in Bioinformatics - 14. Details of Training/ Workshop organized and total no. of user trained

379 One training program is scheduled to be organized during Feb. 12-16, 2008. No. 10.

15. Impact shown by your centre on the growth of biotechnology and allied areas. In this you may highlight the details like number of paper published/ number of papers published with the help of your centre, how your centre is promoting various activities of your organization and neighboring institutions, manpower trained, tools developed, patents & copyrights acquired and other services offered etc.

16. Future activities:

¾ To organize more training programs. ¾ Developing new tools and adding to the resources that aid in the ¾ analysis of the data. ¾ Getting aware of the fine tools of bioinformatics and making aware of the same to the students from neighboring academic institutions. ¾ Exploring the various databases and anlysing the structure and function of biomolecules ¾ Getting access to the newly discovered bio-molecules and pathways ¾ Getting updated in the field of genomic tools and data to analyze the biological systems

Additional Details: Name of the Coordinator: Prof. U. N. Dwivedi Postal Address: Department of Biochemistry, Lucknow University, Lucknow -226007 Phone Number: 0522-2740132 Mobile: 09415022445 Email: [email protected] lkouniv.ac.in

Name of Contact Person(s): Prof. U. N. Dwivedi Email: [email protected]

380 Madras Christian College, Chennai Coordinator : Dr. D. Arul Samraj

1. Summary of the progress made by the centre from its inception The Centre has been established in the dept. of Zoology with the help of Rs.20 lakhs released by DBT during the year 2006-07 and commissioned on 22, March 2007. An Extension Facility was also established in the Dept. of Botany during April 2007. The facility is well utilized both for teaching and for carrying out P.G. and M.Phil dissertation work.

2. Major research activities in Biotechnology and its related fields at your institution M.Phil and M.Sc. dissertation work – listed under item no. 15.

3. Area of Specialization of the centre Thrust area – Genemic Studies, Proteomics studies & drug designing

4. Major activities of the centre during the year 2007-08 4.1. Establishment of the facility 4.2.Teaching Bioinformatics-special paper to UG PG along with dissertation 4.3. Workshop to the Biology Teachers of Higher Secondary Schools to introduce Bioinformatics during June 14 – 16, 2007 4.4. Workshop to the Faculty of MCC on the utility of Bioinformatics Infrastructure Facility established at MCC on August 13, 2007.

5. Infrastructure facilities in the Bioinformatics Centre B. Computer & Communication facility a. All Hardware and Software were purchased and installed according to the specifications provided by DBT and in certain cases an higher configurations were purchased.. b. All terminals are provided with DVD writer, and in addition, Web Cam and Head Phone thereby facilitating Video Conferencing. c. All in one Laserjet and Duplex printers have been installed. d. An online UPS has been provided with more than two hrs backup. e. 2Mbps Broad Band internet connectivity has been provided by BSNL Dataone. Wireless Dial up internet connectivity has also been provided by TATA INDICOM as a standby connectivity. f. All these are housed in an independent air conditioned room. g. The entire premises of the Dept. of Zoology has been provided with wireless internet connectivity by WiFi Technology and Note Book Computers are used in all class rooms; thereby roaming internet facility is made available in and around the Dept. of Zoology. It is possible to access the BIF server from the class rooms itself through this facility of Wireless Networking while utilizing the terminals of BIF simultaneously. It is also possible to share documents. h. An Extension Facility has been provided to the Botany Dept. by allocating a portion of the funds. The entire campus is to be connected with LAN facility shortly so that the Server of the BIF could be accessed from any part of the Campus (365 Acres campus) 381

C. Scientific Software packages D. Databases & other information resources 6. Details about staff members working in the centre (Name of the staff, Designation, Specialization and period of working. Please indicate their absorption status) Ms. Jancy Joy Christy has been appointed as Research Asst. with effect from Jan 18, 2008..

7. Types of services provided Teaching, guiding dissertations, workshop for Biology teachers of Hr. Sec. Schools, unlimited utility by all Biology-related students

8. Educational activities with details of placement 9. Initiative to validate the outcome of bioinformatics resources 10. Collaborative works/ initiatives 11. Databases/ Software packages developed 12. Papers published or presented in the conferences with reference D G Thomas 2007, Splicing in DNA Computing, Proceedings of the National Conference on Emerging Trends in Automata (ETA ’07), Rajiv Gandhi College of Engineering and Technology, Puducherry, 6th October 2007, pp. 14 – 41.

13. Initiation of R&D activities in Bioinformatics 14. Details of Training/ Workshop organized and total no. of user trained Biology Teachers of Higher Secondary Schools – 12 Teachers Faculty of MCC – 20

15. Impact shown by your centre on the growth of biotechnology and allied areas. In this you may highlight the details like number of paper published/ number of papers published with the help of your centre, how your centre is promoting various activities of your organization and neighboring institutions, manpower trained, tools developed, patents & copyrights acquired and other services offered etc. 15.1. Research in various aspects of Biotechnology has been encouranged from the year1990 which is evident from the following Research contributions 15.2. List of M Phil Dissertations in the area of Bioinformatics: a. Hephzibah Swapna Chenchiah 2006 A basic study of inhibin alpha subunit (INHA) using bioinformatic tools. b. Reeba Mathew 2006 Genomic and proteomic studies on Inhibin. c. Anulin Christhudoss 2005 Bioinformative studies on STAR protein in steroidogenesis using bioinformative tools. d. Rebecca Merlin 2005 Proteomic studies on 17β hydroxyl steroid hydrogenase using bioinformative tools. e. Satya Priya 2005 ‘On Circular Splicing Languages’ f. Hepzibah Simon 2004 Genomic and proteonomic studies on 3β hydroxyl steriodohydrogenase using available bioinformative tools. 382 g. Kalaivani C 2000 A Study on splicing operation. 15.3. List of M Sc dissertations Sawmsung Zuali 2007 Characterization of Gene for Haemophilia using Bioinformatics tools Pradeepa Jane 2006 Multiple sequence analysis of protein - Rhodopsin from five different species of fire ants. Mini M K 2004 Characterization and prediction of the protein pitx2 in Homo sapiens and Gallus gallus. Marshal Joe 1997 Seroprevalence of HIV among the rural population of Chengalpat and South Arcot Districts. Cynthia Anupa Isacc 1992 Transferrin polymorphism in Cattle. Baishali Basu 1991Isolation and partial characterization of plasmid DNA from Nocardia asteriodes, Xanthomonas oryzae.

16. Future activities Genomics studies, Proteomics studies, Multiple sequence analysis, Drug Designing, DNA Computing (Studies on the splicing operation and Splicing Languages of Circular DNA). Apart from the above mentioned areas the following specific studies will be undertaken • Students will be trained to collect, assemble and analyze the available data in the varied upcoming areas under Bioinformatics • Students will be motivated to develop a different software to relate and compare different proteomics and genomics data. • Database on the fauna and flora of MCC campus. • Introduction of Optional – Bioinformatics for M.Phil program from 2008- 09. • Introduction of M.Sc. in Bioinformatics during 2009-10. • Introduction of Bioinformatics as an add-on course.

Additional Details: Name of the Coordinator: Dr. D. Arul Samraj, Madras Christian College, Chennai 600 059, (+91) 9444 284670; [email protected] Website: mccbioinformatics.htmlplanet.com Name of Contact Person(s): Dr. (Mrs.) C. Joyce Priyakumari, Associate Coordinator, Bioinformatics Infrastructure Facility, Madras Christian College, Chennai 600059. (+91) 9444 149280; [email protected]

383 Maharani’s Science College for Women, Bangalore Coordinator : Mrs. Kavitha B

1. Summary of the progress made by the centre from its inception The Bioinformatics Infrastructure Facility in the college was set up the in Dec 2006. The facility now has 2 servers, 10 PC’s, a network printer, scanner and copier. A dedicated internet connection has been provided to the facility. Software has been procured along with Pfam database. Training programs have been conducted frequently. Last year saw various programs including Workshops for both undergraduate and Post graduate students and faculty from various colleges in Bangalore The facility also conducted a two month certificate course for B.Sc. Students.

2. Major research activities in Biotechnology and its related fields at your institution M.Phil Student is being guided for her M.Phil dissertation- An assessment of airborne fungal allergens in indoor environment: A bioinformatics approach. 3. Area of Specialization of the centre - Microbiology 4. Major activities of the centre during the year 2006-07 Two workshops for students and one for teachers have been conducted. A certificate course for two months duration on Basic Bioinformatics for Final B.Sc. students of our college was conducted from 1st Sep to 21st Oct 2007 in two batches.

5. Infrastructure facilities in the Bioinformatics Centre ¾ Computer & Communication facility- 2 servers, 10 desktops with internet connection ¾ Scientific Software packages- Genious Pro Ver.3.5.6 ¾ Databases & other information resources- Pfam Database for Geneious

6. Details about staff members working in the centre : At present we do not have dedicated staff for the facility. The faculty of the Microbiology Department are involved in the activities of the facility

a. Name of the staff: Mrs. Kavitha B Designation: Senior Scale lecturer and Head of the Department Specialization: Environmental Microbiology Period of working: Since 1992, appointed by Karnataka Public Service Commission

b. Name of the staff: Mr. Arun Jyothi Mathias Designation: Senior Scale lecturer Specialization: Environmental and Medical Microbiology Period of working: Since 1996, appointed by Karnataka Public Service Commission

c. One RA will be shortly appointed 384 7. Types of services provided Training programme for B.Sc. students, M.Sc Students and faculty Access for browsing for research material is being provided for M.Phil Students

8. Educational activities with details of placement- 9. Initiative to validate the outcome of bioinformatics resources - 10. Collaborative works/ initiatives - 11. Databases/ Software packages developed - Nil 12. Papers published or presented in the conferences with reference - Nil 13. Initiation of R&D activities in Bioinformatics- A database for airborne fungal allergens in indoor environment is being attempted. 14. Details of Training/ Workshop organized and total no. of user trained Date Training Participants Organized by No. of programme users trained 10th April 2007- One day M.Sc. Orsby Engineering Pvt. 20 workshop Students Ltd., Bioware division 18th and 19 April Two day Faculty Orsby Engineering Pvt. 20 2007 workshop Ltd., Bioware division 23rd and 24th April Two day B.Sc. Department of 14 2007 workshop on Students Microbiology Sep and Oct 2007 Two months B.Sc. Department of 21+ 21 (2 course Students Microbiology batches)

15. Impact shown by your centre on the growth of biotechnology and allied areas. Over 75 students and 20 teachers have been trained in the field of Bioinformatics. There have been enquires from schools and colleges to schedule. The facility provides for literature survey to M.Sc. and M.Phil students. 16. Future activities Two months course will be continued during Feb- Mar 2008. Workshop for teachers is being planned during Feb 2008. A state level workshop is being planned for in the month of Aug. With over 15 new faculties being posted to our college, those interested will also be given training in bioinformatics. Additional Details: Name of the Coordinator: Mrs. Kavitha B Postal Address: Department of Microbiology, Maharani’s Science College for Women, Palace Road, Bangalore- 560001 Phone Number: 080-22371416

385 Email: [email protected] Website: www.mscwb.org Name of Contact Person(s): Same as above

386 Maulana Azad National Institute of Technology, Bhopal Coordinator : Dr. K. R. Pardasani

1. Summary of the progress made by the centre from its inception: The Department of Mathematics, MANIT Bhopal has already conducted a number of activities in the area of Bioinformatics, before it received funding from DBT for the BIF Centre. MANIT is already running M.Tech. programme in Bioinformatics since July 2006 and started B. Tech. Program in Bioinformatics from this session i.e. July 2007. MANIT is also conducting Ph.D programme in bioinformatics. MANIT also intends to start B.Tech and M.Tech programmes in the disciplines like Biotechnology, Genetic Engineering,Biomedical engineering, Bioengineering and Pharmacy. MANIT has already been organizing short term training programs in bioinformatics since 2004.

2. Major research activities in Biotechnology and its related fields at your institution :The institute plans to develop a versatile research team in the following areas of computational biology-

1 Thermal modeling of cancer 2 Modeling gene expression 3 Datamining 4 Modeling and analysis of Biological sequences. 5 High performance computing for bioinformatics. 6 Computational phylogenetics 7 Neuroinformatics

3. Area of Specialization of the centre : Computational Biology. 4. Major activities of the centre during the year 2007-08 : 1. Organized 12th Annual Conference of Gwalior Academy of Mathematical Sciences& All India Symposium on Computational Biology during April 6- 8, 2007. 2. Organized National Workshop on Bioinformatics during May 21-25,2007 3. Organized National Workshop on Cheminformatics during May 28-June 1,2007

5. Infrastructure facilities in the Bioinformatics Centre A. Computer & Communication facility: 10 PIV computers along with one medium server, 1 laser printer and 1 Desk-jet printer and one medium server and 1 Photocopier and scanner 1 server high end (Procurement under process) B.Scientific Software packages: At present we use online and free software’s like BLAST, CLUSTALW, PHYLODENDRON, RASMOL, Primers 3, EMBOSS, Webcutters etc. Recently we have purchased GCG Accelyrs software. C. Databases & other information resources:

387 The online databases like NCBI, EMBL, PDB etc are accessed through internet.

6. Details about staff members working in the centre (Name of the staff, Designation, Specialization and period of working. Please indicate their absorption status) : There are 10 Research Fellows working in the area of Bioinformatics.

Name of staff Designation Specialization Period of working Dr.K.R.Pardasani Professor & Head Computational 23 years Biology, Data Mining 7. T Dr.Namita Srivastava Assistant Professor ComputationalGeno 19 years ype mics,Intergral Transforms s of Dr.Madhvi Shakya Head Department Biomathematics, 18 years of Bioinformatics Biocomputing ser MrsUsha Chauhan Lecturer Computational 7 years Phylogenetics vic Mr.Chandan K.Verma Lecturer Modelling 9 years es Gene Expression provided: i. Training programmes/ workshops in the areas of bioinformatics to provide exposure to basic skills of bioinformatics to the students of biotechnology/life science, physical sciences and IT, from other institutes of our region and country. ii. Guiding research for Ph.D degree and in Educational programmes in the areas of Bioinformatics . iii. Consultancy.

8. Educational activities with details of placement: MANIT is running B.Tech,M.Tech and.Ph.D programmes in Bioinformatics Three students of M.tech got placement in Tata Consultancy Services (TCS) and Wipro.

9. Initiative to validate the outcome of bioinformatics resources : (i) Feedback of participants in training/workshops. (ii) Feedback of students and research scholars of educational programme.

10. Collaborative works/ initiatives : We have developed collaborations with institutes like- ƒ Bhopal Memorial Hospital and Research Centre, Bhopal. ƒ JALMA, National Institute for Leprosy and other Mycobacterium Diseases, Agra to create databases for their data. International collaborations (Initialized): • Dr.Tulpupko, Department of Bioinformatics, Tel Aviv University, Isreal. • Dr.Tom Kirkwood, Director and Dr.Anil Wipat , Head department of Bioinformatics, University of New Castle, U.K • Dr.Roman Borisyuk, Director, Centre for theoretical and computational Neuroscience, University of Plymouth, U.K 388 • Dr.Daanvon Altan, University of Dundee, U.K

11. Databases/ Software packages developed :We have developed Softwares for : 1.Haplotyping 2. Molecular cutters 3.Codon usage analysis.

12. Papers published or presented in the conferences with reference :

Papers published-5 Presented in the conferences-30

13. Initiation of R&D activities in Bioinformatics : Since the faculty and students of MANIT are strong in the computational skills therefore we will also focus on software development in the areas of bioinformatics during 11th five year plan. We have Ph.D scholars with backgrounds of mathematics, biotechnology, computer science and statistics. We have faculty in the areas of mathematics, biotechnology, computational science, IT and statistics .Thus we have a very good interdisciplinary group to carry out teaching, research and software development in the area of bioinformatics. We plan to develop computational techniques and softwares for analysis of biological sequences to identify miRNA, siRNA, Epitopes, egritopes, other molecular markers etc with their role in genomic and proteomic networks, drug designing, diagnostics and therapeutics.

14. Details of Training/ Workshop organized and total no. of user trained : S.N Training/ workshops No. of participants 1 Organized National Workshop on Bioinformatics 100 during May 21-25,2007 2 Organized National Workshop on 100 Cheminformatics during May 28-June 1,2007

15. Impact shown by your centre on the growth of biotechnology and allied areas. In this you may highlight the details like number of paper published/ number of papers published with the help of your centre, how your centre is promoting various activities of your organization and neighboring institutions, manpower trained, tools developed, patents & copyrights acquired and other services offered etc. :

Among all the NIT’S, MANIT, Bhopal has taken lead by starting B.Tech, M.Tech and PhD programs in the area of bioinformatics. Also MANIT has taken lead among all NIT’s in organizing short term training programmes in the area of bioinformatics since july 2004.The institute has developed collaborations with the institutes like Bhopal Memorial Hospital and Research Centre, Bhopal, JALMA, National Institute for Leprosy and other Mycobacterium Diseases, Agra to form interdisciplinary groups for carrying research in the areas of mutual interest. We have developed interdisciplinary research groups.

389 16. Future activities: 1. Proposed National Workshop on Bioinformatics during March 10 – 14, 2008. 2. Proposed National Workshop on Cheminformatics March 17 – 21, 2008. 3. International conference on Emerging Horizons of Mathematical and Computational Sciences along with international Symposium on Computational and Systems Biology during Dec 18 to 21, 2008.

17. Additional Details: Name of the Coordinator: Dr.K.R.Pardasani Postal Address: Professor and Head Department of Mathematics, MANIT, Bhopal Phone Number: 0755-2671633 Mobile: +91- 9425358308

Email: [email protected], [email protected] Website: www.manit.ac.in

Name of Contact Person(s): Dr.K.R.Pardasani

390 Narendra Deva University of Agriculture & Technology, Faizabad Coordinator: Prof. K.N. Singh

1. Summary of the progress made by the centre from its inception

The Project “Bioinformatics infrastructure Facility (BIF) for the Biology Teaching through Bioinformatics (BTBI) was sanctioned on 7th September 2007 wide letter no. BT/BI/25/001/2006 to Department of Plant molecular Biology & genetic Engineering, Narendra Deva University of Agriculture & Technology, Kumarganj, Faizabad (U.P.). Tenders for servers, Computers furniture have been invited.

2. Major research activities in Biotechnology and its related research fields at your institution

A) Novel protein corresponding cysteine protease inhibitor (CPI) has been identified from N terminal sequencing and its homology with other protein established. B) Sequence characterization of one the novel Rgene fragment is in process.

3. Area of specialization of the centre

Plant Molecular Biology with specific reference to Biotic and Abiotic Stress and transformation

4. Major activities of the centre during the year 2006-07 a) Protein Purification and raising antibody against Cysteine Protease Inhibitor (CPI) b) Identification of iron rich rice varieties with low phytic acid c) Development of Mapping Population for Drought, Submergence, Salinity in rice and also temperature tolerance in wheat (Under pipeline)

5. Infrastructure facilities in the Bioinformatics centre A. Computer and communication facility B. Scientific software packages : Tenders invited for all items C. Database and other information resources

6. Details about staff members working in the centre (Name of the Staff, Designation, Specialization and period of working. Please indicate their absorption status)

Faculty Member Designation Area of Specialization Working Absorb Since tion Status Dr. K.N. Singh Prof. & Head Gene isolation and its 2005 Yes [email protected] manipulation Dr. Ramji Singh Associate Molecular Biology, 2005 Yes [email protected] professor Disease resistance, Biochemistry Dr. D.K. Dwivedi Associate Genetics, Molecular 2005 Yes [email protected]. professor breeding, Quantitative in Genetics 391 Dr. R.P. Singh Assistant Proteomics of pigeon 2005 Yes [email protected] professor pea to control pod borer m Dr. Nawaz Ahmed Khan Assistant Controlling YSB in rice 2005 Yes [email protected] professor through transgenic approach Dr. Shambhoo Prasad Assistant Abiotic stresses 2005 Yes [email protected] professor (drought, flood, heat m etc.) Dr. Manish Kumar Singh Prog. Asstt. Molecular Biology, 2005 Yes manishsinghmk@hotmail. Submergence tolerance com Dr. C.S. Pandey Prog. Asstt. Plant tissue culture, 2005 Yes [email protected] horticulture-Pomology, Plant Propagation Dr. Pramila Pandey Prog. Asstt. DNA fingerprinting, 2005 Yes [email protected] Biotic Stress Dr. Poonam Yadav Contres(III) Molecular Marker 2007 Yes [email protected] Technology om Mr. Rajiv kumar Singh Contres (II) Transformation and 2007 Yes [email protected] Transgenic Technology m

7. Types of services provided : Teaching and Research

8. Educational activities with details of placement

M.Sc. Biotechnology Program and this Department is established in year 2004 and from year 2008 this M.Sc. Biotechnology Program is being run with the help of Department of Biotechnology, GOI. Two batches of M.Sc. students are passed out and third Batch is pursuing so far. Number of intake is restricted to ten. Placement Details of our students are as follows:

Sr. Name of the Year of Place where appointed Nature of No. Student pass Job outs 1. Prashant Vikram 2006 International Rice Research Ph.D. Institute (IRRI), Philippines, Scholar Manila, 2. Md. Shamim 2006 Indian Institute of Pulse SRF Research (IIPR) Kanpur 3. Neha Singh 2006 Indian Institute of Pulse SRF Research (IIPR) Kanpur 4. Tarranum Nissar 2006 National Botanical Research SRF Institute (NBRI), Lucknow 5. Onkar Singh 2006 NRC on Plant Biotechnology, SRF Pusa, New Delhi 6 Aniruddh Tiwari 2006 Bajaj Hindustan Pvt. Ltd., Trainee Muzaffar Nagar, U.P. Officer 7. Shivam priya 2006 Industrial Toxicological SRF Research Center, lucknow 8. Amit Kumar 2007 Navodaya Vidyalaya Teaching Barabanki, U.P. 392 9. Brijesh Verma 2007 Eriscon, Bangalore Research 10. Vishal Singh 2007 Industrial toxicology Research SRF Centre (ITRC), Lucknow,

9. Initiative to validate the outcome of Bioinformatics resources

10. Collaborative works/initiatives

11. Databases/ Software Packages Developed ----- NA-----

12.Papers published or presented in the conference with reference

Dr. K.N. Singh National Seminar on molecular approaches for crop improvement Feb. 7th – 8th ,2007

International rice Symposium , IARI , New Delhi, October 2007 Dr. Ramji Singh National Seminar on molecular approaches for crop improvement Feb. 7th – 8th ,2007 Annual Zonal meeting of Indian Phyto pathological society & National Symposium on Advancing frontiers of Plant Disease Management Nov. 15-17, 2007 Dr. Ramesh Pratap DBT sponsored training on Gene closing Techniques and Automated Singh DNA Sequencing Department of Genetic Engineering School of Biotechnology organized By SRM University, Kattankulathur Tamil Nadu June 4 to24, 2007 National Seminar on Molecular approached for crop improvement Feb 7-8, 2007 National Symposium on Recent trends in Plan Science and Haerbal Medicine. Dec., 17-18, 2007 Dr. C.S. Pandey National Seminar on Molecular Approaches for crop improvement Feb. 7-8th 2007 organized by Deptt. of PMB & GE, NDUAT, Faizabad Workshop On Agricultural Biotechnology Advanced Tissue Culture Techniques for crop improvement, 21-22 Feb., 2007, Organized the Energy and Resource Institute (TERI) New Delhi. National Symposium on Research Trends in Plant Science and herbal Medicine, Dec. 17-18, 2007. Organized by NDUAT, Faizabad in Collaboration with APSI, India Muzaffar Nagar (U.P.) Dr. Nawaz Khan “Participated in training courage on construction of CDNA library and its screening” organized by ICAR, under advance studies in Biochemistry from Biochemistry, IARI, New Delhi from 5-25, Jan., 2006 Participated in 74th annual meeting society of biological chemistry (India) at CDRI Lucknow from Nov. 7-10, 2005 Participated in international Symposium conference on Post Harvest Technology and Value addition in cereals, pulses & oilseed at CSAU&T, Kanpur , Nov., 27-30, 2006 Participated in National symposium on Molecular approaches for crop improvement at NDUAT, Kumarganj, Faizabad from 7-8 Feb 2007. Dr. Shambhoo Activity participated in National Seminar on Molecular approaches for Prasad crop improvement at Dept. of PMB & GE, NDUAT, Kumarganj, Faizabad from 7-8 Feb., 2007 Participated in winter school training on “Molecular Breeding approaches for rice improvement” at CRRI Cuttak, Orissa from Sep. 10th -30th, 2007.

393 Dr. Poonam Yadav Participated in International Symposium on “Post Harvest technology and value addition in cereal, pulses & oil seeds ” at CSAU&T, Kanpur Nov., 27-30, 2006 Participated in National Symposium on “Molecular approaches for crop Improvement” at NDUAT, Kumarganj, Faizabad from, 7-8, Feb, 2007 Dr. D.K. Dwivedi National Seminar on Molecular Approaches for Crop Improvement, NDUAT, Kumarganj, Faizabad (7-8 Feb., 2007) International Symposium on InterDrought – II: Integrated approach to sustain and Improve Plant Production Under Drought Stress at University of Rome “La Sapienza” Rome, Italy (24-28 September, 2005) th 18 Scientific Conference of the Federation of Crop Science Societies of the Philippines (2-6 May, 2005) International workshop on Resilient Crops for Water-limited Environments at CIMMYT (24-28 May, 2004) Molecular Breeding approaches for rice improvement, CRRI (10-30 Sept, 2007) Planning Rice Breeding Programs for Impact, IRRI (7-18 Feb, 2005) Radiation Safety Course held at IRRI by the Department of Science and Technology, Philippine Nuclear Research Institute (1-5 March, 2004) Microarray and Bio-informatics: Applying Genomic Technologies to Identify Induced and Natural Variation in Stress-Response Genes, IRRI (23-26 February, 2004) Dr. Manish Kumar National Seminar on molecular approaches for crop improvement Singh Feb. 7th – 8th ,2007, N.D.U.A.T., Kumarganj, Faizabad, U.P. Km. Pramila National Seminar on molecular approaches for crop improvement Pandey Feb. 7th – 8th ,2007 N.D.U.A.T., Kumarganj, Faizabad, U.P.

13. Initiation of R&D activities in bioinformatics : Just initiated

14. Details of training/ workshop organized and total number of user trained Program has just started and very soon and in this calendar year training will be organized with intake of the ten participants.

15. Impact shown by your centre on the growth of biotechnology and allied areas. In this you may highlight the details like number of papers published/ number of papers published with the help of your centre, how your centre is promoting various activities of your organization and neighboring institutions, manpower trained, tools developed, patents and copyrights acquired and other services offered etc.

Few publication in Biotechnology has just started and coming up these are as follows: Md. Shamim, N.A. Khan and Singh, K.N. (2007). Controlling Yellow Stem Borer in rice using cysteine protease inhibitor from jack fruit seeds – an alternative to Bt. approach. IRRI News Letter (communicated)

Ashutosh Singh, Kapildeo N. singh, A.L. Yadav and Prashant vikram. (2007). PCR based diagnostics of a geminivirus causing leaf curl disease in papaya. Plant Archives. 7 (1): pp 87-89.

394 Jitendra Pratap Singh, Shambhoo Prasad, K.N.Singh and Randhir Singh (2007). Screening of heat tolerant wheat varieties by membrane thermo stability index in relation to yield and yield attributing trairs. International Journal of Plant Sciences. Vol.2: 159-165.

Till date there is no any publication in Bioinformatics.

16. Future activities

• Gene prediction • Promoter analysis • Various software application like QTL cartographer, NT SYS, secondary structure prediction etc. • Homology Search

Additional details: Name of the Coordinator: Prof. K.N. Singh, Prof. & Head, Department of Plant Molecular Biology & Genetic Engineering

Postal Address: Narendra Deva University of Agriculture & Technology, Kumarganj, Faizabad, 224 229, U.P. INDIA

Phone No. 05270-262123 Mobile: 9450767369 Email: [email protected] Website:

Name of the contact person(s): Prof. K.N. Singh, Prof. & Head, Department of Plant Molecular Biology & Genetic Engineering Email: [email protected]

395 National Institute of Pharmaceutical Education and Research, Chandigarh Coordinator : Prof. P.V. Bharatam

1. Summary of the progress made by the centre from its inception

Carried out research on Drug Design using Bioinformatics using Homology Modeling, Molecular docking, virtual screening are the focus of the work. The targets of interest are Peroxisome Proliferating Activating receptor (PPARα,γ,δ), Glycogen Synthase Kinase (GSK3), DHFR, hERG, acetylcholineesterase, etc. The therapeutic areas of interest are Diabetes, Malaria, arrhythmia, Alzhemier, etc. The drugs of interest are pioglitazone, rosiglitazone, metformin. Chemical processes like tautomerism in drugs, reaction mechanism for the synthesis of drugs, etc. were also studied.

2. Major research activities in Biotechnology and its related fields at your institution

Target identification in Insulin resistant diabetes, Target identification in drug resistant Leishmania, Pharmaceutical biotechnology, Microbiology & biotechnology, Recombinant DNA technology, Protein stabilization, Downstream processing, Nonaqueous enzymology Genomics, Proteomics, Bioinformatics and systems biology,

3. Areas of Specialization of the centre

Computer Aided drug design using sequence analysis, Structural bioinformatics, Molecular Docking Receptor based pharmacophore mapping, Virtual screening using molecular docking

4. Major activities of the centre during the year 2007-08

Workshop on target identification and target validation was conducted during 14-16 March 2007. A symposium on Bioinformatics for pharmacology was conducted as a part of Annual conference of Indian Pharmaceutical Society, SAS Nagar (2nd Nov. 2007). A workshop is scheduled to be held during 13-15 March, 2008.

5. Infrastructure facilities in the Bioinformatics Centre

Computer & Communication facility PCs – 10 Server -1 Printers – 2 Storage Space – NAS – 1TB Xerox machine Networking among all the systems

Scientific Software packages Drug design packages available from NIPER: MOE, SYBYL (QSAR, Maping, docking, Unity,) Catalyst, Gaussian, Spartan, Amber 396 Databases & other information resources available from NIPER. CCSD (Chemoinformatics) GCG (Bioinformatics)

6. Details about staff members working in the centre (Name of the staff, Designation, Specialization and period of working. Please indicate their absorption status)

Prof. P.V. Bharatam, Prof. in Med. Chem. (Coordinator) – specialization in computer aided drug design using molecular docking, pharmacophore mapping, QSAR, Electronic structure methods, etc. Dr. C.G. Mohan, Asst. Prof. in Pharmacoinformatics – specialization, pharmacoinformatics, structural biology, electronic structure analysis, toxicoinformatics, etc.

7. Types of services provided Scientific studies based on metabolic processes (oxidation using CYPs, FMN), pharmacophoric generation, molecular docking, QSAR analysis. Toxicoinformatics based prediction of toxic profile of compounds.

8. Educational activities with details of placement The BIF center contributes heavily to the M.S. Pharm. (Pharmcoinformatics) programme of NIPER. 25 MS students and 9 Ph.D. students are using this facility. All the students of the previous batch of M.S. Pharm. (Pharmcoinformatics) who graduated in July 2006 have found placements. 60 % are in industry, 40% joined academic research.

9. Initiative to validate the outcome of bioinformatics resources. Computational designed drugs have been synthesized and biologically evaluated and found to be promising. 10. Collaborative works/ initiatives Collaborating with scientists at Medicinal chemistry and pharmacology department of our institute. Collaborating with Punjab University, Chandigarh and Guru Nanak Dev University, Amritsar. International Collaboration with scientists at University of Turku, Finland.

11. Databases/ Software packages developed Alzhemier’s disease database: From Genome to Drug

12. Papers published or presented in the conferences with reference Modelling and Informatics in the Design of Anti-Tuberculosis (TB) Agents, G. Ranganath, D. Pohani, S. Sundriyal, P.V. Bharatam. J. Computer Aided Drug Design (submitted). Metformin and Glitazones: Does Similarity in Biomolecular Mechanism Originate from Tautomerism in these Drugs? S. Sundriyal, S. Khanna, R. Saha, P.V. Bharatam, J. Phys. Org. Chem. 2007 (in print). Computer Assisted Methods in Chemical Toxicity Prediction C.G. Mohan, T.Gandhi, D.Garg, R. Shinde, Mini Review in Medicinal Chemistry, 2007, 7, 499-507. 397 XML in Motion from Genome to Drug; Available from Nature Precedings C.G. Mohan, < http://dx.doi.org/10.1038/npre.2007.287.1 > (2007)

13. Initiation of R&D activities in Bioinformatics Target identification and validation, CADD, Cluster and High Performance computing Indo-Finland research collaboration is initiated in the area of structural bioinformatics, CADD and software development. Development of therapeutically useful databases.

14. Details of Training/ Workshop organized and total no. of user trained Workshop on Target Identification and target validation : 14 – 16, March 2007 : 50 participants Symposium on Bioinformatics during IPS annual convention : 2 Nov. 2007 : ~1000 participants

15. Impact shown by your centre on the growth of biotechnology and allied areas. The researches at the biotechnology department at NIPER extensively use the bioinformatics facilities. Several papers and patents were generated during 2007 with the collaborative effort.

16. Future activities

Research focus on drug design using pharmacoinformatics, including structural bioinformatics, molecular docking, pharmacophore mapping, electronic structure, metabolome informatics and toxicoinformatics, etc.

Workshop to be conducted in 13 -15 March 2008 in Pharmacoinformatics.

Name of the Coordinator: Prof. P.V. Bharatam, (on behalf of Director NIPER) Department of Medicinal Chemistry A-208,Natl. Inst. Pharm. Edu. Research. Postal Address: S.A.S. Nagar -160 062 Phone Number: 0172-2214684 Extn. 2018 Fax No.: 0172- 2214682 Email: [email protected] Website: www.niper.gov.in

398 Orissa University of Agriculture and Technology, Bhubaneswar Coordinator : Dr.P.N.Jagadev

1. Summary of the progress made by the Centre from its inception: The project on “Creation of Bioinformatics Infrastructure Facility (BIF) for the promotion of Biology Teaching through Bioinformatics (BTBI) scheme of BTIS net” was implemented on 3rd November, 2006 in the P.G Department of Bioinformatics, OUAT, Bhubaneswar with 100% support from the Department of Biotechnology, Government of India, New Delhi. During the last year (i) a well furnished computer lab with internet facility was established for the project with two high end server and one medium end server, ten numbers of PCs with operating system like Windows 2003 Enterprise server/Redhat Linux and needful software like Microsoft visual studio 2005, MS Office 2007, SQL and one scanner, one HP Laser Jet 3055 printer, one HP DeskJet D2360 printer, one photo copier are available for the project work. 2. Major research activities in Biotechnology and its related fields at your institution: The Orissa University of Agriculture and Technology is offering a two year regular course with an intake of ten students each year, selected through the entrance examination conducted by the JNU leading to M.sc. (Ag.) degree in Agricultural Biotechnology with the 100% support of the Department of Biotechnology, Ministry of Science and Technology, Government of India. The major research activities in Biotechnology are molecular marker technology, protein profiling, DNA fingerprinting, tissue culture, transformation of rice and potato etc. The fields of research in Bioinformatics sequence analysis, computational biology and development of biological databases besides offering a two years regular course with intake capacity of 32 students each year selected through career weightage basis leading to M.Sc. degree in Bioinformatics on self-finance scheme of the University since 2002. 3. Area of Specialization of the Centre: Biotechnology & Bioinformatics. 4. Major activities of the centre during the year 2006-07: During the year 2006-07 four Post-Graduate students (Bioinformatics) of this University have done their dissertation project works in the areas of database development on medicinal plants, Fusarium species, rice crop and soil informatics. Thirty two numbers of Post-Graduate students (Bioinformatics) have also passed from this department by doing their theses works in leading labs of different institutions /organizations of the country. 5. Infrastructure facilities in the Bioinformatics Centre: A. Computer & Communication facility: Thirty-seven PCs with 2048 kbps internet connectivity in the Department of Bioinformatics and ten numbers of PCs, two numbers of high-end servers and one medium end server with operating system in the project are available. B. Scientific Software packages : GCG Wisconsin package, java, LINUX, UNIX, XL stat, Antivirus packages are available- sponsored by OUAT C. Databases & other information resources: Oracle 10G, Microsoft SQL Server, Ricebase, Fusabase.

6. Details about staff members working in the centre: BTISnet-DBT project SL.No. Name of the staff Designation Specialization Period of 399 working 1. Mr. S.N.Rath RA Computational Biology 17.01.2008 onwards PG Department of Bioinformatics 1. Ms.L.kanungo Asst.Proff. Proteomics 29.08.2006 Onwards 2. Mr.S.k. Pradhan Asst.Proff. Molecular modeling 01.05.2007 onwards 3. Ms.S.Mohanty Asst.Programmer Computer Science 17.04.2006 Onwards 4. Mr.M.Garanayak Data Entry Operator ------15.01.2003 onwards * The absorption status of the above staffs is on contractual basis.

7. Types of services provided: The centre has provided the facilities of computer lab and twenty four hours internet facilities (fiber optics)to the post-graduate students and teachers/scientists of the sister departments like Biotechnology, Pathology, Horticulture, Soil Science and Biochemistry, Plant Breeding and Genetics etc. for their dissertation and research work, besides rendering the computational knowledge to them. 8. Educational activities with details of placement: Each year, 32 Nos. of M.Sc. (Bioinformatics) students are passing out of this department and placed in different reputed organizations and companies of repute and also in off campus interview. During the last year our student are at JVK Bio Science, Hyderabad, Mahatma Gandhi Institute of Medical Sciences, Wardha, RCM, Bhubaneswar, GIET, Gunupur, Orissa, KBRC, Cuttack etc. 9. Initiative to validate the outcome of Bioinformatics resources: Actions have been taken to validate the Bioinformatics resources. For example booklet was developed for the initial years (2002-05) of theses research works of students. 10. Collaborative works/initiatives: In the year 2006-07 students done their dissertation different reputed institutions and laboratory like, RRL, Bhubaneswar, Wingene, Banglore, ITRC, Lucknow, WB University, Kolkata, Biotech Park, Lucknow, ISI, Kolkata, GVK Biosciences, Hyderabad, Satya Informatics, secunderabad, MGIMS, sevagram, wardha for their partial fulfillment of M.Sc. Bioinformatics degree. 11. Databases / Software packages developed: One CD-ROM database on rice genotypes available at OUAT research station is developed. 12. Papers published or presented in the conferences with reference: i) Paper entitled “BioRec: A biological record retrieving tool” accepted for poster presentation in InCoB (Sixth International Conference in Bioinformatics) held at Hong Kong during August 27- 30, 2007. ii) Paper entitled “Fusabase: A database for identifying species Fusarium” accepted for poster presentation in InCoB (Sixth International Conference in Bioinformatics) held at Hong Kong during August 27-30, 2007 13. Initiation of R&D activities in Bioinformatics: After getting this project this department has taken initiatives to develop various CD-ROM database on Biotechnological research work, identification

400 tools for bacterial plant pathogens, database on rice genotypes of Orissa and Fusarium are developed in the department of Bioinformatics. Initiation to develop an online database on medicinal plants has also been taken. 14. Details of Training/ workshop organized and total no. of user trained: A 3days National Workshop-cum Training was successfully organized from 9-11 March, 2007 with 31 numbers of participants and 15 Nos. of Resource Person from different R &D organizations and Institutions of National repute. 15. Impact shown by your centre on growth of biotechnology and allied areas: Our centre is helping the students of this university and other Universities like Amity University for their dissertation and works in the biotechnology and allied areas. 16. Future activities: i) To organize hands on training and seminar for familiarizing the applications of Bioinformatics in biology teaching. ii) To establish collaboration with other institutions and BTISnet centres for information resources and expertise. iii) Development of on-line databases of field and horticultural crops.

Additional Details:

Name of the Coordinator : Dr.P.N.Jagadev Postal Address : Head, Post Graduate department of Bioinformatics, Orissa University of Agriculture and Technology, Bhubaneswar-751003, Orissa Phone Number : 0674-2530418, 09861128437 Fax : 0674-2391424/ 2394762 Email : [email protected] [email protected]

Name of Contact Person : Dr. Sashikala Beura, Associate Professor Dept. Horticulture, OUAT, Bhubaneswar-751003, Orissa. Email: : [email protected]

401 Presidency College, Chennai Coordinator : Prof. S. Rajarajan

1. Summary of the progress made by the centre from its inception The Bioinformatics Infrastructure Facility (BIF) Centre at P.G & Research Department of Microbiology & Biotechnology, Chennai was established on 28 March 2007. The Centre had conducted two workshops. 1) State level Workshop for 12- days on Bioinformatics for the Government College Teachers from March 28th to April 10th 2007 2) A National workshop for 11- days on “The Application of Bioinformatics in Drug discovery and Drug development" for the benefit of Research scholars and made an indelible impact on the target group about the activity of the centre. In addition, the centre had created database on Antibiotics of microbial origin and will be available in website from January 2008. The centre provides free internet facility to all the students & all needy departments of the college. 2. Major Research activities in Biotechnology and its related fields at your institution Discovery of newer drugs from herbal source for microbial diseases in human is one of the major thrust area in biotechnology conducted in P.G and Research Department of Microbiology & Biotechnology. Screening of the potential medicinal plants, subsequent isolation of the active principles (at chemistry Department) and testing the efficacy of the active principle (drug) in relation to the Pathogenomics of the microbe. Few research scholars are working on the pharmacogenomics of efficacious drugs for very common diseases like Diabetes, hypertension, Tuberculosis, Chickugunya etc. In addition, in vitro cultivation of important cell lines for the estimation of toxicity of drugs and in vitro antiviral assay are also carried out. 3. Area of Specialization of the Centre:Drug discovery & Drug development. 4. Major Activities Of The Centre During The Year 2007-2008: Conducted two workshops and created a database (as mentioned in item 1) 5. Infrastructure Facilities in the Bioinformatics Centre: a) Computer and communication Facilities: The centre is equipped with 10 Desktop computers (IBM). 1 High end server (IBM), 1 Middle end server (IBM), with 1 HP Color Laser printer (5-in-1 model – Copy, scan, fax, print, imaging) and with software packages like Symantec Antivirus, Symantec Antivirus, MS Windows Vista, Media Kit, MS SQL server, MS SQL server cal 2005, Redhat enterprise linux, MS Windows, MS windows 2003, MS visual studio, MS office 2007, 1 Inkjet printer.7.5kva UPS with VSNL high speed internet connectivity to all needy departments. The centre has been provided with split air conditioner (2 ton).

Telephone :044-64542545 Telefax:044-28589621 Email:[email protected] Website : www.bifcpresidency.net.in b) Scientific software packages: CLC BIO Combined Workbench. c) Database & other information resources: Created a database for the first time in India on Bioinformatics of antibiotics from microbes and this will be uploaded in the website by the end of January. 6. Details of staff members working in the centre: Sl. Name of the Designation working since Absorption No. staff status (yes/no)*

402 1. Miss. M. Niraja Asst. Coordinator December 2006 yes Research September 2006 Associate 2 Miss. L. Anitha Data Entry March 2007 yes Operator

7. Type Of Services Provided Four major types of services are provided 1) Free Internet facility for PG / Research Scholars/ Teachers at the centre 2) Internet facility to all needy departments 3) Free utilization of softwares on Bioinformatics 4) Training programme. Also it enables the P.G. Students of Government colleges, Government aided colleges to obtain required information on Bioinformatics. Thus promoting the discipline of Bioinformatics among colleges in and around Chennai. Text books and reference books on various areas of Bioinformatics are available in the centre for the benefit of students / Teachers / Researchers. 8. Educational activities with details of placement: Students of M.Sc Applied Microbiology & Biotechnology utilize this facility for core elective paper on Bioinformatics. Besides this, students of M.Sc., M.Phil. and Ph.D. utilize for their research data. Many of the students are well placed in other software & knowledge process outsourcing companies. 9. Initiative to validate the outcome of Bioinformatics Resources: A register is maintained on the users and membership card with finger print entry facility is being issued to the users. 10. Collaborative Works/ Initiatives: Collaborative work on Drug discovery & Drug development with TANUVAS (Tamil Nadu University of Veterinary Animal Sciences) for development of drugs for veterinary animals and with Meenakshi Medical University have been agreed in December 2007. 11. Databases/ software packages developed: Developed a database for the first time in India on the Bioinformatics of antibiotics from microbes. Further, a database on vaccines is being developed. 12. Papers published or presented in the conferences with reference: 1) Rajarajan. S. “Application of Bioinformatics in drug discovery and drug development” presented at the national Conference on bioinformatics tools for gene and protein analysis on 7-8 September, 2007 at Srimathi Indira Gandhi College, Tiruchirapalli, Tamil Nadu. 2) Rajarajan. S., “In Vitro antimicrobial assay of Medical Plants – (M.K.Nambiar oration) 28th Annual Conference of India Association of Biomedical Scientists 21st Sept. 2007, Bharathidasan University, Tiruchirapalli. 3). Amerjothy. S “Antimycobacterial properties of Leaf extract of Pithecellobium dulce Benth”. pp. 392-395. 42 (6) Indian Drugs. 4) Amerjothy. S. “In vitro assay of antifungal and antitubercular activities of the leaf extract of Pithecellobium dulce”. XXVIII – All India Botanical Conference BSI - Dehradun – 2005. 5) Amerjothy. S. “Pharmacognosy and Pharmaceutical Potential of Some Plant Galls”,National Seminar on Recent Advances inPlant Biology, Abstract, p. 83, July 2006, Pondichery University, Pondicherry.

403 6) S. Amerjothy “Pharmacognostic investigation on leaves of “Pithecellobium dulce (Huamuchil) A promising anti-tuberculosis drug” pp. 265 – 275 with S.D. Shanmuga Kumar et al. in the book Recent Trends in Plant Sciences. 7) Natarjan. C, Senthil Kumar R, Niraja M, Rajarajan. S “In vitro antiviral efficacy of lyophilized extracts of anthospira platensis (Spirulina Platensis) on human herpes virus – 2 (HH-V / HSV – 2) in comparison with acyclovir”. South Zonal conference of Medical Microbiologist Sozocon – Micro 2008 20th January 2008 at Srimanakula Vinayagar Medical College, Pondicherry. 8) Ganesh. B, Bakthasingh Lazarus. Y, Rajarajan. S “ Study on the isolation and characterization of the etiological fungus from onychomycotic infections at a hospital in chennai and their in vitro susceptibility to a herbal mixture to antifungal agents”. South Zonal conference of Medical Microbiologist ,Sozocon – Micro 2008 20th January 2008 at Srimanakula Vinayagar Medical College, Pondicherry. 9) Praveen Irudiyaraj. R, Bakthasingh Lazarus. Y, Rajarajan. S. “In vivo experimental study on development of cutaneous hypersensitivity in albino mice after exposure to aerosolized antigen of Aspergillus spp”. South Zonal conference of Medical Microbiologist Sozocon – Micro 2008 20th January 2008 at Srimanakula Vinayagar Medical College, Pondicherry. 13. Initiation Of R&D Activities In Bioinformatics The Bioinformatics centre of DBT, Presidency College and the Virology Department of King Institute of Preventive Medicine, Chennai have agreed to work together in its R & D activities on Bioinformatics. 14. Details of training/ workshop organized and total no. of user trained: As mentioned in item (1) The total number of user trained in first workshop was 10 and in the second workshop was 20. 15. Impact shown by your centre on the growth of biotechnology and allied areas. In this you may highlight the details like number of paper published/ number of papers published with the help of your centre, how your centre is promoting various activities of your organization and neighboring institutions, manpower trained, tools developed, patents & copyrights acquired and other services offered etc.

Through its activity and conduct of workshops it evoked interest on bioinformatics in Tamil Nadu in relation to Drug discovery & Drug development. In addition the facility has been used for the below mentioned activities M.Sc. dissertations: 61, M.Phil. dissertations: 57 Ph.D. thesis completed: 14, Papers published using this facility: 37 Database created using this facility: 2 databases No of teachers who availed this facility: 63, PG students – 215, Research scholars – 94 16. Future activities: As this prestigious institute is to be elevated into a University from 2008 - 2009 Post Graduate & P.G Diploma programmes in Bioinformatics will be started. Summer school programme for higher secondary students & teachers on Bioinformatics will be conducted on Drug discovery & Drug development. This will make an effective impression on the young minds to venture into Bioinformatics and appreciate its role in Drug discovery & Drug development. The centre will establish interconnectivity and exchange of information with 404 other centres working on Drug discovery & development. Databases on Drug from plant / animal / mineral sources will be created with the coordination of other departments.

Additional Details: Name of the Coordinator: Prof. Dr. S. Rajarajan Postal Address: College House, No.100, Kamarajar Salai Presidency College, Chepauk, Chennai – 600 005. Phone Number: 044- 28547839, Mobile: 9282321575 Fax Number: 044-28589621 Email: [email protected] Website: www.bifcpresidency.net.in Name of Contact Person(s): Miss. M. Niraja Email: [email protected]

405 Presidency College, Kolkata Coordinator : DR. Abhijit Datta

1. Summary of the progress made at BIOINFORMATICS INFRASTRUCTURE FACILITY (BIF-BTBI) at Presidency College, Kolkata (NAAC A+ Accredited and College with Potential for Excellence) Centre since its inception: The Centre has started working under the guidance of Dr. T. Madhan Mohan, Advisor, DBT, during the last quarter of 2006. Following points are to be mentioned: 1. Inauguration of the site has been done (One Bioinformatics Centre, to accommodate 20 terminals and another Server room with four terminals) in the Central Library Building, Presidency College, Kolkata. 2. The EC meetings have been convened as per DBT guidelines; 3. LAN, 24x7 - 2 Mbps Internet connectivity and graphics facility of the Bioinformatics Laboratory are working full time. 4. Procurement of the hardware and software has been completed as per recommendations by the expert members. 5. List of Experts in the field of Bioinformatics is under processing, required for the Workshop / Training Program to be conducted by BIF, Presidency College, Kolkata from time to time; 6. Probable schedule of the Workshops / Training Program to be taken up during the next financial year is under formulation; 7. Designing of the website bioinfopresidencycollegekolkata.edu.in is under construction; 2. Major research activities in Biotechnology and its related fields at Presidency College, Kolkata: A full fledged Plant Biotechnology Laboratory runs in the College, working on various medicinal plants viz. Jatropha, Chlorophytum, Swertia and other horticultural plants including Orchids. Plant Molecular Biology group is working on Cashew genome in collaboration with Haldia Institute of Technology, West Bengal. Bioinformatics work group from different constituent departments of the college is growing to make out some inroads in near future. 3. Major activities of the centre during the year 2007-08: Formally Inaugurated on Founder’s Day, National Workshop conducted on Bioinformatics: Genomics & Proteomics Plexus 8 - 9 Dec 2007 in the Bankim Sabhagriha which was inaugurated by Dr. T. Madhan Mohan and a National Workshop on Clinical Research & Clinical Database Management is being held during 31 Jan - 2 Feb 2008. 4. Infrastructure facilities in the Bioinformatics Centre: Computer & Communication facility: One IBM Server 226 has been installed as per DBT specifications; Ten Desk tops are installed as terminals as per DBT specifications; One HP Workstation is being installed for modeling works; Software to run these systems purchased as per DBT specifications; One independent Broadband (2 Mbps) connection with unlimited download facility is running for the users / students; One Fortigate Firewall has been installed for net security of the Centre. Scientific Software packages: None purchased so far; Databases & other information resources: Under consideration. 5. Details about staff members working in the centre: 406 Research Assistant: Sayak Ganguly, M.Sc.; Diploma in Bioinformatics. Laboratory Assistant: Priyanka Dhar, M.Sc. 6. Types of services to provide: Downloaded packages are being made available to the Under Graduate and Post Graduate students of different Bio-Science Departments as well as to the Research Scholars of the College and other Institutes of the locality. In future all types of facilities will be offered depending on the availability of the suitable Software. 7. Initiative to validate the outcome of bioinformatics resources: A high profile Advisory Committee has been constituted to formulate the future course of action at this Centre. With the help of suggestions of the honourable members the facilities are being designed to cater not only the students of Presidency College, Kolkata, but also the students of the nearby Government Colleges, other affiliated Colleges and share with other National Institutions. The excerpts of the suggestions were proposed along with the EFC inputs. 8. Collaborative works / initiatives: Collaborative work has already been proposed with partner Dr. T.C. Ghosh of BIC, Bose Institute and collaboration with other Institutes viz. IOCB, Bangalore and Birla Institute of Technology etc. is under consideration. BIF, Presidency College and IOCB have held a workshop on Clinical Research & Clinical Database Management at the Derozio Hall, Presidency College, Kolkata. 9. Initiation of R&D activities in Bioinformatics: R & D programmes on RNAi, Dof Domain and other interesting storage proteins are being initiated. Two communications have been made and others are in the pipeline. Proposals from Research work groups have been invited from different Bio-Science Departments of the College, to be carried out utilizing the Bioinformatics Infrastructure Facility at Presidency College, Kolkata. 10. Details of Training / Workshop organized and total no. of user trained: One National workshop was conducted on Bioinformatics: Genomics & Proteomics Plexus during 8-9 Dec 2007 in the Bankim Sabhagriha, Presidency College, Kolkata with 48 participants. Inaugural address was delivered by Dr. T. Madhan Mohan and the list of speakers includes Prof. Pinak Chakrabarti, Dr. Subhasish Mukherjee, Dr. Debasish Mukherjee, Dr. Kunal Mukhopadhyay and Somak Ray. Another National Workshop on Clinical Research & Clinical Database Management is being held during 31st Jan – 2nd Feb 2008 in collaboration with IOCB, Bangalore with ~ 150 participants. 11. Future activities of this Centre will include: As proposed in EFC inputs Summer School / Winter School on Bioinformatics for Research Scholars and Students, Training Programmes for Post graduate, Under Graduate students and Teachers from the Undergraduate Colleges, Post Graduate Departments of different Colleges and Universities. National level Seminars, Workshops on emerging fields of Bioinformatics. Offer Post M.Sc. Traineeship/Studentship to the students coming from different Bioscience disciplines. To conduct research in the areas viz. Dedicated and derived Genomic/Clinical/ Biotechnology Database Development, Analyses using Bioinformatics tools, In silico Modelling and Development of study modules for different levels of teaching. To introduce (Memorial) Lecture Series in Bioinformatics. To observe and celebrate BIOINFO-DAY each year, as annual meet, to attract 407 students in this field. This Centre aspires to become full fledged Bioinformatics Centre in near future.

Name of the Coordinator: DR. ABHIJIT DATTA Postal Address: PRESIDENCY COLLEGE 86/1, COLLEGE STREET KOLKATA 700073 Phone Number: +919830116667 email: [email protected]

408 Sardar Vallabh Bhai Patel University of Agriculture & Technology, Meerut Coordinator : Prof. Raghvendar Singh

1. Summary of the progress made by the centre from its inception : The project entitled “Establishment of Bioinformatics Infrastructure Facility (BIF) for the promotion of Biology Teaching Through Bio-informatics (BTBI)” was sanctioned in the month of September 2006. The Bioinformatics lab was established and furnished. The web site for the BIF is created and the same is linked with our university (SVBPUA&T, Meerut) web-site. The two week training programme on “Database and Software application in biological sciences” was prepared. The six month teaching and practical courses on Information Technology and Bioinformatics had been taught to the B.Tech (Biotech) students of the university. The summer training on Bioinformatics was given to the B.Tech student. The visit of the expert scientist on Bioinformatics research in the area of structural & computational biology was organized under VSAP. The development of the database on milk protein and rice is in progress and will be completed shortly. Genomics and proteomic study on wheat, rice and potato is in progress. 2. Major research activities in Biotechnology and its related fields at your institution: College of Biotechnology is established consisting of eight specialized department as Pathology & Microbiology, Cell Biology, Biochemistry and Physiology, Immunology & Defense Mechanisms, Recombination Techniques, Department of Fingerprinting, Commercial biotechnology and Department of Genetic Engineering to carry out major research and teaching activities respectively. 3. Area of Specialization of the centre : Biotechnology The objective of the College of Biotechnology is to train the students in different biotechnology techniques and research areas like Finger printing, Cell biology, Tissue culture of medicinal and other important crops of western U.P. Molecular characterization, diagnosis and detection of pathogens, Genetic of various traits, tagging and mapping of agriculturally important gene(s), functional analysis of different mechanism, gene manipulation and expression. 4. Major activities of the centre during the year 2007-08 The major activities were establishment of Bioinformatics Lab, Creation of Web-site, organization of BTISnet Teaching/Training / Workshop, visit of scientist under VSAP, initiation for development of databases and collaborative Ph. D. research projects and Participation in Meeting/ Seminar /Conference. 5. Infrastructure facilities in the Bioinformatics Centre : The Bioinformatics lab is furnished with total ten Desktop computer system, two Servers, two Laser Printer, internet connectivity and On-line UPS with research and teaching material projection facility. 6. Details about staff members working in the centre (Name of the staff, Designation, Specialization and period of working.

409 Name of the staff Designation Specialization Absorb. status Dr. Raghvendar Singh Prof. & Head Immuno.& Biochem. Univ. employee Dr. Jitender Singh Asst. Professor Biotechnology Univ. employee Dr. Akash Tomar Asst. Professor Recombinant Tech. Univ. employee Mr. Deepak Sisodia Asst. Professor Information tech. Univ. employee Mr. Gyanendra Singh Project fellow Information tech. No* 7. Types of services provided : Teaching, training and research 8. Educational activities with details of placement: B.Tech (Biotech) in progress and M.Tech (Biotech) with specialization in seven different departments is approved and under process of its implementation. 9. Collaborative works/ initiatives: Ph. D. Research project with Ch. Devi Lal Univ. , Hisar. 10. Initiation of R&D activities in Bioinformatics : proteomic and genomic study on lactoferrin, whey proteins, Dictyostelium discoidium. 11. Details of Training/ Workshop organized and total no. of user trained Total 60 students of B.Tech (Biotechnology) were trained and the training on “Database and Software application in biological sciences” is proposed in this year. 12. Future activities: • To support and promote different on going teaching programme of the university in the subjects of information technology, bioinformatics and biotechnology. • To provide a facility to different on going research programmes on mandatory crops and other potential areas of research in the field of biotechnology and bioinformatics of the university. • Establishment of Agri-Information center for quick transformation of advance agricultural technology for the farmers of western U.P. • To prepare the information resources, databases on research advances on wheat, rice, vegetable and dairy husbandry. Training on advances in Biotechnology and Bioinformatics research including proteomics and genomics. • Development of website portal with several functionalities such as database searching, teaching protocols, email support, user login, Query questions and solutions and other standard information tools etc. The development of softwares related to the bioinformatics as per the requirement of users of the universities. • To organize a refresher and Orientation courses on advances and development in the field of bioinformatics research and to provide studentship ant traineeship for the graduate and Post-graduate students of Biotechnology and Bioinformatics. • Advance Diploma and post graduate degree course will be started in Bioinformatics if approved. 13. Additional Details: Name of the Coordinator: Raghvendar Singh, Prof. & Head Postal Address: Department of Immunology & Defense Mechanism, College of Biotechnology, Sardar Vallabh Bhai Patel University of agriculture & Technology, Meerut Phone Number: 0121-2411534 Mobile: 9410816513 Email: [email protected] Name of Contact Person(s): Dr. Jitender Singh, Co-coordinator Email: [email protected]

410 Sant Gadge Baba Amravati University, Amravati Coordinator : Dr. Prasad A. Wadegaonkar

1. Summary of the progress made by the centre from its inception Bioinformatics infrastructure Facility was established at Sant Gadge Baba Amravati University This facility is housed in Post Graduate Department of Biotechnology. Servers, PCs and other hardware are procured from HP through DGS&D and 256 kbps internet leased line is obtained from BSNL. This facility was inaugurated on 28th December 2007 by Hon’ble Vice Chancellor Dr. (Ms.) Kamal Singh, in the presence of Dr. Gulshan Wadhwa, Principle Scientific Officer and Information Officer, Apex Centre, DBT, New Delhi. 2. Major research activities in Biotechnology and its related fields at your institution Department of Biotechnology, SGB Amravati University is actively engaged in research mainly in the area of microbial and plant biotechnology. DST has sanctioned Funds DST-FIST Scheme. Prof. M.K. Rai and his group’s research is focused on the microbial growth promoters using chlorophyll fluorescence as a biomarker (Biophysical Phenotyping). Dr. P.A. Wadegaonkar and his research group is working on the root organ and suspension cultures of those medicinal plants, such as Withania somnifera (UGC sponsored), Artemisia annua (DRDO sponsored) and Rauwolfia serpentina, Catharanthus roseus, Morinda citrifolia and Zinziber species for production of secondary metabolites using bioreactors. Dr. (Mrs) A.S. Patil and her group is working on bio-bleaching of paper pulp. 3. Area of Specialization of the centre 4. Major activities of the centre during the year 2006-07 Establishment of infrastructure. 5. Infrastructure facilities in the Bioinformatics Centre Computer & Communication facility Server (High end) HP ML350 G4/G5 Xeon Daul processor - 01No. Server (Medium end) HP ML110G3 Pentium IV configuration - 01No. Desktops HP DX2060 Intel Pentium Dual Core 2.8 GHz - 10 Nos. Laser Printer (Network) HP 2420 DN - 01 No. Desk-Jet Printer HP BJ1200 d - 01 No. Scanner Flat bed HP 2400 - 01 No Lease Line 256 kbps Scientific Software packages Bio-edit, ClustalW, GeneDoc, RasMol, TreeView, ACD/Chemsketch, Fermisym, Polymath Databases & other information resources o Flora of Melghat Reserve Forest (S&T Cell, Govt. Maharashtra Funded) o Database of Phyto chemicals (On going) o Database of Industries India involved in phyto chemicals (On going) 6. Details about staff members working in the centre (Name of the staff, Designation, Specialization and period of working. Please indicate their absorption status) - nil 7. Types of services provided BIF has collection of books in PDF format on Bioinformatics, Genetics, Molecular Biology, Biochemistry, Immunology etc. and other teaching 411 resources in flash animations, which are loaded on server and made available to students through LAN. BIF is also providing Internet access and literature search facility for academic purpose. 8. Educational activities with details of placement 9. Initiative to validate the outcome of bioinformatics resources 10. Collaborative works/ initiatives – With the collaboration of Bioprocess Laboratory, Department of Biotechnology, Sant Gadge Baba Amravati University, attempts have been to integrate the available in silico and wet lab facility for Metagenomic Research. 11. Databases/ Software packages developed • Database of Phytochemicals (On going) • Database of Industries India involved in phytochemicals (On going) 12. Papers published or presented in the conferences with reference 13. Initiation of R&D activities in Bioinformatics – Initiation has been taken to integrate the wet lab facility of Biotechnology Department and in silico facility of BIF. 14. Details of Training/ Workshop organized and total no. of user trained Training Program on Bioinformatics and Information Technology was organized from December 28-30, 2007. Total 15 participants were trained during the period. During the training period special lectures were delivered by Dr. Gulshan Wadhwa, Principle Scientific Officer, New Delhi, Dr. Shekhar Mande, Scientist, CDFD, Hyderabad and Dr. (Mrs.) Sharmila Mande, Head, Biological division, TCS, Hyderabad. Along with participants, over 150 students, research scholars and teaching faculty attended the lectures. 15. Impact shown by your centre on the growth of biotechnology and allied areas. Ten PG students and Research scholars, who used the computational facility of BIF, have been selected and representing the university in Inter-University Research Festival “Awishkar”, at SNDT University, Mumbai. 16. Future activities To organize Training/Workshops for familiarizing the applications of Bioinformatics in Biology teaching and learning activities. To provide infrastructure facility to research students and graduate and postgraduate students of the university. Completion of databases. To establish linkages with BTISnet of DBT and make available the knowledge resources to the students, researchers and teaching faculties.

Additional Details: Name of the Coordinator: Dr. Prasad A. Wadegaonkar Postal Address: Coordinator, Bioinformatics Infrastructure Facility, Sant Gadge Baba Amravati University, Amravati 444602 Phone Number: 0721-2662207 ext 267 Mobile: 09422157263 Email: [email protected], [email protected] 412

413 Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow Coordinator: Dr. Sita Naik

1. Summary of the progress made by the centre from its inception. Since the project was initiated under the BTISnet program w.e.f. 22nd September 2006, a computer network has been set up consisting of servers and 14 machines. Various softwares have been procured and installed. The center (a) provides bioinformatics support facilities to the entire institute and neighboring institutions, (b) has designed an in-house database of research activities of SGPGI containing searchable lists of completed and ongoing intramural and extramural projects undertaken at SGPGI since 1988, (c) organized two training courses on bioinformatics and (d) begun two projects using bioinformatics tools. 2. Major research activities in Biotechnology and its related fields at your institution SGPGI is a premier medical teaching and research institution. Several departments, including immunology, genetics, neurology, pathology, microbiology, gastroenterology and urology have active research programs. 3. Area of Specialization of the centre Research and educational activities in of Biomedical information sciences 4. Major activities of the centre during the year 2007-08 The Centre organized the following courses during the year: i. Three week course in Bioinformatics from 8th -26th October, 2007. Objective of the course was to provide introduction and overview bioinformatics to the medicos. ii. Two-day training cum workshop titled “First course in Bioinformatics: Introduction, Principles & Applications” on 1st-2nd December 2007. The main objective of the course was to impart the introductory knowledge about principles underlying bioinformatics and practical application of bioinformatics tools and techniques for gene and protein analysis to the students, researchers and medical personnel. 5. Infrastructure facilities in the Bioinformatics Centre Computer & Communication facility Sl. No Equipments 1 CISCO 1700 Series Router 2 CISCO 2950 Series Switch 3 XEON 3.2 GHz Processor dual processor with 2GB RAM, 72X5 GB HDD 4 2Mbps Internet connectivity through VSNL Lease Line 5 Fourteen PCs: Intel Pentium IV with 1GB RAM, 80GB HDD 6 Hp LaserJet P3500dn Printer 7 HP Color LaserJet 3800 Printer 8 HP Scanjet 8290 digital flatbed scanner 9 Xerox Copier WC 420 CP 10 Sharp Digital DLP Multimedia Projector

Scientific Software packages Licensed Software OS and Packages

414 Sl No. Name 1 Redhat Linux Enterprise Edition 4 2 Microsoft Visual Studio Professional Edition 3 Microsoft ISA Server 4 MS Window 2003 Server Edition 5 MS SQL Server 2005 Standard Edition 6 MS Office 2007 Professional Plus 7 Semantic Antivirus Corporate Edition 8 Discovery Studio 1.6 9 GCG Package

Free Software OS and Packages Sl No. Name 1 Fedora Core 8 2 BIOLinux 4 Live DVD 3 DNA Linux 4 BioBREW 5 The Quantian Scientific Computing Environment 7.9

Free Bioinformatics Software Downloaded software from World Wide Web ftp sites under General Public License: BioEdit, spdbv, rasmol, Cn3D, Jemboss, Emboss, NCBI BLAST, Treeview, Phylip, MEGA, DAMBE, ClustalW, Chimera

6. Details about staff members working in the centre

Name Designation Specialization Period of Absorption work status Aditya N. Senior Bioinformatics June 2007Temporary Sarangi Research Officer Bhawna Rathi Research Bioinformatics October Temporary Officer 2006

7. Types of services provided The centre provides computational facilities, bibliographic searches, bioinformatics related services like primer design, analysis of DNA and protein Sequence, database development to researchers and medicos. More than 50 users from various department of SGPGIMS and near by universities in Lucknow has been using this facility. Centre is organizing short term training program in bioinformatics for students, researchers and medicos.

8. Educational activities with details of placement. The Institute considers the requests from universities and colleges for project work towards partial fulfillment of the respective postgraduate degrees. Currently one student from Integral University is undergoing dissertation work on “Insilico protein structure prediction and Bioinformatics strategies for disease gene identification”. 415 9. Collaborative works/ initiatives Efforts are on to carry out collaborative initiatives with medical universities at Lucknow and would like to join hands with other BTIS Centers. 10. Databases/ Software packages developed The Centre has designed in house database for highlighting the research achievements of SGPGI which contains searchable lists of completed and ongoing intramural and extramural projects undertaken by the faculty at SGPGI from 1988. Database also includes the lists of past and current PhD students enrolled at SGPGI under various departments. 11. Initiation of R&D activities in Bioinformatics: Current work is going on Insilico studies of Hepatitis E Virus using bioinformatics tools and techniques. Center is developing BiomedLinux Live DVD based on knoppix, which will contain the free pre installed bioinformatics and biomedical software packages for biomedical, molecular and evolutionary data analysis. The centre is also developing its local WWWBLAST Server. 12. Details of Training/ Workshop organized and total no. of user trained

Sn. Training Name Duration No of trainee 1 01 course in Bioinformatics 8 -26,October, 2007 22 2 First Course in Bioinformatics, 1-2,December, 16 Introduction, Principles and 2007 Applications 3 Second Course in Bioinformatics, 22-24 February, Introduction, Principles and 2008. Applications 4 Workshop titled ‘Computers and March 17-19, Informatics in Medicine’ 2008

13 Impact shown by your centre on the growth of biotechnology and allied areas. The Centre has designed in house database for highlighting the research achievements of SGPGI. The centre had organized 01 Credit Course in Bioinformatics [8 – 26 October 2007] and workshop cum training on “First Course in Bioinformatics: Introduction, Principles and Applications [1-2 December 2007]. In these two training programs 38 students, researchers and medicos were trained. 14 Future activities The centre plans to hold short term training programs and workshop for students, researchers and academicians on a regular basis. It also proposes to start diploma and certificate course in the field of Biomedical Informatics for which permission has been taken from the Institute’s Academic Board. A meeting of curriculum committee is planned in Feb 2008 and the courses are expected to start from the coming academic year. Centre will find linkages with different research organizations, universities to promote bioinformatics education and research. Centre will develop various software tools and databases related to medical sciences.

Additional Details: 416 Name of the Coordinator: Dr. Sita Naik Postal Address: Department of Immunology SGPGIMS, Raibareilly Road Lucknow-226014 Phone Number: +91 522 2668700, 2668800, 2668900 Email: [email protected] Website: http://biomedinfo.sgpgi.ac.in/

Name of Contact Person(s): Dr. Sita Naik Email: [email protected]

417 Shri Mata Vaishno Devi University (SMVDU), Katra, Jammu Coordinator : Prof. (Dr.) V. Verma

1. Summary of the progress made by the centre from its inception As it is a new centre after receiving the grant efforts have been made to procure the hard and softwares. In the meantime a room has been earmarked for housing the centre in the new Block A recently constructed in the university and furniture for the same has been ordered. The following equipments have also been ordered: • Servers – 2 Nos. • Work Stations – 4 Nos. • Computers – 10 Nos. In addition all the infra structural facilities required for the centre are already have been put in place/ are in the process of installation.

2. Major research activities in Biotechnology and its related fields at your institution School of Biotechnology at SMVDU is carrying out research in different fields and currently has running following research projects • Project on Bioprospecting of actinomycetes from selected niches of North Western Himalayas in J&K state. Funded by J&K state DST. PI Prof. V. Verma • Project on Exploitation of microbial biodiversity of North Western Himalayas for novel enzymes, bioactive molecules and biotransformation processes. Funded by DBT, New Delhi. PI Prof. V. Verma & Dr. Ahmed Kamal, IICT, Hyderabad • Project on Molecular and biochemical characterization of ACC gene in Jatropha curcas. Funded by DST, New Delhi. PI Dr. Dhiraj Vyas, lecturer. • Project on Strengthening of botanical garden at SMVDU. Funded by Ministry of Environment & Forests, New Delhi. PI Dr. PI Dr. Dhiraj Vyas, lecturer. • Project on Establishment of Herbal Garden-Trikuta Hills at SMVDU campus. Funded by National Medicinal Plants Board, Department of Health & Family Welfare, New Delhi. PI Dr. Sharda, lecturer 3. Area of Specialization of the centre The centre envisages to work on the following areas: • Identification of novel ORFs from North Western Himalayas; • Development of databases for the novel actinomycestes inhabiting North Western Himalayas; • Development of databases on Medicinal Plants of J&K state. 4. Major activities of the centre during the year 2007-08 418 Establishment of Bioinformatics Centre in the university. 5. Infrastructure facilities in the Bioinformatics Centre • Computer & Communication facility Ordered • Scientific Software packages Ordered • Databases & other information resources In process 6. Details about staff members working in the centre (Name of the staff, Designation, Specialization and period of working. Please indicate their absorption status) Presently no temporary staff is working in the centre 7. Types of services provided - NA 8. Educational activities with details of placement- First batch of B.Tech IBT is expected to graduate in 2009 9. Initiative to validate the outcome of bioinformatics resources - NA 10. Collaborative works/ initiatives Research collaborations have been initiated/already working with the following institutes: • IIT, Delhi; • IICT, Hyderabad; • IMTech, Chandigarh; • University of Jammu, Jammu; • University of Kashmir, Srinagar. 11. Databases/ Software packages developed - NA 12. Papers published or presented in the conferences with reference: Publications: 1. Sharada, M., Ahuja , A., Suri, K.A. Vij, S.P, Khajuria, R.K., Verma, V. and Kumar, A. (2007) Withanolide production by in vitro cultures of Withania somnifera (Linn) Dunal and its association with differentiation. Biologia Platarum 51(1): 161-164. 2. Kumar, J., Verma, V., Shahi, A.K., Qazi, G.N. and Balyan, H.S. (2007) Development of Simple Sequence Repeat Markers in Cymbopogon Species. Planta Medica 73(3): 262-266. 3. Soror, S. H., Verma, V., Rao, R., Rasool, S., koul, S., Qazi, G.N. and Cullum, J. (2007) A cold-active esterase of Streptomyces coelicolor A3(2): from genome sequence to enzyme activity. J Indus. Microbiol Biotechnol. On-line access no. DOI 10.1007/s10295-007-0224-6. 4. Verma, V., Smelcerovic, A., Zuehlke , S., Hussain, M.A., Ahmad S.M., Ziebach , T., Qazi, G. N. and Spiteller, M. (2008) Phenolic constituents and genetic profile of Hypericum perforatum L. from India. Biochemical Systematics and Ecology 38(3):201- 206

Presentations: 419 • V. Verma, Impact of Biotechnology Research on Biodiversity, Proceedings of the National conference on Hiamlayan Biodiversity- Concerns & Issues Oct 27-29, 2007 at BGSB University, Rajouri (J&K). • V. Verma, Biology of Cancer – an over view, Proceedings of the International Symposium on Genetic Instability and cancer, July 22-26, 2007 at University of Kashmir, Srinagar. • V. Verma, Need for molecular characterisation of the biocontrol species for IPR and patent purposes, Proceedings of the National Conference on Fungal Diversity: Impact & Exploration & 34th annual meeting of Mycological Society of India from Oct 5-6, 2007 at Thapar University, Thapar Technology Campus, Patiala-147004. • V. Verma, Impact of Biotechnology Research on Biodiversity, Proceedings of the National conference on Hiamlayan Biodiversity- Concerns & Issues Oct 27-29, 2007 at BGSB University, Rajouri (J&K). • V. Verma, The concept of gene manipulation called Directed Evolution, Proceedings of the National symposium on Biophysics: Biphysics in Medicine & Biology from Nov.15-17, 2007 at Punjab University, Chandigarh.

13. Initiation of R&D activities in Bioinformatics The following work has already been initiated: • Development of databases for the novel actinomycestes inhabiting North Western Himalayas; • Development of databases on Medicinal Plants of J&K state. • Course in Bioinformatics in B.Tech (IBT).

14. Details of Training/ Workshop organized and total no. of user trained - NA 15. Impact shown by your centre on the growth of biotechnology and allied areas. In this you may highlight the details like number of paper published/ number of papers published with the help of your centre, how your centre is promoting various activities of your organization and neighboring institutions, manpower trained, tools developed, patents & copyrights acquired and other services offered etc. • The BIF centre of the university will cater to the needs of Under/post graduate and research students of various disciplines of the university. • The centre is also actively collaborating with the institutes/universities in the region for research as well as joint collaborative studies. • The centre is also planning to organize a joint workshop in collaboration to Department of Biotechnology, University of Jammu, Jammu.

16. Future activities • Besides, research we propose to initiate Post Graduate Diploma in Bioinformatics in collaboration with leading national Biotechnology/Bioinformatics industry (s). • Establish a Chair in Bioinformatics at Professor/ Associate Professor level.

420 17. Additional Details: Name of the Coordinator: Prof. (Dr.) V. Verma Postal Address: Dean College of Sciences, Director School of Biotechnology, Shri Mata Vaishno Devi University (SMVDU), Katra

Fast track postal address: PRO Office of SMVDU,15-C (2nd Ext.) Gandhi Nagar, Opp. Bahu Plaza, Jammu 180003

Phone Number: (Direct) 01991 285691, (PABX) 01991 285524,285535, 285699 ext.2129 Mobile: 094191 31814, E mail: [email protected] , [email protected] Website: www.smvdu.ac.in

421 Sri Padmavati Mahila Visvavidyalayam, Tirupati Coordinator : Prof. M. N. Reddy

1. Summary of the progress made by the centre from its inception : This is only a Bioinformatics infrastructural Facility (BIF) Centre, which is still under the process of establishment. All the arrangements have been made for the procurement of necessary equipment, establishment of the Lab etc., and the facility will soon be ready in all respects.

2. Major research activities in Biotechnology and its related fields at your institution : The major areas of research activity in the Departments of Biotechnology and Applied Microbiology and Sericulture in the University include -Agricultural Biotechnology, Molecular Biology, Animal Biotechnology and Seribiotechnology

3. Area of Specialization of the centre : Not Applicable – as it is only a BIF Centre 4. Major activities of the centre during the year 2007-08 : The Facility is still in the process of establishment 5. Infrastructure facilities in the Bioinformatics Centre : Computer & Communication facility Scientific Software packages Databases & other information resources The BIF Centre is in process of establishment. Arrangements have been made to procure Computers and specific software soon.

6. Details about staff members working in the centre (Name of the staff, Designation, Specialization and period of working. Please indicate their absorption status) : Not applicable – as it is only a BIF Centre. The position of Research Associate sanctioned in the 2007-’08 budget, is to be filled up shortly. 7. Types of services provided : The facility is yet to be started to open for utility by the students of different Life Sciences Departments.

8. Educational activities with details of placement: Not allocable as it is only a BIF Centre 9. Initiative to validate the outcome of bioinformatics resources : Not applicable 10. Collaborative works/ initiatives : 422 To be initiated once the facility is established in all respects, 11.Databases/ Software packages developed : Not Applicable 12.Papers published or presented in the conferences with reference : Not Applicable 13. Initiation of R&D activities in Bioinformatics : Not Applicable 14. Details of Training/ Workshop organized and total no. of user trained : Not Applicable

15. Impact shown by your centre on the growth of biotechnology and allied areas. In this you may highlight the details like number of paper published/ number of papers published with the help of your centre, how your centre is promoting various activities of your organization and neighboring institutions, manpower trained, tools developed, patents & copyrights acquired and other services offered etc. : Not Applicable 16. Future activities: • To conduct Workshops/Training programs atleast twice in a year for the target groups of women students/researchers/scientists/Faculty in Biotechnology/Bioinformatics/Microbiology and other Life Sciences, to make them proficient and more competent for catching employment opportunities available / being generated with increasing industrialization of the Biotech field/Institutions as they started attracting experts from academia

• To provide effective training/awareness to the students of Life Sciences to gain knowledge in handling different tools/techniques used in Bioinformatics and their applications in Modern Biology, to develop professionalism in them , as there is lot of demand for women Bioinformatics professionals with Biotechnology/Microbiology by many upcoming/newly established gene hunting companies, larger pharmaceutical companies etc.

• To train the students to get to know the applications of Bioinformatics and use of computers and Data Banks in Modern Biology especially in the fields of Molecular Biology, Industrial Biotechnology, Agricultural Biotechnology, Animal Biotechnology, Mulberry Biotechnology etc.

• To make the students confident in gaining knowledge in tools/techniques in Bioinformatics underlying the strategies and scientific approaches essential for understanding biological problems and successful implementation of computer programs through guided practical training.

• Inviting experts in the field to deliver Lectures and conduct demonstrations on relevant topics, followed by hands-on sessions in computer lab

423 Additional Details : Name of the Coordinator : Prof M N Reddy Postal Address: Department of Microbiology, S P Mahila Visvavidyalayam, Tirupati-517 502, Andhra Pradesh Phone Number: 0877 6576759 Mobile: 09849085596 Email: [email protected] Name of Contact Person(s): Coordinator as above

424 Sri Venkateswara College, (University of Delhi) Coordinator : Dr. N. Latha

1. Summary of the progress made by the centre from its inception Bioinformatics Infrastructure Facility at Sri Venkateswara College Inaugurated on July 27, 2007 2. Major research activities in Biotechnology and its related fields at your institution. • PG Diploma in Biochemical Technology – funded by DBT • Research Projects under DRDO, DBT and UGC Grants 3. Area of Specialization of the centre ¾ Teaching & Training Activities ¾ Research Activities – Computer aided drug design 4. Major activities of the centre during the year 2007-08 ™ Teaching & Training Activities ƒ Add on Course in Bioinformatics : 4 months Short Term Course for graduates 25 final year students pursuing degree programs in Biochemistry, Botany, Zoology, Physics at Sri Venkateswara College were selected based on an aptitude test. This 4 month course covers lectures by experts working in the area of Computer Fundamentals, Genomics, Proteomics and In silico drug design. In addition, hands-on session exposes the students to various Bioinformatics tools & softwares available in the public domain. ƒ Short Term Training Programme in Bioinformatics: 6 months duration for post-graduates The following students are undergoing training program for 6 months in the Bioinformatics Facility at Sri Venkateswara College. Name of the Trainee Affiliated Institution Project 1. Nidhi Jatana Banasthali Vidyapith, Protein Structure Rajasthan Prediction 2. Indrakshi Bhan Amity University, Proteomic Analyses Noida ™ Workshops Organized : ƒ Bioinformatics Workshop for School Teachers – Jan 3-4, 2008 To promote teaching of biology through Bioinformatics, a 2-day Bioinformatics Workshop for School Teachers was organized at Bioinformatics Facility, Sri Venkateswara College. Around 20 participants from various recognized schools in Delhi & around attended the workshop wherein lectures as well as hands on training session was provided in the field of Genomics, Proteomics & In silico drug design. The workshop was 425 inaugurated by Dr. T. Madhan Mohan, Adviser, DBT and Prof. K. Muralidhar, Department of Zoology, University of Delhi.

5. Infrastructure facilities in the Bioinformatics Centre Computer & Communication facility The existing infrastructure includes the following hardwares/other Equipments.

S. No Items No. 1. Sun Workstations M2 18 2. Servers (1- High End Compute & 2 1- Web Server) 3. Laser Network Printer 1 4. Gigabit Switch for LAN 1 5. UPS ( 10KV) 1 6. Internet Connectivity ( MTNL Broadband) Unlimited

Scientific Software packages ¾ Schrodinger package for Protein modeling & Analysis ¾ BioBox from SUN that includes Glimmer, Artemmis, TCoffee,etc.

Databases & other information resources ¾ Bioinformatics Books – 20 6. Details about staff members working in the centre (Name of the staff, Designation, Specialization and period of working. Please indicate their absorption status)

Name Designation Date of Joining Salary Mr. Sarvesh Jangid Research Assistant 24 Sept, 2007 Rs.11000 + 30% HRA

7. Types of services provided: Training & Research Colloborations 8. Educational activities with details of placement: see section 4 9. Initiative to validate the outcome of bioinformatics resources 10. Collaborative works/ initiatives Project Colloborating Scientist Commencement Homology Modeling of proteins Prof.. Anil. K. Tyagi Dec 2007 derived from Mycobacterium Department of Biochemistry tuberculosis University of Delhi South Campus Bioinformatics Analyses of Dr. P. Hemalatha Reddy Nov 2007 Calmodulin –like protein from Reader, Dept. of Biochemistry Mycobacterium tuberculosis Sri Venkateswara College 426

11. Databases/ Software packages developed : NIL 12. Papers published or presented in the conferences with reference : NIL 13. Initiation of R&D activities in Bioinformatics : Submitted a project to DBT as a part of COE proposal 14. Details of Training/ Workshop organized and total no. of user trained Bioinformatics Workshop for School Teachers – Jan 3-4, 2008 Number of users-20 15. Impact shown by your centre on the growth of biotechnology and allied areas. 16. Future activities: Training & Research Name of the Coordinator: Dr. N. Latha Postal Address: Reader, Department of Biochemistry, Sri Venkateswara College Phone Number: 011-24113129 Mobile: 9891900122 Email: [email protected] Website: www.svcollege.net

Name of Contact Person(s): Dr. A. Sankara Reddy, Principal, Sri Venkateswara College Email: [email protected]

427 Sri Venkateshwara Institute of Medical Sciences, Tirupati Coordinator: Dr. A. Umamaheswari

1. Summary of the progress made by the centre from its inception:

Bioinformatics infrastructure facility at SVIMS was formally inaugurated on 10th March, 2007. On this occasion, the BIF centre organized a guest lecture on “Machine learning methods and their Applications in Biology” and Prof.S. Ramakumar, Chairman, Bioinformatics Centre, Indian Institute of Science, Bangalore acted as a key resource person. The centre was made open to the students, faculty and researchers of SVIMS, Tirupati to retrieve the literature and utilize the infrastructure available at BIF, SVIMS. The infrastructure facility is being utilized by the departments of Bioinformatics, Biotechnology, Anatomy, Physiology and Nursing. In collaboration with BIF, SVIMS, the department of Biotechology, SVIMS conducted a workshop on “Molecular Biology tools” for 29 participants from different states and institutions of Tirupati, in which one full day was earmarked for bioinformatics tools dealing with genome sequence analysis. Nine students of the Department of Bioinformatics, SVIMS were utilized the BIF infrastructure facility in pursuing their project works dealing with identification of drug targets in pathogens, simple sequence repeats, homology modeling and docking of proteins.

2. Major research activities in Biotechnology and its related fields at your institution: Stem cell technology and drug target identification.

3. Area of Specialization of the centre: Molecular modeling, Drug designing and sequence analysis.

4. Major activities of the centre during the year 2007-08:

• The Centre is helping M.Sc. and Ph.D. students of Bioinformatics in teaching, research projects and finalizing their dissertations/thesis. • Organized a guest lecture • Organized a workshop • Providing internet facility to the staff, research scholars and P.G students of the institute.

5. Infrastructure facilities in the Bioinformatics Centre: a. Computer & Communication facility : i. SERVER (High end) for Database/Application Server- 1 No. ii. 2. SERVER (Medium) for Porxy & File Server - 1 No. iii. 36 GB Server iv. DESKTOP MACHINES -22 v. HP LASER JET 2420 PCL6 PRINTER - 1 No. vi. DESKJET PRINTER - 1 No. vii. SCANNER – 2 No viii. PHOTO COPIER – 1 No. ix. 10 KVA UPS x. Wipro LQ DX Gold Printer 428 xi. Canon Printer xii. Local Network Connection xiii. 13.BSNL Dataone Broad band internet

b. Scientific Software packages:

c. Databases & other information resources: Nil

6. Details about staff members working in the centre (Name of the staff, Designation, Specialization and period of working. Please indicate their absorption status)

Sl. NO. NAME OF THE STAFF DESIGNATION

1. Dr. A. Umamaheswari Coordinator of BIF 2. Dr. S.A.A. Latheef Information Officer 3. K. Bhavana System Analyst

7. Types of services provided: As partial fulfillment of graduation requirements, ten students of M.Sc. bioinformatics carried out their dissertation work utilizing Bioinformatics Infrastructure Facility. In addition, ten more students of M.Sc. Biotechnology have utilized the facilities of the centre in collecting literature and utilizing Bioinformatics tools. Furthermore, Ph.D. students of bioinformatics, biotechnology, microbiology, biochemistry, cardiology, medicine, neurology, plastic surgery, CT surgery and institute staff are utilizing these facilities for research work.

8. Educational activities: Bioinformatics Centre in the Department of Bioinformatics, SVIMS University, is mainly involved in educational activities. The department is offering M.Sc. and Ph.D. courses in Bioinformatics.

9. Initiative to validate the outcome of bioinformatics resources: With the available infrastructure we identified drug targets in pathogens causing infections ranging from tuberculosis to endocarditics. We are modeling and analysing drug target proteins by utilizing academic softwares like modeler 9v2 and with the available Bioinformatics Infrastructure Facility.

10. Collaborative works/ initiatives: Nil 11. Databases/ Software packages developed: Nil 12. Papers published or presented in the conferences with reference: Nil

429 13. Initiation of R&D activities in Bioinformatics: Reserch activities carried out by the centre are as follows: a. Homology modeling of cobrotoxin and human G-protein activated inwardly rectifying potassium channel-4 and molecular docking with blocker 3,4 – pyridine diamine. b. Substractive genomic approach for the identification of novel drug targets in human pathogen Leptospira interrogans copenhagani str Ficrouz L 1-130. c. In silico identification of potential drug targets in human pathogen Mycobacterium tuberculosis H37Rv. d. Identification, Abundence, Distribution and Analysis of simple sequence repeats (microsatellites) in the genomes of Leptospira. e. A comparative study of selected scorpion toxins: binding mode of toxins with modeled receptor and docking of scorpion toxins with L- carnitine”. f. Analysis of Genomes of Brucella sps Brucella melitensis and Brucella suis on simple identification abundance and distribution. g. Studies on putative in silico drug targets and homology modeling in organisms (Legionella pneumophila and Tropheryma whippelii ) causing endocarditis. h. Identification of drug target proteins and homology modeling in organisms (Coxiella burnetti and Brucella abortus ) causing infective endocarditis. i. study on genomes of organisms ( Neisseria gonorrhoeae and Brucella melitensis ) causing infective endocarditis: identification of drug targets and homology modeling.

14. Details of Training/ Workshop organized and total no. of user trained The bioinformatics Centre has organized a guest lecture on “Machine learning methods and their applications in Biology” by Prof. S. Ramakumar, Chairman of Bioinformatics Centre, IISc, Bangalore. The department of Bioinformatics collaborated with the department of Biotechnology, SVIMS in conducting a workshop on “Molecular Biology tools” for 29 participants from different states and adjoining regions and Ph.D. students of our institute.

15. Impact shown by your centre on the growth of biotechnology and allied areas. In this you may highlight the details like number of paper published/ number of papers published with the help of your centre, how your centre is promoting various activities of your organization and neighboring institutions, manpower trained, tools developed, patents & copyrights acquired and other services offered etc. The facility is catering to the needs of staff of the centre assisting in theoretical and practical training provided to the students of M.Sc. Bioinformatics, M.Sc. Biotechnology and B.Sc. Nursing. The department of Bioinformatics utilized the BIF lab in offering the following courses to M.Sc. Bioinformatics students: a) Biostatistics b) Computer Fundamentals c) C++ language and its applications d) OOPS Programming and databases 430 e) Functional Proteomics and Genomics f) Perl Programming g) Molecular Modeling and Drug Designing

Apart from this the lab was used by students of M.Sc. Biotechnology by offering two subjects. a) Biostatistics b) Fundamentals of Computers and Bioinformatics The lab was also used to provide hands on training to the students of B.Sc. Nursing who have registered the following courses: a) Computer Fundamentals b) Fundamentals of Computers and Information Technology

16. Future activities 1. To organize workshops, guest lecturers, training programs in Bioinformatics. 2. Enhance the research activities and subscribe to online Journals and Softwares. 3. Tata Consultancy Services (TCS) has launched Tata Bio-Suite, a portable, versatile software package for life sciences and drug discovery. This Bioinformatics software is aimed at facilitating life science research through information technology. As this software runs on LINUX we have recently installed a new Pentium with LINUX on it. We are in the final stages of procuring this software, which will provide higher capability for computations in the areas of sequence analysis and drug designing.

Name of the Coordinator: Dr. A. Umamaheswari

Postal Address: Dr. A. Umamaheswari Co-ordinator of BIF Department of Bioinformatics SVIMS University Alipiri Road Tirupati – 517 507

Phone Number: 0877 2287727 Fax.No: 0877 2286803 Email: [email protected] Website:http://svimstpt.ap.nic.in

Name of Contact Person: Dr. A. Umamaheswari Email: [email protected]

431 Tezpur University, Tezpur Coordinator: Dr. B. K. Konwar

1. Summary of the progress made by the centre from its inception The BIF was established in 2007 with the objective of assisting the M Sc Molecular Biology and Biotechnology students. The allotted 10 computers and the photocopier were purchased and installed. Students are using the computers for the course “application of computers in Biotechnology”.

2. Major research activities in Biotechnology and its related fields at your institution Plant-based medicinal and aromatic compounds, petroleum biotechnology, yeast genomics, bacterial enzymes for industrial application, malaria immunogenetics, oncogenomics, enzymology of snake venom and computational genomics.

3. Area of Specialization of the centre Computational genomics and database on plant and microbial diversity 4. Major activities of the centre during the year 2007-08 Establishment of the Centre with procurement and installation of computers

5. Infrastructure facilities in the Bioinformatics Centre A. Computer & Communication facility: 10 computers purchased and installed. Server installation will take some more time due to some administrative and electrical problems. B. Scientific Software packages: Procurement of DNA star etc. C. Databases & other information resources: Medicinal plant and Petroleum microbe database

6. Details about staff members working in the centre (Name of the staff, Designation, Specialization and period of working. Please indicate their absorption status)

Mr. K. Hazarika, Technical Officer, TU – additional responsibility (part-time) Mr. Dhiraj Sarmah, Computer Engineer, TU – additional responsibility (part- time)

7. Types of services provided: as teaching aid to M Sc students and research use for Ph D scholars.

8. Educational activities with details of placement: The first batch of 18 Biotechnology students attending the course ‘Use of computers in Biotechnology” in the BIF passed in the year, 3 of them secured DBT-JRF; 13 were selected for Ph D in different national institutes and Universities; 2 obtained industrial placement. 9. Initiative to validate the outcome of bioinformatics resources 432 10. Collaborative works/ initiatives: with the Department Computer Science and Engineering 11. Databases/ Software packages developed: Not yet, but proposed to develop in collaboration with the Dept. of Computer Science. 12. Papers published or presented in the conferences with reference Das, D., Satapathy, Occurrence of all nucleotide Curr Sci 2006, 90: S. S., Buragohain, combinations at the third and the first 22 – 24. A. K. and Ray, S. K. positions of two adjacent codons in open reading frames of bacteria Verma, S. K., Das, Compositional Symmetry of DNA Curr Sci. 2005. D., Satapathy, S S , Duplex in Bacterial Genomes. 89:374- Buragohain, A. K. & 384 Ray, S.K. Das, D., Verma, S. An Altered G + C% Region Within Curr Sci 2005, 88: K. & Ray, S. K. Potential Hemagglutinin ORFs of 786 – Ralstonia solanacearum. 792. Ray, S. K. Riboswitch: A New Mechanism of Curr Sci. 2004, 87: Gene Regulation in Bacteria 1168- 1169.

13. Initiation of R&D activities in Bioinformatics: Computational genomics 14. Details of Training/ Workshop organized and total no. of user trained: to be taken up in 2008.

15. Impact shown by your centre on the growth of biotechnology and allied areas. In this you may highlight the details like number of paper published/ number of papers published with the help of your centre, how your centre is promoting various activities of your organization and neighboring institutions, manpower trained, tools developed, patents & copyrights acquired and other services offered etc. Research on computational genomics has been continued with publication of 4 papers and presentation of 1 paper in a Conference at CCMB. 16. Future activities: To start M Sc in Bioinformatics after the sanction of the 11th 5-year plan, Manpower training Additional Details: Name of the Coordinator: Dr. B. K. Konwar, Professor and Head Postal Address: Dept. of Molecular Biology & Biotechnology, Napaam, Tezpur, Sonitur - 784028 433 Phone Number:03712-267172 Mobile:9954449468 Email: [email protected] Website: www.tezu.ernet.in Name of Contact Person: Mr Kalyan Hazarika Email: [email protected]

434 University of Allahabad, Allahabad Coordinator : Prof. Dwijendra Gupta

1. Summary of the Progress made by the Center from its inception M.Sc. Program in Bioinformatics started here with our own resources in 2002 is presently running in its 6th Batch. Besides, Bioinformatics is being taught in B.Sc.(Applied Science).Three laboratories have since been added. One Molecular biology Lab and 2 Advanced level Bioinformatics Laboratories for M.Sc.(Bioinformatics) and B.Sc. Applied Science students. Besides, for experimental laboratories in Biochemistry, Molecular Biology and Biotech-nology, the existing facilities in the Departments of Biochemistry and Biotechnology are being used. Yet another Computer Lab for M.Sc. Bioinformatics students has 30 advanced desktop computers and with internet service. We have procured the hardware( one High-end Database /Application Server, one Medium –end Proxy /File Server, 10 Desktop P-IV Systems as provided in the Sanction Order of DBT. This Facility is being set up in the space provided in Institute of Interdisciplinary Studies situated in the Faculty of Science. The softwares suggested by the DBT have also been procured. 2. Major Research activities in Biotechnology and its related fields at University of Allahabad Fields of Research in Biotechnology: There are four independent research groups working in Biotechnology and related areas, i.e. Nanobiotechnology, Nanophosphors, GPI anchors etc (Prof. D.K.gupta, Dr.Shanthy Sundaram,Dr Avinash Pandey and Dr. Anjana Pandey . These projects have become operational as regards the procurement of the equipment is concerned.

3. Area of Specialization of the center Fields of Research in Bioinformatics & Computational Biology: Molecular Modeling, Structural Bioinformatics, Metabolic Network Reconstruction, Molecular Docking, Promoters of Cold-Stress Genes in insects

4. Major activities of the Center during 2006-07: An International Collaboration is already in force between University of Allahabad ( Prof. D.K. Gupta and Prof. A.K.Gupta) and University of Cagliari ( Prof. Paul la Colla).

5. Infrastructure facilities in the Bioinformatics Center: A. Computer and Communication facility We are also in the process of setting up a 16-node Red-Hat Linux Cluster (with Beowulf configuration) for the Bioinformatics Computing lab. The whole system will be used as the very high-end computing system for bio-molecular dynamics, genomics and computer-aided structure prediction and computer-aided drug design.

435 B.Scientific and Software packages: GenoCluster version 1.0 procured from Jalaja Technologies, Bangalore for functional Genomics and Proteomics . Red Hat and MS ISA 06 are the other softwares we have procured. C. Databases and other information resources: We are developing our database of activities of the Center of Bioinformatics that includes the projects carried out by the students as part of requirement of curriculum, research papers published by the Biotechnology and BioinformaticsCenters as well as any softwares that we may develop in the meanwhile.

6. Details about staff members working in the Center Presently, we have only one person temporarily employed as Office Assistant on fixed emoluments( Rs 5000 per mensem). UGC has given 8 faculty positions (Professor 1, Readers 2, and Lecturers 5) which remain to be filled. Presently, the core teaching faculty comprises of faculty drawn from different departments vide infra: CORE TEACHING FACULTY OF BIOINFORMATICS 1. Professor Ashok K.Gupta (specialty:Macromolecular Structure, DNA-Protein interactions, Computational Biology, Evolutionary Computing and Bioinformatics) 2. Professor Dwijendra K.Gupta, ( Recombinant DNA, Membrane Molecular Biology, Cell Biology, Immunology, Biochemistry and Genomic DNA and cDNA cloning techniques. Besides, hands-on experience in the area of Genomics and Proteomics and Nano- biotechnology). 3. Dr.Shanthy Sundaram, (Immunobiology, protein structure-function and Genomics and Proteomics 4. Professor Anoop Chaturvedi ( Econometrics, Time series, Life Testing and Reliability, and Liner Models). 5. Professor P.N.Pandey ( Differential Geometry, Biomathematical Modeling. 8 . Dr.K.N.Uttam (specialty is Diatomic Molecular Spectroscopy).

7. Types of Service provided: None yet 8. Future activities: 1. We are developing our website 2. We will also seek link with worldwide institutions that store primary and secondary biological databases, like, Incyte and UniGene, SWISS-PROT, PDB, NDB, GENES and DIPand BIND etc. Among these are National Center for Biotechnology Information (USA), Universities of Kyoto and Tokyo, European Bioinformatics Institute etc. The inter-action may include summer training of our students and researchers in these international laboratories in different areas of Genomics and Proteomics, Transcriptomics and Metabolomics.

9. Educational activities with details of placement An International Collaboration is already in force between University of Allahabad ( Prof. D.K. Gupta and Prof. A.K.Gupta) and University of Cagliari ( Prof. Paul la Colla). A number of passed out students are working towards their doctoral degrees on prestious Italian Govt fellowships in Universities of Cagliari,and Turino( Italy) ,in Brno (Czech Republic) and University of South Bohemia (Czech Republic) and a Swiss University.

10.Initiative to validate the outcome of bioinformatics resources 11.Collaborative works/ initiatives 12.Databases/ Software packages developed -- None 436 13. Papers published or presented in the conferences with reference 1. In silico Determination of potential drug target for curing meningococcal disease” ESFConference on Biomedicine: International Conference on “Synthetic Biology-Design, Programming, and optimization of Biological Systems” Sant Feliu de Guixols (Spain) Nov 23-28, 2007.

14. Initiation of R&D activities in Bioinformatics 15. Details of Training/ Workshop organized and total no. of user trained As the facility is yet to become operational, the Workshop proposed to be organized here in September 2007 has been postponed to sometime in March 2008.

16 Impact shown by your centre on the growth of biotechnology and allied areas. M.Sc. Students from different Universities outside Uttar Pradesh are training in this Department for their Major projects. The Bioinformatics Infrastructure Facility has not been operational as there has been inordinate delay in processing of paperwork for purchase of computer items at various university offices. Finally, the process for purchase and set up of the hardware( one High-end Database /Application Server, one Medium –end Proxy / File Server, 10 Desktop P-IV Systems and softwares as provided in the Sanction Order of DBT, has been completed. Also, the site where the Facility is to be operational is under preparation and could not be completed for want of funds.

17. Future activities As the facility is yet to become operational, the Workshop proposed to be organized here in September 2007 has been postponed to sometime in March 2008. Some of the financial requirements based on Budget provision are appended to this Progress Report.

Additional details :M.Sc. Bioinformatics program has a novel feature amongst all the teaching programs run at this University, i.e. it is credit-based. The courses are divided into level 0, level 1, level 2, and level courses. Each course has an appropriate minimum requirement. There is a minimum number of credits(12) that each student has to complete in each semester

Name of Coordinator: Professor Dwijendra Gupta Postal Address: Prof. Dwijendra Gupta, Coordinator, Center of Bioinformatics Institute of Interdisciplinary Studies, Nehru Science Center & Head, Department of Biochemistry, Faculty of Science University of Allahabad, Allahabad 211002 (U.P.) Phone Number: 0532-2461861(o), 09335150718(Cell), Fax # 0532-2545733 Email: [email protected] [email protected] Website: www.alldunivpio.org www.allduniv.edu

437 University of Bangalore, Bangalore Coordinator : : Prof. Geetha Bali

1. Summary of the progress made by the centre from its inception An independent laboratory has been earmarked. The laboratory has been equipped with computer tables and chairs. The room has been airconditioned. The sanctioned number of desktops with TFT monitors, 2 servers, Laser Jet and Ink jet printers, scanner and some software has been purchased. The computers have been networked. Sanction for the purchase of UPS (5 KVA 2 nos.) has been granted by the university and the same is being installed. Permission is being sought for installation of the UPS and necessary wiring. Internet connection has been established. The Advisory committee has been constituted. A meting of the advisory committee is being convened to evaluate the progress and discuss the Bioinformatics software to be purchased.

2. Major research activities in Biotechnology and its related fields at your institution a. Drought resistance in peanut plants b. Anti cancer properties of Embelin and Curcumin c. Bioactive peptides in Helicoverpa armigera and their potential as biopesticides d. Bioremediation of water contaminated with electroplating industrial effluents e. Use of Nanoparticles for diagnostics f. Developing subunit vaccine for Blue tongue virus

3. Area of Specialization of the centre : Nanobiotechnology/Plant Biotechnology/ Animal Biotechnology/Environmental Biotechnology/ Medicinal Plants

4. Major activities of the centre during the year 2007-08 In the process of being established 5. Infrastructure facilities in the Bioinformatics Centre Computer & Communication facility HP Pentium IV Server: HPML 110G3 (Sl. No.5) HP Pentium IV Server: HPML 350 G4/G5 Processor Intel Xeon DP 3.2 GHz, 800 MHz FSB (Sl. No.38) Hard Disk Drives LJ 2420 DN Laser Jet Printer Monochrome Resolution 1200 x 1200 dpi, paper size A4, memory 32MB printing speed 24 PPm, 1 parallel port with inbuilt duplex with network card 10/100 (Sl. No.143) Desk Jet Printer 2360: Inkjet Printer Resolution 1200 x 600 dpi, paper size A4, Printing speed 17 PPM B/W and 9 PPM Colour, 1 USB Scan Jet 5590 : Scanner Flat Bed A4 Size with USB Port with CD Technology: Scanner Flat Bed Tupe, A2 Size, Res. 600 x 600 dpi, preview/scan speed 7 sec, colour depth 48 bit USB port with inbluilt ADF (50 page) (Sl. No.172) 512 MB RAM for PIV Computers (Sl. No.47); TFT Monitors* (10 Desktops + 2 servers) Scientific Software packages

438 Windows 2003 Server Software (5 users) (Item No.87) Additional CAL License (15 users) Red Hat Linux Standrad (Sl. No.105) Microsoft SQL Server Standard (Sl. No.110) Additional CAL License (15 users) Anti Virus For Server (Itemm No.91) Microsoft ISA 2006 software Microsoft Visual Studio 2005 Professional With Net (5 user) Additional CAL License (15 user) Microsoft Office 2003: Professional MOLP with Media & Documentation Others are being purchased 6. Databases & other information resources 7. Details about staff members working in the centre (Name of the staff, Designation, Specialization and period of working. Please indicate their absorption status) University has been requested to appoint a full time staff specialized in Bioinformatics.

8. Types of services provided Will be provided once established completely. 9. Educational activities with details of placement Bioinformatics is being taught as one complete paper in M.Sc. courses 10. Initiative to validate the outcome of bioinformatics resources Training programmes will be organized as basic level for UG and PG students and advanced training for doctoral students to undertake research in Bioinformatics. Implementation of Bioinformatics projects and employment of bioinformatics in biotechnology research will be a good indicator. Biotechnology research will be initiated.

11. Collaborative works/ initiatives Discussions were held at Bangalore University and at the Department of Computer Science and systems for initiating collaborative programmes Engineering, Andhra University.

12. Databases/ Software packages developed : Not yet 13. Papers published or presented in the conferences with reference 1. Atmaram, T.N. Geetha Bali & K.M. Devaiah, Integration and expression of Bluetongue VP2 gene in somatic embryos of peanut through particle bombardment method Vaccine.(Elsevier)24, PP2994-3000, 2006

2. Atmaram, T.N.& Geetha Bali Recombinant expression of partial bluetongue VP2 protein in E.coli, Virus Genes 35:265-271(2007)

3 S. Dwarakanath, J.G.Brunoulatha, T.N.Atmaram & Geetha Bali, Ab-QD conjugates exhibit enhanced antibacterial action vs. unconjugated Quantum Dots, Folia Microbiol 52(1) 01-04, 2007

439 4. K.M. Devaiah, Geetha Bali & T.N. Atmaram, Identification of two new genes from drought tolerant peanut variety that is up regulated in response to drought, plant growth regulation 52:249-258(2007)

14. Initiation of R&D activities in Bioinformatics Bioinformatics is being employed for current ongoing research on peanut plants etc. More programmes are in the process of implementation

15. Details of Training/ Workshop organized and total no. of user trained : Not Yet 16. Impact shown by your centre on the growth of biotechnology and allied areas. In this you may highlight the details like number of paper published/ number of papers published with the help of your centre, how your centre is promoting various activities of your organization and neighboring institutions, manpower trained, tools developed, patents & copyrights acquired and other services offered etc. Intensive efforts will be made once the center is fully established.

17. Future activities: Organizing training programmes, Implementing R&D in Bioinformatics

Additional Details: Name of the Coordinator: Prof. Geetha Bali Postal Address: Department of Microbiology, Bangalore University, Bangalore 56056 Phone Number:080 - 22961462 Mobile: 9845242396 Email: [email protected] Name of Contact Person(s): Prof. S.K. Sarangi Email: Phone No. 080-22961461 [email protected]

440 University of Calicut, Kerala Coordinator: Dr. M. V. Joseph

1. Summary of the progress made by the center from its inception The Department of Biotechnology, University of Calicut has established the Bioinformatics Facility with the financial support from DBT, Government of India in the year 2006-07.

2. Major research activities in Biotechnology and its related fields at your institution A separate Department of Biotechnology has been established in 1995 with the financial support from DBT, Government of India to start Postgraduate programme in Biotechnology having Bioinformatics in the Course curriculum. The department is activity engaged in research in the area of plant Biotechnology, Immunology, Cell and Molecular Biology/recombinant DNA technology.

3. Major activities of the centre during the year 2007– 08 The BIF centre is being fully utilized by the faculty and research scholars for their research activities. As a part of their research activities a few cloned sequences have been deposited in the GenBank for which the accession numbers have been obtained.

4. Infrastructure facilities in the Bioinformatics center

a. Computer and Communication facility The department has 23 computers having 24 hours broadband internet facility with LAN and UGC infonet facility.

b. Scientific software packages Vector design (SimVector), primer premier, and free down loadable software packages are available. A few more software packages are in the process of procurement.

5. Details about Staff members working in the centre a. Dr. M. V. Joseph Microbiology & Immunology 1996 onwards Professor Secondary metabolites Head & Co-ordinator b. Dr. P.R. Manishkumar Cell and Molecular Sr. Lecturer Biology & recombinant 1996 onwards DNA technology c. Mr. C. Gopinathan Bioprocess technology 1996 onwards Sr. Lecturer d. Dr. S. Pyroja Molecular Neurobiology 2002 (on Leave)

6. Details of Training/Workshop organized and total number of user trained The BIF at Calicut University has conducted three days workshop on Application of Bioinformatics tools in biological research for the faculty 441 members and research scholars. A total number of 25 participants have been given training in this area.

7. Impact shown by your Centre on the growth of biotechnology and allied areas Four number of clone sequences have been deposited in the GenBank for which accession numbers have been obtained. Authors Title of the Article Journal Year Martin K P and Joseph Trichopus zeylanicus subsp. travancoricus ribosomal GenBank 2007 Madassery protein L16 (rpl16) mRNA, chloroplast EU057718 gi|155965995|gb|EU057718.1|[155965995] Martin K P, Gupta S, Ophiorrhiza prostrata tryptophan decarboxylase (tdc) GenBank 2007 Zhang C-L, Slater A gene gi|155965997|gb|EU057719.1|[155965997] EU057719 and Joseph Madassery Martin K P and Joseph Ophiorrhiza prostrata strain albino tryptophan GenBank 2007 Madassery decarboxylase (tdc) gene, EU057720 gi|155965999|gb|EU057720.1|[155965999] Kumar M P R, Manish Physarum polycephalum sequence new GenBank 2008 JPR, Rabindran R M EU371923

8. Future activities The department would like to conduct training programme in Bioinformatics for the teachers, post graduate and research students in Biological Sciences. We would like to databases of some important medicinal plants and microorganisms.

Additional details:

Name of the coordinator: Dr. M. V. Joseph Professor Department of Biotechnology University of Calicut P.O., 673 635 Kerala State Telephone No. 0494 -2401972: Fax: 0494 -2400269, 0494 -2400361 Email: [email protected] [email protected]

442 University of Hyderabad, Hyderabad Coordinator : Prof. Anand K. Kondapi

1. Summary of the progress made by the centre from its inception The BIF has been set-up in November 2007. The first activity of the BIF was in collaboration with CR Rao Advanced Institute of Mathematics, Statistics and Computer science, in conducting an “Instructional Workshop in Bioinformatics and Drug discovery” from Dec 16-19 2007. During the four days, two workshops are held one on “Statistical methods in Bioinformatics” and second one was on “Drug Discovery”. The workshop was attracted by large number of young talents throughout India and the lectures were delivered by Eminent scientists from India and abroad including Prof. C R Rao himself. The workshop was inaugurated by Dr. T. Ramasami, Secretary, DST and Dr. T. Madan Mohan, Advisor DBT has addressed in Valedictory function. The topics discussed in the workshop were related to use of various statistical methods and packages such as R-Package, SAS Genomics in analysis of data collected from bioinformatics, genomics and proteomics experiments. Drug discovery workshop covered the topics on quantum mechanics, classical mechanics. molecular mechanics, semiemprical methods, molecular dynamics, homology modeling, threading, Molecular docking and Computer aided drug design. The workshop followed with an International conference on Bioinformatics and Drug discovery, which was inaugurated by Smt. D. Puradereswari, Honorable Union HRD Minister of State. The conference has covered various aspects of system biology, drug discovery including metabolomics, genomics, proteomics, drug design, Clinical and translational research and critical issue of clinical trails etc. It was attended by participants from academics and Industries. The scientists actively working in academia and industry from India and abroad have participated in the conference. In addition, the PhD students and M.Tech students have registered and actively using the facility for research and teaching.

2. Major research activities in Biotechnology and its related fields at your institution

3. Area of Specialization of the centre Systems Biology and Drug Discovery

4. Major activities of the centre during the year 2007-08 Instructional workshop in Bioinformatics and Drug discovery (16-19 Dec, 2007) International Conference on Bioinformatics and Drug Discovery(19-22 Dec, 2007)

5. Infrastructure facilities in the Bioinformatics Centre Computer & Communication facility 2 HP servers, 10 HP Desktops, 2 printers & FAX with LAN network Scientific Software packages 443 SYBYL with QSAR from Tripos (3 Licenses), Biosuite from TCS (1 License) GOLD (1 License) from CCDC Ltd. (Under University Funds) Public domain software Open Eye, R package, Autodock Databases & other information resources: Public domain databases.

6. Details about staff members working in the centre (Name of the staff, Designation, Specialization and period of working. Please indicate their absorption status) Name Designation Specialization Period of working Anand K. Kondapi Professor Molecular therapeutics Since June 1993 K. Ramesh Naik Tech. Assistant System Administration Adhoc from April, 2007

7. Types of services provided (1) Modeling and drug design (2) Statistical analysis

8. Educational activities with details of placement : M.Tech and PhD programs

9. Initiative to validate the outcome of bioinformatics resources Through Short-term projects to the students of Bioinformatics and computer sciences from outside University.

10. Collaborative works/ initiatives: A proposal for conducting periodical training program in collaboration with CR Rao Advanced Institute for Mathematics, Statistics and Computer sciences, being proposed to the DBT.

11. Databases/ Software packages developed: To be taken up 12. Papers published or presented in the conferences with reference: Work just started.

13. Initiation of R&D activities in Bioinformatics: In house database on plant system is being created.

14. Details of Training/ Workshop organized and total no. of user trained Instructional workshop in Bioinformatics and Drug discovery (16-19 Dec, 2007) 95 students trained

15. Impact shown by your centre on the growth of biotechnology and allied areas. In this you may highlight the details like number of paper published/ number of papers published with the help of your centre, how your centre is promoting various activities of your organization and neighboring institutions, manpower trained, tools developed, patents & copyrights acquired and other services offered etc.

The facility is just started for the use of the PhD students and M.Tech. students. We are in process of using the facility for research and Teaching in Drug Discovery and Systems Biology. The publications, dissertations and meeting presentations will be reported in Coming year. We are also in the process of developing a database on plant systems to cater the community.

444 16. Future activities: 5. Training programs in Drug Discovery, Systems Biology and Statistical methods in Proteomics and genomics will be periodically conducted in every year. 6. Databases on plant systems being created

Additional Details: Name of the Coordinator: Prof. Anand K. Kondapi Postal Address: Department of Biotechnology, School of Life Sciences, University of Hyderabad, Hyderabad 500046 Phone Number:040-23134571; Mobile:9246152654 Email: [email protected] Website: www.uohyd.ernet.in Name of Contact Person(s): Prof. Anand K. Kondapi Email: [email protected]

445 University of Jammu, Jammu Coordinator : Prof. M. K. Dhar

1. Summary of the progress made by the centre from its inception:

The BIF at University of Jammu, was set up in January 2007 as the Bioinformatics Infrastructure Facility (Training Code: JUBIF-01) under the Biotechnology Information System Network (BTISnet) programme of the Department of Biotechnology, Government of India. During the first four months, we set up the Bioinformatics lab and made it functional for the use of students, research scholars, faculty and research scientists. During the last six months, the Coordinator delivered lectures in various departments of the University and also the affiliated colleges. The Centre organized demonstrations, hands on training sessions and awareness programmes on applications of Bioinformatics in solving the biological problems. Bioinformatics is one of the courses in the M. Sc programmes in Biotechnology, Biochemistry and Microbiology running in the University of Jammu since last couple of years. The Bioinformatics centre extended full support in conducting various hands on sessions and was involved in teaching a full fledged course in these programmes. The Bioinformatics Centre offered the dedicated internet facility and training to the students, research scholars for using the online and offline softwares, tools to assist in their research programmes.

2. Major research activities in Biotechnology and its related fields:

The centre is focusing mainly on In silico analysis using Bioinformatics softwares. The centre promotes Bioinformatics awareness. Research projects and interdisciplinary research in collaboration with wet lab Biotechnology research programmes are being carried out.

3. Area of specialization of the centre:

The main area of specialization is Genome and Proteome Analysis.

4. Major activities of the centre during the year 2007:

During 2007, the Coordinator delivered lectures to the College and University teachers during the inter-disciplinary refresher courses held in the Departments of Physics, Computer Sciences and Information Technology and Environmental Sciences, of the University of Jammu and also the affiliated college namely Government Degree College for Women, Udhampur. The Centre organized short training sessions and awareness programmes on applications of Bioinformatics in solving the biological problems. The Bioinformatics centre extended full support in conducting various hands on sessions and was involved in teaching full fledged course on Bioinformatics in M. Sc Biotechnology, M. Sc Biochemistry and M. Sc Microbiology programmes of the University. The Bioinformatics Centre offered the

446 dedicated internet facility and training to the students, research scholars for using the online and offline softwares, tools to assist in their research programmes.

5. Infrastructure facilities in Bioinformatics Centre: a. Computers : Twenty (Desktop machines) b. Printers : Two c. Scanners : One d. Communication facility : Telephone connection,

B. Scientific software packages : NTSys, PHYLIP, TREE VIEW, RAPDPLOT

C. Databases and other information resources Databases acquired: Under process

Books on Bioinformatics: (Department of Biotechnology Library)

Title Author 1. Introduction to Bioinformatics Krawetz and Womsle 2. Bioinformatics: A modern approach Srinivas 3. Algorithms in Bioinformatics Benson 4.Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins Andreas D. Baxevanis 5. Bioinformatics (A Beginner's Guide) Clavene 6. Bioinformatics Concepts Skills and Applications Rastogi,S.C 7.Essentials of Genomics and Bioinformatics Sensen, C.W 8.Bioinformatics Sequence and Genome Mount, David 9. Bioinformatics Approaches and Applications Chakraborty 10.Bioinformatics Sequence Structure and Databanks Higgins and Taylor 11.Introduction to Bioinformatics Attwood and Smith 12.Bioinformatics Methods and Protocols Misener and Krawetz 13.Bioinformatics and Genomes Current Perspectives Andrade 14.Protein Analysis and Design Ruth Hogue Angeletti 15.Bioinformatics Sequence and Genome Analysis (2nd Edition) David W.Mount 16.Bioinformatics Pevsner, Jonathan 17.Bioinformatics and Molecular Evolution (Latest edition) Attwood and Higgs 18.Bioinformatics Lesk 19.Instant Notes Bioinformatics D.R.Westhead,J.H Parish &

447 R.M Twyman 20.Introduction to Bioinformatics (Indian edition) Arthur M.Lesk 21.Fundamental Concepts of Bioinformatics Dan E Krane, Michael L.Raymer 22.Bioinformatics Genes Proteins and Computers C.A Orengo,D.T Jones & J.M Thornton

23.Bioinformatics Basics Applications in Biological Lukas K Buehler,Hooman H. Science and Medicine (Second edition) Rashid

24.Principles of Bioinformatics P Shanmughavel

Journal: Science Trends in Biotechnology Indian Journal of Biotechnology 6. Details about staff members working in the centre:

Name Designation Specialization Period of Absorption working status Prof. M. K. Dhar Head Genomics and Permanent Biotechnology Proteomics Faculty & Coordinator Bioinformatics Centre Mohit Kumar R. A Bioinformatics/ Temporary Sharma Data Analyst

7. Types of services provided: The Centre offers training on fundamental topics in Bioinformatics for technical staff and students of Jammu University. Literature search, sharing of resources, support to R&D activities in Biotechnology for PG student projects, imparting teaching in Bioinformatics for PG students. Creation of awareness among undergraduate and post-graduate students and faculty regarding the basics of Bioinformatics and its applications is the major focus.

8. Educational activities with details of placement: As a part of the M Sc program, the centre conducts Bioinformatics courses for M.Sc students of the University of Jammu.

9. Initiative to validate the outcome of bioinformatics resources: The large number of users at the Centre and the research activities validate the outcome of bioinformatics resources. 448

10. Collaborative works / Initiatives:

11. Databases/Software packages developed:

12. Papers published or presented in the conference with Reference: Two papers have been submitted for presentation during 3rd J&K Science Congress to be held w.e.f. 26 to 28th February, 2008 in the University of Jammu, Jammu.

Title of the Papers: 1. Using Bioinformatics tools to create a database of transcription factors binding sites. Mohit Kumar Sharma and V. B. Bajic 2. Cloning and functional analysis of carotenoid biosynthesis genes from carrot Khalid Zaffar Masoodi and Manoj K. Dhar

13. Initiation of R&D activities in Bioinformatics: The BIF is promoting Bioinformatics awareness and has initiated dedicated research programmes in Bioinformatics.

14. Details of Training / Workshops organized and total no. of users trained: The Centre conducted various hands on sessions and was involved in teaching full fledged course on Bioinformatics in M. Sc Biotechnology, M. Sc Biochemistry and M. Sc Microbiology programmes of the University.

Department Users Trained Biotechnology 12 Biochemistry 7 Microbiology 8

15. Impact shown by the centre on the growth of biotechnology and allied areas: The Centre has initiated several programmes for introducing Bioinformatics to the students as well as faculty of the University. The usage of e-mail and Internet has increased notably and the facilities of the Centre are widely made use of for presentations and other research activities. The softwares available are being used for phylogenetic analysis by several research scholars. 16. Future activities: The focus will be on research activities in Bioinformatics. The Centre proposes to conduct three day workshop for University and college teachers during first week of February 2008. The other routine services of the Centre would be continued efficiently.

Additional details:

449 Name of the Coordinator: Prof. M. K. Dhar

Postal address : Department of Biotechnolgy University of Jammu, Dr. B.R.Ambedkar Road Jammu -180006

Phone Number: 91-191- 2433655, 91-191-2456534 Fax: 0191-2456534 E-mail: [email protected], [email protected]

450 University of Kalyani, Kalyani, West Bengal Coordinator : Dr. Alpana Seal

1. Summary of the progress made by the centre from its inception : The centre was inaugurated on 28th March,07 .The inauguration was coupled with one workshop on “Application of Bioinformatics in Molecular Modeling, Data Analysis and System Biology” .The centre is now being used by researchers, M.Sc. students and project workers from this University and other Universities/Institutions. Training programs in bioinformatics and computational biology has been arranged. Scientific Software package GCG was bought and installed. Other scientific program packages, free for academicians have been installed. Recently another national workshop on “Macromolecule Ligand Interaction & Drug Design” has been arranged and another national workshop on “System Biology” will be arranged in this financial year.

2. Major research activities in Biotechnology and its related fields at your institution :

Department of Biochemistry and Biophysics: ¾ Molecular modeling of sulfur compounds metabolizing proteins (in collaboration with Bose Institute, Kolkata): Sulfur compounds are metabolized by an operon called sox operon. It codes for a number of proteins. A considerable progress in the genetics of sulfur lithotrophy is noted but the structural details of the proteins are not available. To predict the biochemical aspects of the proteins involved molecular modeling technique is employed. ¾ Molecular modeling of protease inihibitor interaction. ¾ Molecular Mechanism of Artificial Transformation of E.coli with Plasmid DNA. ¾ siRNA technology for knocking down a gene (in collaboration with SINP, Kolkata)

Department of Molecular Biology and Biotechnology: ¾ Molecular Phylogeny of Indian Shad Tenualosha ilisha inferred using mitochondrial DNA partial gene sequences. ¾ Molecular Breeding of Rice with Special Reference to Marker Assisted Gene Pyramiding for Biotic Stress Resistant. ¾ An Investigation on Somaclonal Variance of certain Aromatic Plants using Biochemical and Molecular Approaches. ¾ An Investigation on in vitro selection of Aluminium Stress Resistance of a leguminous crop and its rhizobial counterpart for their potential exploration in acid soil tract. ¾ An exploration of in vitro somatic embryogenesis of two important medicinal plants and their biomodulatory mechanism. ¾ Identification of DNA markers associated with disease and pest resistant in Mulberry. ¾ A study on induction of somatic embryos and over-expression of SAM Decarboxylase in Limonium sinensis through transgenesis.

3. Area of Specialization of the centre:

451 I. Molecular Modeling, II. Computational Biology

4. Major activities of the centre during the year 2007-08: ¾ One national workshop was arranged during 2nd – 4th January, ’08. ¾ Another national workshop will be arranged in March,’08 ¾ Some local training programs have been arranged to introduce Bioinformatics in the neighborhood. ¾ GCG programme package has been installed. ¾ Other free scientific programme packages (SHELX, WINZIP, XtalView, Rasmol, ClustalW etc.) have also been installed. ¾ Trying to interact with local hospitals and other local institutions to generate Medical & Pharmaceutical Databases and to start collaborative work.

5. Infrastructure facilities in the Bioinformatics Centre : A. Computer & Communication facility: 1) Ten P(IV) Lenovo desktop Computers with 17” TFT monitors 2) One highend (X236) and one medium (X226) IBM server 3) One Canon black & white copier cum printer 4) One HP colour laser printer 5) One HP scanner 6) One APC Smart RT-5000 UPS with 16 batteries 7) Sony L.C.D. projector. Internet Connection: Opted for BSNL Broadband (2 MBPS) connection (annual).

B. Scientific software packages: Operating System Softwares: Purchased and installed as recommended by DBT. Scientific Software: 1) Purchased and installed Acclerys GCG package. 2) Installed Shelex-97 package. 3) Some software free for academicians has been installed.

C. Databases & other information resources: Developed one database on the enzyme Dehydrogenase. 6. Details about staff members working in the centre (Name of the staff, Designation, specialization and period of working. Please indicate their absorption status): None at present. It’s a newborn centre. No staff member is attached with it till now. Two faculties of the Department of Biochemistry and Biophysics are working for the Centre in addition to their normal duties at the department.

7. Types of services provided: Till now we trained the students only. Project workers are also using the facility. 8. Educational activities with details of placement: Training students, arranging national workshops, initiated research activities. We will start summer training programme also.

452 9. Initiative to validate the outcome of bioinformatics resources: We have initiated.

10. Collaborative works/ initiatives: Initiatives has been taken to collaborate with nearby Institutions and other research institutes in Kolkata.

11. Databases/ Software packages developed: Till now one database on dehydrogenase has been developed.

12. Papers published or presented in the conferences with reference: Work is going on.

13. Initiation of R&D activities in Bioinformatics: Nothing started yet.

14. Details of Training/ Workshop organized and total no. of user trained: We have arranged one national workshop and trained thirty two participants in the current financial year. We will arrange another one in March,’08.Training of University students are also going on in regular basis.

15. Impact shown by your centre on the growth of biotechnology and allied areas: In this you may highlight the details like number of paper published/ number of papers published with the help of your centre, how your centre is promoting various activities of your organization and neighboring institutions, manpower trained, tools developed, patents & copyrights acquired and other services offered etc:

I. Five papers were published in last year in collaboration with other research institutes. II. Training programmes for University students in bioinformatics and in computational biology are going on in regular basis. III. We are trying to collaborate with other nearby institutions with the view to develop various databases needed for this locality. IV. One national workshop has been arranged in which thirty-two participants were trained. V. A database on dehydrogenase has been developed.

16. Future activities: We plan to Research on: ¾ Modeling studies of membrane system. ¾ Structural Bio-informatics to develop novel drug molecules. ¾ Cluster and self assembly study. ¾ Protein – ligand interactions. Develop databases required for this locality in association with other Institutes. Train students and research workers in this field. Provide service especially in this locality related to database search, sequence analysis, use of bioinformatics tool and software packages.

453 Additional Details:

Name of the Coordinator: Dr. Alpana Seal Postal Address: Department of Biochemistry and Biophysics, University of Kalyani, Kalyani 741235, W.B. Phone Number: 033 2582 3405(O), 033 2321 2106(R) Mobile: 9830795655 Email: [email protected], [email protected] Website: None Name of Contact Person(s): Dr. Alpana Seal Email: same as above

454 University of Madras, Chennai Coordinatior : Prof. D. Velmurugan

1. Summary of the progress made by the centre from its inception An international conference on “Computational drug discovery in pharma R&D” has been conducted on July 2007. About 350 candidates were participated in the conference. A technical assistant has been appointed in the BIF. The following items has been purchased as per the DBT sanction rule 1. Hardware including 10 systems,2 servers, printers and scanners. 2. Software-GLIDE from Schrödinger, Bangalore. [Quotations are invited for the purchase of other softwares like windows 2003 server with license and Red Hat Linux enterprise edition 4 or higher version.] 3. Books on Bioinformatics 4. Furnitures and stationeries required for site preparation

2. Major research activities in Biotechnology and its related fields at your institution Medical Biotechnology and diagnostics of infectious diseases Aquaculture Biotechnology, Enzymology, Environmental biotechnology.

3. Area of Specialization of the centre Structural Bioinformatics. Molecular modeling and drug designing. Molecular dynamics

4. Major activities of the centre during the year 2007-08 An international conference on “Computational drug discovery in pharma R&D” has been conducted on July 2007. About 350 candidates were participated in the conference.

5. Infrastructure facilities in the Bioinformatics Centre Computer & Communication facility-10 systems and 2 servers Scientific Software packages- Molecular docking softwares like GLIDE, Hex, Auto dock, Modeling softwares like Swiss PDB viewer, Modeller, visualization softwares like Pymol , Rasmol, web lab Viewer and chemical drawing softwares like ISIS Draw, Chemsketch etc. Databases & other information resources- Purchased about 100s of Books in Bioinformatics (V.C has assured for shifting to the new building with larger space. Internet connection will be provided in the new building)

455 6. Details about staff members working in the centre (Name of the staff, Designation, Specialization and period of working. Please indicate their absorption status) Sruthi Govind, Technical Assistant, MSc Bioinformatics from August 2007 Represented BIF in four international conferences and the research work has been presented. (Details are given in 12)

7. Types of services provided Training will be given on the following areas 1. Three dimensional structure determination of drug molecules 2. Molecular modeling 3. Molecular Dynamics 4. Structure based drug designing 5. QSAR studies

8. Educational activities with details of placement : -- 9. Initiative to validate the outcome of bioinformatics resources The research work done in BIF will be published as scientific papers soon. A three days International symposium on structural bioinformatics will be convened on first week of march wherein atleast 6 delegates will be invited from the following institiutes.1.Genomics centre,Yokohama,Japan 2.SPring Riken Harima, Japan 3.National University of Singapore,Singapore.

10. Collaborative works/ initiatives Molecular modeling studies for the compounds from marine resources, Centre for Marine Diversity, Kerala University, Kerala, is being undertaken to develop potential anticancer/anti malarial drugs.

11 Databases/ Software packages developed : -- 12.Papers published or presented in the conferences with reference 1. Presented a paper on Crystal structure analysis and molecular modeling studies of four novel beta lactam derivatives in the international symposium on Applied Bioengineering conducted by sathyabhama University, Chennai. 2. Presented a Poster on “Molecular docking studies of HCV NS5B polymerase inhibitors” in the international symposium on Bioinformatics and computational Biology conducted by Kerala University, Kerala 3. Presented a Poster on “Docking studies of Sulphonamide derivatives with human Carbonic anhydrase as target” in the international symposium on recent trends in macromolecular structure and function conducted by University of Madras, Chennai. 4 Presented a Poster on Molecular Crystal structure analysis and molecular modeling studies of four novel beta lactam derivatives inhibitors in the international symposium on “structural Bioinformatics- structure and function of Macromolecules” conducted by Sri Ramakrishna college of Arts And Science For Women, Coimbatore. 5. A paper on “Antiviral Drug design: Modeling studies of HIV Integrase with dihydroxy- pyrimidine analogues and N- Methyl Pyramidone analogues as inhibitors” was accepted by Jadavpur university, Kolkotta and will be presented in the National Seminar on crystallography.

456 13. Initiation of R&D activities in Bioinformatics Many requests are being received from many colleges for making use of the centre for 3 months major projects during summer .Once internet connection has been set up this will be pursued. Since the Coordinator is applying for a project in structural Bioinformatics wherein 2 project assistants are requested, R &D work will begin after the recruitment of the project fellow who wll later register for PhD in the University

14. Details of Training/ Workshop organized and total no. of user trained An international conference on ”Computational drug discovery in pharma R&D“ has been conducted on 26th july 2006. About 350 candidates were participated in the conference . 15. Impact shown by your centre on the growth of biotechnology and allied areas. In this you may highlight the details like number of paper published/ number of papers published with the help of your centre, how your centre is promoting various activities of your organization and neighboring institutions, manpower trained, tools developed, patents & copyrights acquired and other services offered etc. Project is being submitted by the Coordinator, BIF on High throughput crystallography and structural genomics. Once we move to the new building, 3 days workshop will be convened and after that research work will be carried out in the field of Molecular modeling with novel biomolecules as potential drug candidates.

16. Future activities Research students will be admitted to work on areas like QSAR, Structural Bioinformatics etc

Additional Details: Name of the Coordinator: Prof.D.Velmurugan Postal Address: Dr.D.Velmurugan, Centre of Advanced Study in Crystallography and Biophysics, University of Madaras, Chennai-25 Phone Number: 044-22202772 Mobile:09841075847 Email:[email protected] Website: Name of Contact Person(s): Prof.D.Velmurugan, Sruthigovind Email: [email protected] [email protected]

457 University of North Bengal Coordinator: Arnab Sen

1. Summary of the progress made by the centre from its inception: Since its inception in November 2006, we have marched forward steadily. The centre has every modern facility of information and communication including necessary hard ware and software. There were a number of publications in journals and posters presented in national and international conferences on the relevant areas.

2. Major research activities in Biotechnology and its related fields: At NBU major research activities are clustered around the fields of molecular genetics, microbial biotechnology, plant tissue culture, immunology, microbial genomics, transgenics, genomics and proteomics of nitrogen fixing bacteria and food pathogenic bacteria.

3. Area of specialization of the centre: Bioinformatics, microbial genomics, molecular modeling.

4. Major activities of the centre during the year 2007-08: A National Level Workshop on Bioinformatics will be held from 18th-20th January 2008. Another National level workshop has been planned in the month of March. The Coordinator Dr. Arnab Sen has set up International collaboration with the University of New Hampshire, USA. He along with Prof. Louis Tisa (Department of Microbiology, UNH, USA) has been working towards complete genome sequencing of five Frankia strains. Considerable amount of work relating to the characterization of bacteria on the basis of codon usage and phylogeny has been done and are expected to be published in the coming days. Recruitment of research fellows/ associates is in process.

5. Infrastructure facilities in the Bioinformatics Centre: Computer and communication: 10 PCs with OS One High end server and a Medium end server Scientific and Software packages: Two Windows 2003 Server with license, 10 Windows XP Professional with license, Microsoft ISA Server 2005 for Proxy Server, one Microsoft Visual Studio, .NET, MS SQL Server (Std.), MS Office 2003, 10 Quick Heal AVG Antivirus Package. GENOME BROWSER, CODONS, CODON W, MODELLER 9v1, CLUSTAL W, CLUSTAL X, DNAsp 4.0, MEGA 4.0, TREEVIEW, SPDBV, RASMOL, PHYLIP, PAUP, DAMBE, Jcat, Argus Lab, C++ and PERL. Databases and other resources: One Laser printer (network), one Desk-Jet printer, Internet Lease line.

6. Details about staff members working in the centre: Recruitment of one Research Associate (RA) is in process.

7. Types of service provided: The centre provides access to the faculty members, research scholars and students from nearby universities, colleges and research institutions interested in working in the field of bioinformatics.

8. Educational activities with details of placement: Two PhD students (S. Sur and U.K.Mondal) are currently engaged in their research work utilizing the 458 facility. Besides students and research scholars from other departments, institutes and nearby areas utilize this facility. 9. Collaborative work and initiatives: The Coordinator Dr. Arnab Sen has set up International collaboration with the Department of Microbiology, University of New Hampshire, USA.

10. Databases and softwares developed: We have developed programs for codon usage analysis and another for phylogenetic analysis which would be published in the coming months.

11. Papers published or presented in the conferences /workshops in the year 2007-08: a) Sri. Saubashya Sur participated in a National Workshop (28-30 March, 2007) on ‘Application of Bioinformatics in Molecular Modeling, Data Analysis and System Biology” organized by Bioinformatics Infrastructure Facility, University of Kalyani, Department of Biochemistry and Biophysics. b)Dr. Arnab Sen presented a poster in the 107th Annual General Meeting American Society of Microbiology on “Codon Usage Patterns and Predicted Highly Expressed Genes for Three Frankia Genomes and the Implication on Life Style” held in Toronto, Ontario, Canada from 21-25th May, 2007. c) Dr. Arnab Sen presented a poster in the Boston Bacterial Meetings on “Codon Usage Patterns and Predicted Highly Expressed Genes for Three Frankia Genomes and the Implication on Life Style”. Boston, June 20-21, 2007 Tufts University. d)Dr. Asim Kr. Bothra presented a paper in a National level Workshop on “Fundamental Genomics and Evolutionary Biology” on “Comparative analysis of codon usage patterns and identification of predicted highly expressed genes in five Salmonella genomes” (November 21-23, 2007), DIC, Institute of Life Science, Bhubaneswar. e) Sri. Saubashya Sur participated in a workshop on “Introduction and Scope of Computational biology” (3-5 December, 2007) organized by the Bioinformatics Centre, State Council of Sikkim Science and Technology, Gangtok, as a resource person. Presented a paper on “Bioinformatics Databases” and provided hands on Training.

12.Initiation of R&D activities in Bioinformatics:The Coordinator’s group is actively engaged in research in the field of genomics and proteomics of nitrogen fixing bacteria and food pathogenic bacteria. Protein structure prediction, biological sequence analysis, phylogenetic study, molecular modeling and molecular docking are the major thrust areas. Two PhD students (S. Sur and U.K.Mondal) are actively pursuing their research work. 13. Details of Training/ Workshop organized and total no. of user trained: A National Level Workshop on Bioinformatics will be held from 18th-20th January 2008.

14.Impact shown by your centre on the growth of biotechnology and allied areas: Research publications from the Centre during 2006-07: i) Sur. S, M. Bhattacharya, A. K. Bothra, L. Tisa & A. Sen (2008). “Bioinformatic analysis of codon usage patterns in a free living diazotroph, Azotobacter vinelandii”. ‘ANSI Biotechnology’(in press). 459 ii)Sen. A, S Sur, A. K. Bothra, D. R. Benson, P. Normand & L. S. Tisa (2007) “The implication on life style of codon usage patterns and predicted highly expressed genes for three Frankia genomes. Antonie van Leeuwenhoek” (in press). iii) Sen. G, S. Sur, D. Bose, U. Mondol, T. Furnholm, A. Bothra, L. Tisa & A. Sen (2007) “ Analysis of codon usage patterns and predicted highly expressed genes for six phytopathogenic Xanthomonas genomes shows a high degree of conservation”. ‘InSilico Biology 7, 0039. iv) D. Bose, S. Sur, A.K. Bothra & A. Sen (2007). “Study of the diversity of the heavy metal resistance genes and their codon usage profiling”. ICFAI Journal of Biotechnology 1(3) 49-58. v) Sur. S, A .Sen & A. Bothra (2007) “Mutational drift prevails over translational efficiency in nif operons of Frankia”. Indian Journal of Biotechnology’. (6) 321-328. vi) Mondol. U.K, S. Sur, A. Sen & A.K. Bothra (2007). “Codon Volatility: An Efficient Tool to Detect the Purity of Genes”. ICFAI Journal of Biotechnology 1(2) 45-49.

15. Future activities: Development of software for the analysis of DNA sequencing data and protein. Annotation of five Frankia genomes whose sequencing has been undertaken Bioinformatics analysis of nitrogen fixing and food pathogenic bacterial genomes. Molecular modeling of some nitrogen fixing proteins. Publication of Newsletter and conducting various training programs/workshops in bioinformatics.

Additional details: Coordinator: Dr. Arnab Sen Department of Botany, University of North Bengal, Siliguri-734013 Tel: 0353-2699106; Fax: 0353-2699001 E-mail: [email protected] Deputy Coordinator: Dr. Asim Kr. Bothra Chemiinformatics Bioinformatics Laboratory, Department of Chemistry, Raiganj College (University College) Raiganj- 733134 Phone: 9474441570;e-mail: [email protected].

460 University of Rajasthan, Jaipur Coordinator : Prof. S. L. Kothari

1. Summary of the progress made by the centre from its inception The sanction for the establishment of BIF was issued by DBT through its order number BT/BI/04/055/2001 dated 22-9-06. University in its centre for converging technologies has provided independent accomodation suited for BIF.The area of the facility is about 600 sq. ft.It is provided with four units of split air conditioners. Furniture and site Preparations have been completed. The university has provided one direct telephone line. The executive committee has been constituted. One R.A has been appointed from 01-12-2007.

2. Major research activities in Biotechnology and its related fields at your institution The institution has biotechnology and its related fields of study in the departments of Botany, Zoology, Biotechnology, Microbiology, Chemistry and Centre for Converging technologies (CCT). The broad research activities in these departments include transgenesis, plant tissue culture, secondary metabolites, molecular taxonomy, biodiversity, reproductive biology, microbial genetics, environmental biotechnology, radiation and cancer biology, immunology, biochemistry, and bioinformatics.

The CCT has four components of Converging technologies that are: N : Nanomaterials & Nanotechnology B : Bioinformatics & Biotechnology I : Information & Communication Technology C : Cognitive Neuroscience

3. Area of Specialization of the centre Converging Technologies namely : N : Nanomaterials & Nanotechnology B : Bioinformatics & Biotechnology I : Information & Communication Technology C : Cognitive Neuroscience

4. Major activities of the centre during the year 2007-08 The centre came into existence in December 2006.The R.A joined on 01-12- 2007. The centre will hold a 3 day workshop on “Bioinformatics : Introduction and Application” from 7th-9th feb,2008.

5. Infrastructure facilities in the Bioinformatics Centre

461 Computer & Communication facility : 10 Desktop Computers with all the accessories,1 Hp Laser jet printer & 1 HP Inkjet Printer. Scientific Software packages 1) Microsoft visual studio net Proffesional 2) Microsoft ISA server 2005 for proxy serve with media kit. 3) Freeware (Linux, Apache F Server, My SQL, PHP) Databases & other information resources

6. Details about staff members working in the centre (Name of the staff, Designation, Specialization and period of working. Please indicate their absorption status) Ranjeeta Bonal : R.A : M.Sc (Bioinformatics) : 01-12-2007

7. Types of services provided The 5 Yr integrated course in Converging Technologies take the help of BIF.Other students, research scholars and faculty also take the advantage of the facilities at BIF.

8. Educational activities with details of placement 9. Initiative to validate the outcome of bioinformatics resources 10. Collaborative works/ initiatives 11. Databases/ Software packages developed 12. Papers published or presented in the conferences with reference

13. Initiation of R&D activities in Bioinformatics It is proposed to take Ph.D level students in the subject area of Bioinformatics.

14. Details of Training/ Workshop organized and total no. of user trained A workshop is going to be held in BIF on “Bioinformatics : Introduction and Application” between 7th-9th Feb, 2008. Total no. of participants expected is 25..

15. Impact shown by your centre on the growth of biotechnology and allied areas. In this you may highlight the details like number of paper published/ number of papers published with the help of your centre, how your centre is promoting various activities of your organization and neighboring institutions, manpower trained, tools developed, patents & copyrights acquired and other services offered etc.

462 CCT is providing help to the 5yr integrated course in M.Sc(Converging Technologies) and is on the way to start PhD programmes and M.Sc-Honours in Converging Technologies.

16. Future activities BIF is actively working to start PhD programme & CCT- M.Sc (Honours) Programme is already running.

Additional Details: Name of the Coordinator: Prof. S.L Kothari Name of the Dy. Coordinator : Dr.Ashok .K. Nagawat Postal Address: Bioinformatics Infrastructure Facility Centre for Converging Technologies University of Rajasthan Jaipur-302004

Phone Number: 0141-2712489; 0141-2703439; 0141-2700370

Email: [email protected]; [email protected] Website: www.uniraj.ernet.in

Name of Contact Person(s): Dr.A.K. Nagawat, Dy. Coordinator CCT, Email: [email protected]

463 Vidyasagar University, Midnapur, West Bengal Coordinator : Prof. Bikas Ranjan Pati

1. Summary of the progress made by the center from its inception Bioinformatics laboratory of our center is start to functioning since August’ 2007. Inauguration of center was made by our Hon’ble Vice Chancellor Prof. Swapan Kumar Pramanick and in presence of the chief guest, Prof. Pinak Chakraborty, Co-ordinator of BIF, Bose Institute on 8th October 2007. From the inception of this laboratory our aim was to popularize the Bioinformatics in our surrounding as our center is situated in the remote corner and rural part of West Bengal. We have been able to complete the four training programme in different aspects of Bioinformatics like Structural Bioinformatics, Computational Biology, Database & data mining, and Evolution & Phylogeny.

2. Major research activities in Biotechnology and its related fields at your institution. Biotechnology related research activities of our University are – 1. Microbial enzyme (amylase, tannase, xylanase, chitinase) production and scale up process. 2. Production of microbial polysaccharides and antibiotics. 3. Biofertilizer production and transfer of technology. 4. Anticancer substances from mashroom. 5. Antioxidant and antidiabetic constitute from medicinal plants. 6. Joint forest management (JFM). 7. Development of new fish feed. In the last year we have received two research projects from different funding agencies like UGC, DRDO, New Delhi. 3. Area of specialization of the center a. Microbial fermentation; b. Biofertilizer ; c. Medicinal plants; d. Mashroom polysaccharides; e. Fish feed 4. Major activities of the center during the year 2007 - 08 After establishment of the center we have organized four short-term workshops for different group of students and teachers. Post graduate students, Ph. D. scholars and faculties of different department of our Institute and surroundings are enjoying different softwares, internet and e-journal facilities regularly. Now we are starting some shorts of proteomics research work in our center. 5. Infrastructure facilities in the Bioinformatics Centre Computer & Communication facility In the department there is already five existing computer, two printers (one laser and other dot matrix) and one scanner. Apart from these, 10 computers, one printer, one scanner and one copier machine procured from the BIF scheme and all are functioning. Twenty four hours internet facility and one dedicated telephone (no. 03222 – 274173) is available in this center. a.Scientific software packages Target to install the following softwares - Sequence analysis software: EMBOSS, Phylip 3.6, MEGA 2.0, TreeconW, Boxshade, OMIGA 2.0 Molecular modeling software : 464 MSI Insight II, Modetter, Procheck, Chemsketch, Rasmol, Swiss PDB viewer. b.Databases & other information resources Some free software collected from the internet and used regularly –

http://www.ncbi.nlm.nih.gov/Web/Gen GenBank Bank/index.html EMBL http://www.ebi.ac.uk/embl.html DNA sequence motifs TRRD http://www.bionet.nsc.ru/trrd/ ooTFD http://www.isbi.net Gene expression ASDB http://cbcg.nersc.gov/asdb Some specific software could not purchase due to shortage of fund. We can procure it whenever next allotment is available. 6. Details about staff members working in the center (Name of the staff, Designation, Specialization and period of working. Please indicate their absorption status). There is no permanent staff in our center. Following departmental faculty and staff are actively engaged in this center – Prof. B. R. Pati (Head of Microbiology Department & Coordinator of BIF center) Dr. K. C. Mondal (Faculty, Microbiology Department) Dr. D. Banerjee (Faculty, Microbiology Department) Dr. P. Das Mohapatra (Staff, Microbiology Department) Mr. J. Chalak (Staff, Microbiology Department) Mr. Biplab Chakraborty, [Information scientist] BE (Computer Science) Mr. Krishnakanta Ojha, [Technical assistant] Graduate Second installment of BIF grant is very much necessary to appoint a contractual research associate.

7. Types of services provided a. Laboratory supports to our students for learning their course curriculum. b. Internet & e-journal facilities to the PG students, Ph D scholars and faculties. c. Computational facility to all users of the University. d. Short term training & workshops are given to different scientific communities. 8. Educational activities with details of placement. At present we are not able to provide any type of conventional course on Bioinformatics. However our students completed their M. Sc. dissertation works and most of them are now engaged in industry or in research. 9. Initiative to validate the outcome of Bioinformatics resources. As such there is no committee in our center to evaluate the outcome of the Bioinformatics resources. We are planning to request the BIF executive committee of our center to take initiative to evaluate the outcome of biotechnology related works in our University. 10. Collaborative works/ initiatives. The center made primary discussion to tie-up with Bioinformatics center, Bose Institute, Kolkata for exchange of resource person, software and others. 465

11. Databases/software packages developed. We are not able to develop any software / databases from our center. We have only collected free and available softwares from the internet. 12. Papers published or presented in the conferences with reference Paper Das Mohapatra Production of tannase by the Journal of Applied Microbiology P.K., Mondal K.C. immobilization of Bacillus 102, 1462- 1467, 2007 and Pati B.R. licheniformis KBR6 in Ca-alginate beads. Das Mohapatra Effect of amino acids on tannase Journal of Microbiology, P.K., Mondal K.C. biosynthesis by Bacillus licheniformis Immunology and Infection. and Pati B.R. KBR6. (Accepted) K. Krishna Prasad, Immobilization of Pleurotus ostreatus Indian J. of Biotechnology S. Venkata Mohan, 1804 on PUF cubes: Influence of (Accepted). B. R. Pati and P. N. mycelial growth pattern on laccase Sarma. yield. S. M. Mandal, K. C. Optimization of IAA production by a Res. J. Microbiol (In Mandal, B. R. Pati Rhizobium isolate from V. mungo. press), 2007

S. M. Mandal, K. C. A rapid colony screening method for the Ind. J. Microbiol, 47, Mandal, B. R. Pati detection of arsenate reducing bacteria 2007

S. M. Mandal, K. C. Production and composition of Biotecnol. Lett 29, 1271-1275, Mandal, B. R. Pati extracellular polysaccharide synthesized 2007. by a Rhizobium isolate of Vigna mungo.

S. M. Mandal, K. C. Optimization of cultural and nutritional Res. J. Microbiol 2 (3) 239-246 Mandal, S. Dey, B. conditions for Indole 3-acitic acid (IAA) (2007). R. Pati Production by Rhizobium sp. isolated from root nodules of Vigna mungo (L.) Hepper. S. M. Mandal, ,B. R. Letter: Influence of experimental Eur. J. Mass. Spectrom 13. 165- Pati, A.K. Ghosh, parameters on identification of whole cell 171 (2007). A.K.Das. Rhizobium by matrix assisted laser desorption/ionization time of flight mass spectrometry. Debdulal Banerjee, Tannase Production by Aspergillus Acta Microbiologica et Keshab.C. Mondal, aculeatus DBF9 Through Solid State Immunologica Hungarica 54 (2): Bikas R. Pati. Fermentation. 159-166 (2007) Debdulal Banerjee Optimization of Tannase Production by Journal of Microbiology and and Bikas R. Pati. Aureobasidium pullulans DBS66. Biotechnology 17 (6) 1049- 1053 (2007) Publication in proceedings 1. Pradeep K. Das Mohapatra, Keshab C. Mondal and Bikas R. Pati. 2007. Solid state fermentation for tannase production by Bacillus licheniformis KBR6. Proceeding of the International Conference on New Horizons in Biotechnology [NHBT-2007], pp 131-132. 2. Parag Dandapat, Pradeep K. Das Mohapatra, Chiranjit Maity, Bikas R. Pati and Keshab C. Mondal. 2007. In vitro antimicrobial activity of leaf extracts of Anacardium occidentale (L) against human pathogens. Proceeding of the National Seminar on Medicinal Plants, pp 27. 3. Chiranjit Maity, Sapdip Samanta, Chandrani Mishra, Sasmita Jana, Pradeep K. Das Mohapatra, Bikas R. Pati and Keshab C. Mondal. 2007. Production and partial characterization of amylases by a local bacterial isolate, Bacillus sp. CKB19 under immobilization in Ca-alginate beads. Proceeding of the International Conference on New Horizons in Biotechnology [NHBT-2007], pp 244. 4. Mahapatra S, Manna S, Dey BK, Pandey A, Roy S, Basu M, Banerjee D. 2007. Endophytic fungal assemblage in tulsi (Oscimum sanctum) plant. Proceeding of 2nd Asian Congress on Mycology & Plant pathology, pp 436. 5. Banerjee D, Roy S, Mahapatra S. 2007. Antimicrobial activities of some endophytic bacteria isolated from Vinca rosea and Centella asiatica. Proceeding of joint bilateral seminar on Antimicrobial Drug Resistance and the development of new Antibiotics.

466 13. Initiation of R & D activities in Bioinformatics. Till we are not able to start R & D activities on Bioinformatics. Two M. Sc. students started project work in Bioinformatics in our center with active support of IIT, Kharagpur and Bose Institute, Kolkata. 14. Details of Training / workshop organized and total no. of user trained

Name of the training Nature of Number of programme Participants Participants attended Structural Bioinformatics M.Sc. students: 26 Computational Biology B.Sc. students 28 Database & data mining Biology teachers 20 Evolution & Phylogeny H.S. students 20

15. Impact shown by your center on the growth of biotechnology and allied areas. In this you may highlight the details like number of paper published /number of papers published with the help of your center, how your center is promoting various activities of your organization and neighboring institutions, manpower trained, tools developed, patents & copyrights acquired and other services offered etc. Paper published: 06 Manpower trained: 94 16. Future activities a. Initiation of refresher course for college teachers on ‘Bioinformatics & Advance Biology’. b. Regular workshop and training on different fields of bioinformatics for UG & PG students. c. Purchase of software and appointment of a research associate. d. Introduction of certificate / diploma course on Bioinformatics.

Additional details: Name of the Coordinator (& contact person): Prof. Bikas Ranjan Pati Postal Address: Dept. of Microbiology, Vidyasagar University, Midnapur, WB Phone : 03222-276554/555 (Ext. 477) Fax : 03222 – 275329 / 264338 Mobile: 09232743348 Email : [email protected] Website: www.vidyasagar.ac.in

467 West Bengal University of Technology, Kolkata Coordinator : Prof. Ashoke R. Thakur

H. Summary of the progress: The Dept. of Bioinformatics was founded for PG teaching and research in the year 2005. The courses offered in Bioinformatics – I. M. Tech. In Bioinformatics and II. Post B.SC. Int. Ph.D in Bioinformatics. For details : www.wbut.ac.in , www.utechbiotech.org. A Credit Exchange Programme has been initiated with the Bioinformatics Centre, University of Pune, a COE under DBT, New Delhi. Admission: Students are selected through a written test followed by PI. Intake: 18 (app. By AICTE). Fellowship: Students scoring above GPA 8.0 are awarded a monthly fellowship of 4000 INR. Other Activities: The Department regularly organizes workshops on different topics. Eminent Scientists from different research institutes, Universities, R&D organizations from all over the country delivered seminars on current research topics. The Department has recieved Rs. 26.50 lacs in grants from the DBT, New Delhi for “Eshtablishment of Bioinformatics Infrastructure Facility (BIF) for the promotion Biology Teaching through Bioinformatics (BTBI)”. It is also the DBT nodal centre for Eastern Region and have held the National Eligibility Test for Bioinfo-NET (rechristened BINC). An MoU has been signed for DOEACC-B level programme for M.Sc.(Tech) in Bioinformatics.

I. Major Research Activities in Biotechnology and its Related Fields: Ongoing research stresses on Microbial Biodiversity, Plant Biotechnology(heavy metal homeostasis in plants), Protein trafficking in Giardia lamblia. Human Molecular Genetics and Human Cordblood Stem Cell. Experimental techniques on Molecular Biology and Microbiology to students of M.Sc. In Bioinformatics, Sikkim Manipal University.

J. Areas of Specialization of the Centre: ZTUS – Zero Tolerance in Unlicensed Software

K. Major activities of the centre during the year 2007-2008: 1. Mirror Sites: The University website(www.wbut.ac.in) now hosts mirror sites for: 1. Fedora 2. Ubuntu 3. Mozilla 4. CRAN and 5. OpenOffice. 2.Workshops Organized: Bioiformatics – 5, Biotechnology – 3 on R, QSAR etc. 3. 1st Annual JC Bose Memorial lecture by Sir Gregory Winter (Feb 24th 2007). 4.2nd Annual JC Bose Memorial lecture by Prof. B. Sanyal, honored by the French Govt. with Legion de honor (Scheduled Feb 22nd 2008). L. Research Activities: Ongoing research stresses on Microbial Biodiversity, Plant Biotechnology(heavy metal homeostasis in plants), Protein trafficking in Giardia lamblia. Human Molecular Genetics and Human Cordblood Stem Cell. MD. M. Projects Approved: 1. Design of 'anion recognition' short peptide motifs 2. Molecular Investigation of Heavy Metal Tolerance/ Hyperaccumulation in Plants Growing on the Uranium Tailings Ponds in Jaduguda 3. Role of phosphoinositide in intracellular protein transport of Giardia lamblia 4. Co-ordinated Research & Development Project on the use of Kalanchoe pinnata(Patherkuchi) as a green manure crop to increase the yield of medicinal plants cultivated on degraded wasteland 5. Imparting Training to progressive farmers, growers, women members of self-help groups, traders and educated unemployed youths on cultivation, processing, extraction of medicinal & aromatic plants including entrepreneurship development N. Publications in peer-reviewed National and International Journals: 468 Bioinformatics – 4 2. Biotechnology – 8 3. Presentations in Conferences & Seminars – 4. O. Infrastructure facilities in the Bioinformatics Centre: Computer & Communication facility Hardware – Servers 6, Thin Clients 25, 12 desktops, workstation 1, 30 TFT monitors, 4 switches Scientific Software – EMBOSS, EMBASSY, CLUSTALV, ARB (Phylo. Anal.), Helix packing, netblast, dssp, OpenBabbel, Genoculster(Jalaja Technologies),GROMACS, YASARA, CHARMM, Mopac, VMD, RASMOL,SPDB Viewer, YASARA, RASTER3D, Pymol, AUTODOC, MOLWORKS, Bkchem, Cerius2 from Accelrys Databases and other Information Resources – Our Digital library based on KOHA and D-space platforms permit network bassed access to 13500, e-books & 1800 e-journals from Springer link along with CSIR, Academy of science, Science Direct and IOE journals.

P. Details about staff members working in the centre: ix. Prof. Ashoke Ranjan Thakur, Vice-Chancellor, Microbial Biodiversity & Bioinformatics 4yrs 2.Professor Rabi Majumdar, Advisor, Molecular Biophysics, 2yr 3.Dr. Raja Banerjee, Reader, Spectroscopy & Structural Biology, 2.5 yr 4.Dr. Soumalee Basu, Lecturer, Computational Biology & Bioinformatics, 2.5yrs 5.Mr. Subhrangshu Supakar, Project Officer, Pharm. & Bioinformatics, 2yr. 6.Ms. Aulie Banerjee, Project Officer, Botany & Bioinformatics, ~2yr 7.Ms. Sujata Roy, Project Officer, Molecular Modelling, 1.5 yr 8.Md. Aftabuddin, Project Officer, Protein Networks & Comp. Appl. ~1.5yrs Advisor and project officers are on contractual appointment.

Q. Types of service provided: The centre provides training programmes.

R. Educational activities with details of placement: Cognizant, wipro, IICB, CU, Labvantage, Bose Institute, NIT, DOEACC, Cennexios life sc.

S. Initiative to validate the outcome of bioinformatics resources: T. Placement of students – Cognizant, wipro, IICB, CU, Labvantage, Bose Institute etc U. Research papers – 12 V. Projects – 5

W. Collaborative works/initiatives: We have Ekta Incubation Centre, a Technology Business Incubator which proposes to build on competencies of its own resources and those of the networked incubator Entrepreneurship Development Cell (EDC). Dabur has signed an MOU.M/S Solutron based in USA is a company that specialises in development of software related to Patent database and has signed an Agreement.Hinovation Research Centre Pvt.Ltd. is another incubatee.

X. Databases/software packages developed : None. Y. Papers published/ presented in Conferences with reference: 12 Z. Initiation of R&D activities: Dabur has signed an MOU.M/S

AA. Details or training/ workshop organized and total no of users trained: 5 Nos. on R, QSAR and drug Design, Phyllogenetics.

BB. Impact shown by your centre on the growth of biotechnology and allied areas: Many research papers published, good placement for students, 5 projects awarded.

CC. Future workshops: python, QT, Molecular Dynamics

469

Additional details: Name of the Coordinator: Prof. Ashoke R. Thakur

Postal Address: West Bengal University of Technology, BF-142, Sector-1, Salt Lake, Kolkata -700064 Phone Number: 033-23217578, Fax No.: 2334-1030 Email:[email protected] www.wbut.net, www.utecbiotech.org

Name of Contact Person(s): Prof. Ashoke R. Thakur [email protected]

470 Jawaharlal Nehru University , New Delhi Coordinator : Prof. Alok Bhattacharya,

1. Summary of the progress made by the centre from its inception

Bioinformatics Center (BIC) was established in Jawaharlal Nehru University, New Delhi in 1989 under Biotechnology Information System Programme funded by the Department of Biotechnology, Government of India. The original objective of the center was to provide information to the researchers in Northern Region. In the first decade the Centre assisted biologists by providing bibliographic references with abstracts, retrieving sequences and structural data, analyzing the sequences and structural data, imparting skills in bioinformatics and providing computational facilities for research purposes in any area of bioinformatics. Last few years the BIC- JNU has embarked on research and development in the broader area of Computational and systems biology. The advancements in the field of Bioinformatics is leading to more focused area of study at Systems level. Taking note of this trend BIC-JNU has renamed its centre as Centre for Computational Biology and Bioinformatics (CCBB). Our main objective of human resource development activities and research in frontier areas of computational biology is has taken a shape and recognition within the country. We are also making concrete effort in inter–institutional collaboration in research projects. To keep pace with the development in the field, impetus is given to set up the necessary infrastructure and resources for the academic community

2. Major research activities in Biotechnology and its related fields at your institution Application and development of computational tools and Techniques to analyze, visualize and interpret sequence, structure and gene expression data on a large scale.

3. Area of Specialization of the Centre • Computational Comparative genomics • Large scale Microarray data analysis • Homology modeling and molecular simulation • Systems biology • Evolutionary mechanisms • Computer based drug discovery

4. Major activities of the centre during the year

471 • Faculty recruitment • Setting up of a high performance computing facility • Started M.Tech program in Computational and Systems Biology • Academic activities, such as conference and lectures • Research in Computation Biology

5. Infrastructure facilities in the Bioinformatics Centre

A. Computer Facilities • High Performance Computing Facilities (HPCF) as part of the UPOE, JNU. HPCF will be not only be used by the Bioinformatics community but also by other faculty doing large scale system level simulation. School of Information Technology has signed an MOU with C-DAC Pune to set up a 256 processor Cluster system for high performance computing initiative. • Internet Connectivity : Our host organization has high speed connectivity through Software Technology Park of India (STPI), Noida and a fibre optic based campus wide LAN is fully functional. Beside this SIT – JNU has a connection of 2 Mbps from DBT.72 PCs and 10 serversImplemented Video Conferencing as a method to share teaching and other resources • A specialized library

B. Scientific Software Packages • Discovery Studio Windows & Linux Server, Discovery Studio DS Modeling 1.2, Discovery Studio DS MedChem Explorer 2.2,DS Project KM Plus 1.0, MS SQL Server 2000, What IF,Gold 2.1.2,CORINA Structure Generator 2.6,Catalyst NS (SGI Workstations) 3.1, SYBYL 6.5,Chem Office, SigmaStat 2.0.3, SigmaPlot, MATLAB – Unix & Windows, AMBER 7, Chamm32 C. Databases & other information resources

6. Details about staff members working in the centre (Name of the staff, Designation, Specialization and period of working. Please indicate their absorption status) • University has merged the centre along with the staff w.e.f. 2000

Sl. Name of the staff Designation Specialization Period of # working 01. Dr. N. Subbarao System Analyst Molecular Modeling 1996 02. Dr. A. Krishnamachari Assistant Bioinformatics 1995 Professor 03. Debasish Mondal Accountant Accounts 1997 04. K.Ganesan Technical Computer Hardware 1998 Assistant & Software 05. Arun Kumar Thakur Xerox Operator Xerox / Fax operation 1995 06. Mahesh Ram Office Assistant Office Assistance 1999

7. Type of services provided Provide access to biological databases and tools to research scientists on-site as well as through the network. This is supplemented with trained manpower to guide the new user. The Center has several high-end workstations with considerable storage capacity processing capabilities, and are available for the user community. External

472 users from surrounding institutes and users from within campus routinely use the centers facilities for sequence data analysis as well as use the expertise in different area, such as molecular modeling etc.

8. Educational activities with details of placement We are offering M.Tech and Direct Ph.D programme in the area of computational and systems biology. a) M.Tech in Computational and Systems Biology : Present batch is about 15 students drawn from diverse background. This two year programme grooms them to become professional in the area of Computational Biology. Year Applied Interviewed Admitted 2006-07 576 26 06 2007-08 43 36 12 b) Ph.D in the broad area of computational biology and bioinformatics : During the current year , Ms. Sonika Tyagi became our first Ph.D scholar form the centre and Ms. Anchal Vishnoi submitted her thesis. We expect four students may submit their Ph.D thesis by July 2008. Besides these seven students are currently working on their research problem.

Year Applied Interviewed Admitted 2006-07 17 12 03 2007-08 06 03 01 c) Long-Term and Short-term trainees : Through this programme we provide an opportunity to young minds from any area to work on a specific problem and the duration is generally 3 months for short-term and 6-12 months for long term. We get tremendous response and we plan to strengthen this in the coming year. Year No. of students 2006 29 2007 34 d) Post-Doctoral Fellowship : Our centre also provides fellowship to attract Ph.D scholars from diverse background and motivate them to undertake research investigations in the broad area of computational biology. e) Placements : Majority of the students have gone into Ph.D. program in India and abroad. Some of the places where these students have enrolled for Ph.D. are JNU, IISc, number of Institutes in Europe and USA. Some of the students have joined as faculty including in one Central University. A substantial fraction about 30-40% are in private sector. Many of these students did not stay long in Industry and decided to go for Ph.D. programme. Since we started M. Tech program in 2006 the first of batch of srydents will be graduating in 2008. f) Workshops / seminars/ conferences (a) Participated in eight national workshops: (b) Thirteen Invited Lectures were organized by CCBB (c) Thirteen Lectures were delivered outside JNU

9. Initiative to validate the outcome of bioinformatics resources The number of collaborative projects involving computation biology is increasing as evident from number of publications and we plan to increase this aspect so that larger community can benefit from the expertise.

473

10. Collaborative works/ initiatives A major project involving researchers from AIIMS, JNU, IIT and ICGEB has been initiated i.e Deciphering RNA regulons : Construction, analysis and validation of a miRNA based regulatory network. We have started a “Complexity Group” with an aim to attract researchers working in diverse areas to take up research problems in complexity studies at systems level. Several meetings and seminars have been organized in this regard.

11. Databases / Software packages developed (a) No. of Software Created • http://gopam.jnu.ac.in GOPAm Database contain the relation between Gene, Genbank accession number, Gene Aliases, Chromosomal Location, SwissPort, Accession No. Annotation in Gene Ontologies, UniGene Cluster, UniGene and Locus Link Ref. Seq • MGDD : The database contains divergent regions present in members of tuberculosis complex. SNPs, repeats causing indels are also included in the database. • ABWGC, a comparative genomics method

12. Papers published or presented in the conferences with reference

1. Thakur, V., Azad, R. K., Ramaswamy, R. (2007) Markov models of Genome segmentation Physical Review E. 75, 011915. 2. Srivastava, P. K., Desai, D. K., Nandi, S., Lynn, A. M. (2007) HMM-ModE - Improved classification using profile hidden Markov models by optimising the discrimination threshold and modifying emission probabilities with negative training sequences. BMC Bioinformatics. 8,104. 3. Vishnoi, A., Roy, R., Bhattacharya, A. (2007) Comparative analysis of Bacterial genomes: Identification of divergent regions in Mycobacterial strains using an anchor- based approach. Nucleic Acid Res. 2007;35(11):3654-67. Epub 2007 4. Ramachandran, V., Subbarao, N., Mallick, B. N. (2007) In silico modeling of α1A- adrenoceptor: Interaction of its normal and mutated active sites with noradrenaline as well as its agonist and antagonist. American Journal of Biochemistry & Biotechnology American Journal of Biochemistry and Biotechnology 3 (4):216-224, 2007. 5. Stephen, P., Ramachandran, V., Subbarao, N., Bamezai, R. N. K. (2007) Molecular Modeling Pyruvate Phosphate Dikinase of Entamoeba Histolytica and Insilico Virtual Screening for novel inhibitors. Special Issue in Drug Discovery of Journal of Computer aided Molecular Design (E publicated in Aug. 2007) 6. Anupama Singh, Hemant R. Kushwaha, Pawan Sharma Molecular Modeling and Comparative Structural Account ofAspartyl beta -semialdehyde dehydrogenase of Mycobacterium tuberculosis (H37Rv) Journal of Molecular Modeling (In Press)

13. Initiation of R&D activities in Bioinformatics • Genome analysis using statistical and other methods • Comparative genomics • Systems biology • Microarray and other large scale data analysis • Motif finding and analysis • Pathway analysis and identification of drug targets • In silico drug discovery 474

14. Details of Training / Workshop organized and total no. of user trained • We have already mentioned before under educational programs.

15. Impact shown by your centre on the growth of biotechnology and allied areas. In this you may highlight the details like number of paper published/ number of papers published with the help of your centre, how your centre is promoting various activities of your organization and neighboring institutions, manpower trained, tools developed, patents & copyrights acquired and other services offered etc. a. Some of the papers published by us are getting citation as well as are highly accessed. b. The students produced by us are being considered to be one of the best in the field are working in the top industries and also in top Institutions. c. Some of the potential drugs identified by us by computational methods are currently being experimentally verified. d. The teaching programs are in the forefront of the subject.

16. Future Activities

• Setting of a software development centre : • Setting up of a large scale data analysis centre • Setting up of Interdisciplinary group on complex system • Starting a Ph.D. program with M.Sc./B.Tech as input students • Continuation of Post Doctoral Fellow / Long Term Training Programme in Bioinformatics

Additional Details: Name of the Coordinator: Prof. Alok Bhattacharya, Postal Address: Centre for Computational Biology & Bioinformatics, School of Information Technology Jawaharlal Nehru University Hall # 4, Lecture Hall Complex, New Delhi-110 067 Phone Number:26741699 Mobile: Email: [email protected] Website: http://ccbb.jnu.ac.in/

Name of Contact Person(s): Prof. Alok Bhattacharya, Email: [email protected]

475

National JALMA Institute for Leprosy & Other Mycobacterial Diseases Agra Coordinator: Dr. VM Katoch

Title: Creation of Bioinformatics Infrastructure Facility (BIF) for the promotion of Biology Teaching through Bioinformatics (BTBI) scheme of BTISnet

Installation of Bioinformatic softwares: Following Bioinformatic softwares have been / are being purchased for the facility.

Biointerpreter GeneSpring Geno-cluster Discovery Studio 2.0 GCG

Research work done:

Homology modeling: We have prepared homology models for proteins recently identified in the Institute to have role in efflux mediated drug resistance in Mycobacterium tuberculosis as well as for metabolic proteins of M.leprae.

Phylogenetic analysis: We have done phylogenetic analysis of M.tuberculosis efflux pump proteins. The study was done to investigate close relationship of efflux pump proteins within other genera having similar functions. Phylogenetic analysis of M.tuberculosis was also done based on VNTR typing.

Evolutionary relationship of M.leprae strains: Evolutionary relationship of M.leprae strains has been studied to investigate their origin in India. The copy numbers of micro and minisatellites regions in M.leprae determined by Molecular Biological methods have been correlated with Bioinformatic analysis to investigate their ancestral origin.

Other studies: A number of online Bioinformatic tools have been used for ongoing studies in the Institute like primer designing, BLAST analysis, Transmembrane region prediction of efflux proteins, multiple sequence alignments etc.

Workshop cum Orientation Training Programmes: The Institute has organized three workshops during the period of August to December 2007. The selection of students as well as teaching faculty for Orientation Training cum Workshop was based on a write-up submitted by them covering their present work and motivation for future research / teaching involving Bioinformatic aspects.

1. Bioinformatics Orientation Training cum Workshop held from 27th – 31st August 2007

476 In this training 25 candidates were selected including 8 teachers and 16 students from Agra as well as other cities such as Indore, Bharatpur, Jabalpur and Bhopal. Lectures on advanced tools and techniques related to sequence analysis, genomic data mining, protein modeling, docking and structure based drug designing etc. were given by the Institutional faculty as well as invited speakers from various places like MANIT, Bhopal (Prof. KR Pardasani), Jaypee Institute of Engineering & Technology, Guna (Dr. Neeru Adlakha), AIIMS, New Delhi (Prof. Punit Kaur), JNU, New Delhi (Prof. Alok Bhattacharya) and Madurai Kamraj University, Madurai (Dr. Sanjeev Singh). Hands-on training was also provided in various aspects of Bioinformatics.

2. Short-term Training cum Workshop held from 25th September – 6th October, 2007

This training programme was organized for students studying at the Institute / who had come for short-term training from Agra and nearby regions to provide them exposure about various bioinformatic tools. Twenty students were selected for this training and hands-on training was provided to them alongwith lectures by the Institutional faculty.

3. Bioinformatics Orientation Training cum Workshop held from 24th – 30th December 2007

The selection procedure for the second Bioinformatics Orientation Training cum Workshop was based on same procedure followed earlier. 40 candidates were selected for the training including 9 teachers and 31 students from Agra as well as other cities such as Datia, Lucknow, Meerut, Moradabad and Ghaziabad. The training programme was inaugurated by Prof. VP Saxena, Former Vice Chancellor, Jiwaji University, Gwalior and Lectures as well as hand-on training on various aspects of Bioinformatics were provided by the Institutional faculty as well as invited speakers from various places like MANIT, Bhopal (Prof. KR Pardasani), Jaypee Institute of Engineering & Technology, Guna (Dr. Neeru Adlakha) and CDFD, Hyderabad (Dr. Akash Ranjan).

Dr. VM Katoch Director & Coordinator Bioinformatics Infrastructure Facility (BIF)

477 Ch. Charan Singh University, Meerut Coordinator: H. S. Balyan

1. Summary of the progress made by the centre from its inception: The BIF facility was established in the Department of Genetics and Plant Breeding and is open for use by all biology students. The first workshop will be organized during March 2008 to train students. 2. Major research activities in Biotechnology and its related fields at your institution: Genetic and physical mapping, QTL analysis, Molecular marker assisted selection, gene pyramiding, association analysis, comparative genomics involving wheat, rice, rye, barley, Mycobacterium tuberculosis and M. bovis, database searches, sequence retrieval, in silico correlated gene expression in bread wheat, genome-wide analysis of promoter and coding sequences in Mycobacterium tuberculosis, homology modeling and docking studies for various enzymes, Development of web-based interface for food safety, computer aided drug designing (Cadd); designing of self-assembling peptides 3. Area of Specialization of the centre: The major area of specialization is Genetics, Plant Breeding & Crop Biotechnology. Although master courses in Biotechnology and Bioinformatics are also offered by the university under self-finance scheme. 4. Major activities of the centre during the year 2007-08: The facility is open to all biology students. We also propose to organize a workshop “Databases, data mining and retrieval of information” during March 2008. 5. Infrastructure facilities in the Bioinformatics Centre (i) IBM THINK CENTRE: 10 Numbers; RAM 256 DDR-2 (Make IBM additional 256 MB DDR 2 Ram): 10 Numbers; IBM TFT 17” (in lieu of 17” monitor): 10 Numbers (ii) IBM SERVER with 2 Dual Core Processor: One Number; IBM TFT 17” In lieu of 17” monitor): One Number (iii) IBM SERVER Intel Xeon 3.00 Ghz Dual Core Processor EM 64 T: One Number; RAM 1 GB (Make IBM additional 1GB DDR2 RAM, 2×512 MB): One Number; IBM TFT 17” (in lieu of 17” monitor): One Number (iv) 420 CP Multifunction Xerox Machine: One Number (v) HP Laser Jet Printer (Model 5200 series): One Number (vi) Scanner HP 2400C: One Number (vii) Desk Jet HP 1360 Laser Jet Printer: One Number (viii) Softwares: Windows 2003 Server 10 clients: One Number; Microsoft ISA Server 2005: One Number; Microsoft Visual Studio Standard 2005: One Number; MS SQUL Server 2005 Standard: One Number; MS Office 2003: One Number

6. Details about staff members working in the centre (Name of the staff, Designation, Specialization and period of working. Please indicate their absorption status): The facility is being looked after by the staff of the Department of Genetics & Plant Breeding. Separate staff has not been recruited as yet. 478 7. Types of services provided: The facility is available for all those who are interested 8. Educational activities with details of placement: Not Applicable 9. Initiative to validate the outcome of bioinformatics resources: Not applicable 10. Collaborative works/ initiatives: Not applicable 11. Databases/ Software packages developed: Not Applicable 12. Papers published or presented in the conferences with reference Mohan A., Goyal A., Singh R., Balyan H.S., Gupta P. K. (2007). Physical mapping of wheat and rye expressed sequence tag-simple sequence repeats on wheat chromosomes. The Plant Genome (A supplement to Crop Sci.) 47: 3-13

13. Initiation of R&D activities in Bioinformatics: Not Applicable 14. Details of Training/ Workshop organized and total no. of user trained: A workshop on “Databases, data mining and retrieval of information” will be organized during March 2008 for training of students. 15. Impact shown by your centre on the growth of biotechnology and allied areas: The facility is being put to use by students and scholars as evident by the above publication. The organization of the workshop will also help in training manpower in the use and application of bioinformatics. 16. Future activities: Conduct of workshop Name of the Coordinator: H. S. Balyan Postal Address: Dr. H. S. Balyan, Professor & Head, Department of Genetics & Plant Breeding, Ch. Charan Singh University, Meerut-250 004 Phone Number:0121-2763564 Mobile: 9412515497 Email:[email protected] Website: www.ccsuniversity.org

Name of Contact Person(s): H. S. Balyan Email: [email protected], [email protected]

479 Maharani Lakshmi Ammanni College for Women, Bangalore. Coordinator : Prof. M.B. Nagaveni

1. Summary of the progress made by the centre from its inception: From the time of receipt of grants, our college BIF centre has successfully conducted one national conference and 3 workshops on bioinformatics.

National conference: College conducted two day national conference on computational biology, bioinformatics and life sciences (NCCBL ’07) on May 2 and 3, 2007.

Workshops:

A. 15 days hands-on workshop on “In silico drug designing and molecular modeling, was held with the collaboration with Institute of Computational Biology from July 25, 2007 to August 10, 2007. After the completion of the workshop, students /faculties are well-versed in drug designing softwares as ligand scouts, marvin sketch, smiles, quantum, vmole, autodock, argust lab etc. Sessions were handled by experienced faculties from industries (Biocon, IOCB, Accenture, PDP), academia (IIIT, Hyderabad, Maharani Lakshmi Ammanni College for Women). B. Two days hands-on workshop for faculty members alone, was conducted with the collaboration of Accelrys, Sai foundation, Apsara Innovation specificifally only on GCG wiscon package. C. The other workshop was conducted in collaboration with the company named Orsby Engineering Pvt. Ltd., BIOWARE Division, Bangalore. The workshop was conducted on April 11, 2007 on “Genious Pro” software for Post graduate students for enhancing their bioinformatics skills. This software is used for mainly for teaching basic bioinformatics tools.

Apart from the above mentioned scientific activities, BIF centre made few progresses as listed below:

A. Upgradation of the systems B. Speed enhancement of the systems which has enabled us to use the softwares effectively C. BIF has given free access to undergraduate students, to enable them to have bioinformatics software knowledge and to make them focused towards research D. Using BIF, our colleague, Mr. Sushil Kumar Middha has won first prize in paper poster presentation at international bioinformatics symposium held at Bhubaneshwar. E. Our M.Sc. students Ms. Keya, Ms. Ashwini have presented a paper at national conference “Motif ‘06” at Bharatiyar university at Coimbatore on cystic fibrosis Title of the paper: “CFTR genome analysis with the help of bioinformatics tools”. Authors: Keya M, Ashwini, Sushil Kumar Middha

2. Major research activities in Biotechnology and its related fields at our institution

480 Many faculty members have taken up the research projects for their M.Phil and Ph.D. degrees.

3. Area of specialization of the center : Biotechnology 4. Major activities of the centre during the year 2007-08 BIF centre has successfully conducted 2 days national conference on computational biology, bioinformatics and life sciences on May 2 and 3, 2007, short term training programs for students of our and other colleges. 5. Infrastructure facilities in the Bioinformatics Centre a. Computer and communication facility: 25 computers, A dedicated BSNL line for internet access, High end Server for internet. b. Scientific software packages: Accelrys GCG package, Discovery studio, Quantum software (all are commercial packages and free ware Hex,RasMol,Qmol etc. ) c. Databases and other information resources: PFam (Protein database) 6. Details about staff members working in the centre : Mr. Suhil Kumar Middha : Bioinformatician Mrs. Aruna H.K. : Bioinformatician Mrs. Saraswati B. : Bioinformatician Mrs. Harini : Lab Assistant Mr. Venkatesh : Bioinformatician . (All are appointed on permanent basis since 2006)

7. Types of services provided: We have trained our students and faculty members to use bioinformatics tools for teaching and enhance their bioinformatics skill

8. Educational activities with details of placement Students are placed in companies like Accenture, Apsara Innovation center as bioinformatician, data management professionals etc.

9. Initiative to validate the outcome of bioinformatics resources: Want to collaborate, have discussions and interact with BTISnet Centres and other BIF centers.

10. Collaborative works/initiatives With IOCB we want to do database designing With Apsara Innovation for conducting work shop in future.

11. Databases/software packages developed : Still working

12. Papers published or presented in the conferences with reference:

13. Initiation of R&D activities in Bioinformatics: Initiated database creation

14. Details of Training/workshop organized and total no. of user trained 5 days hands-on workshop on “In silico drug designing and molecular modeling, was held with the collaboration with Institute of Computl. Biology from July 25-Aug 10, 2007.

481 Two days hands-on workshop for faculty members alone, was conducted with the collaboration of Accelrys, Apsara Innovation specifically only on GCG wiscon package.

One day workshop in collaboration with the company named Orsby Engineering Pvt. Ltd., BIOWARE Division, Bangalore Total number of users trained: 130

15. Under progress

16. Future activities Working on database designing and drug designing, Organizing national level workshop on clinical research during March, 2008

Additional details: Name of the Coordinator: Prof. M.B. Nagaveni Postal Address: Maharani Lakshmi Ammanni College for Women, Malleswaram, Bangalore- 560 012 Phone Number: 26692137 Mobile: : 9886205533 Email : nagavenimb_yahoo.co.in

Name of Contact Person: Mr. Sushil Kumar Middha Email: [email protected]

482 University of Kerala Coordinator : Dr.Achuthsankar S. Nair

1. Summary of the progress made by the centre from its inception. The Centre for Bioinformatics was established by the University of Kerala in January 2005 to take up teaching, research and extension activities in bioinformatics and computational biology. This inter-disciplinary centre focuses on the computational applications in biology, drawing knowledge from mathematics, statistics, computer science, information technology, biology and bio-technology. The centre has currently a post-graduate programme (MSc in Computational Biology) and a post-masters programme (MPhil in Bioinformatics) in addition to a research programme leading to PhD in Bioinformatics/Computational Biology. The research areas identified are genomic and proteomic signal processing (applications of digital signal processing), protein sub-cellular localization, chaos game representation of bio-sequences, bio-sequence compression, systems biology and molecular modeling. The Centre has attracted funding from various state and national agencies such as Kerala State IT Mission, Dept of Information Technology, Govt of India, Dept of Bio-Technology, Govt of India, University Grants Commission, Dept of Science, Technology and Environment, Govt of Kerala. In 2006-2007, DBT-BIF was granted to the centre and the first phase of implementation is now complete. A number of programmes were conducted under the auspices of DBT-BIF and the major one was Bioinformatica Indica 08 International Symposium on Computational Biology, Bioinformatics and Synthetic Biology. 2. Major research activities in Biotechnology and its related fields at your institution. Major research activities in Biotechnology and its related fields at your institution The research areas identified are genomic and proteomic signal processing (applications of digital signal processing), protein sub-cellular localization, chaos game representation of bio-sequences, bio-sequence compression, systems biology, Drug Discovery against Hepatitis C virus and isolation and analysis of active compounds present in Trichopus zeylanicus (Arogyapacha).

3. Area of Specialization of the centre Computational Biology & Rational Drug Discovery 4. Major activities of the centre during the year 2006-07 x. Bioinformatica Indica 08: International Symposium on Computational Biology, Bioinformatics and Synthetic Biology. This was a major event with 41 institutions from India and abroad represented. It had 120 participants. Key note address was delivered by Dr Todd Taylor of the Riken Genomic Sciences Centre in Japan. Dr Limsoon Wong from National University of Singapore, Dr Pawan Dhar from Riken Genomic Sciences Centre in Japan (Editor in chief International Journal Systems & Synthetic Biology), Dr Kumar Selvarajoo from University of Kew, Japan, Dr. G. Narahari Sastry, IICT, Hyderabad, India, Dr. D. Karunagaran, IIT, Chennai, India, Dr. D. Swati, Banaras Hindu

483 University, India, Dr. Ramakrishna Ramaswamy, JNU, New Delhi were the key speakers. Proceedings has been published. xi. A number of training programmes/workshops were conducted which are listed in section 13.

5. Infrastructure facilities in the Bioinformatics Centre The centre has a full-fledged Informatics Lab, whereas wet labs are shared with the Life science Depts. Facilities ranging from Gel electrophoresis and RTPCR to electron microscope are at the disposal of the students. In addition, the Rajiv Gandhi Centre of Biotechnology (RGCB) in Thiruvananthapuram also supports our programme with expert human resources and short workshops at their Labs which include DNA & Protein sequencing systems, DNA finger printing facility and Molecular Imager. An excellent collection of over 600 books on Bioinformatics and allied areas are available at the Centre, in addition to facilities of the Campus Library and the University Library. Computer & Communication facility With DBT-BIF funds, 2 servers and 10-node network has been installed. Both broad-band fiber-optic connection and Wi-Fi connection has been established.

Scientific Software packages : Scilab, MATLAB, GenoCluster, GOLD. Databases & other information resources. Through Campus WAN has access to bundled on-line subscription of 1800 Journals.

6. Details about staff members working in the centre (Name of the staff, Designation, Specialization and period of working. Please indicate their absorption status) Dr Achuthsankar S Nair, (Hon. Director, Computational Biology, Since 2005, Permanent) Being appointed Lecturers (2 Nos): Contract Lecturer (1 No): Permanent (UGC) 7. Types of services provided Training, Consultancy 8. Educational activities with details of placement MSc (Computational Biology) – 8 seats: Started in 2008 MPhil (Bioinformatics) – 15 Seats: Placement in SooryaKiran Bioinformatics Pvt Ltd, Kerala Agricultural University, Rajiv Gandhi Centre for Biotechnology, Saurashtra University, Rajkot, 5 students have registered for PhD at the centre.

The MPhil (Bioinformatics) programme has an intake of 15 seats, admits students with masters degree in life science/computer science and all allied areas. The courses include: Bio-Mathematics & Statistics, Web Programming, Computational Genomics, Computational Proteomics and Computer-Aided Drug Discovery, Micro Array Bioinformatics, Introduction to IT (E), Introduction to Life Sciences (E), Algorithms in Computational Biology (E), Applied Bioinformatics (E), Seminar, Project & Viva Voce.

484 The Msc(Computational Biology) programme with an intake of 8 seats, admits students from computing and allied areas (BSc (Computer Science), BSc (Electronics), BCA, BSc Physics and Computer Applications, BSc in any branch with PGDCA, BTech (Biotechnology)). It covers the following courses: Introduction to Life Sciences, Bio Mathematics & Statistics, Bio-Physics, Computational Genomics, Introduction to Biotechnology, Computational Proteomics & Metabolemics, Computational Transcriptomics, Molecular Phylogenetics, Advanced Programming Tools, Computer Aided Drug Design, Micro Array Image Processing, Project & Viva Voce, and Elective courses (Systems Biology, Data Mining, Professional Studies, Synthetic Biology, Advanced Topics, Programming in Perl, Soft Computing methods in Bioinformatics)

9. Collaborative works/ initiatives - Informal Collaboration with Scientists of Riken Genomic Sciences Centre, Japan - Sooryakiran Bioinformatics Pvt Ltd (A company launched by alumni of the centre and incubated in the centre).

10. Databases/ Software packages developed CGRex: A Software for generating CGR Signatures of Biosequences Developed with DIT, Govt of India support)

Contributions to International Data Banks [1] Achuthsankar S Nair , Sugunan V S, Amjesh R, Prasanth V, Theoretical model for the structure of HCV NS3 Protease (Indian Strain), Brookhaven Protein Data Bank, Pdb id :2ijs, Released on 17 Oct 2006. [2] Achuthsankar S Nair , Amjesh R, Theoretical model for the structure of Cholestryl Ester Transfer Protein, Protein Model Data Base, Pmdb id: pm0074708, Released on 30 Oct 2006. [3] Amjesh R., Achuthsankar S. Nair & Sugunan V.S. Homo sapiens isolates of 1 to 19 microRNA, complete sequence. Submitted to NCBI Database. Accession Code: EF629327, EF629328, EF629329, EF629330, EF629331, EF62932, EF629333, EF629334, EF629335, EF629336, EF629337, EF629338, EF629339, EF629340, EF629341, EF629342, EF629343, EF629344, EF629345. [4] Amjesh R, Achuthsankar S Nair, Sugunan V.S, Sequence Alignment of Hepatitis C Virus Indian Strain, European Molecular Biology Laboratory. Align Id-001119.

11. Papers published or presented in the conferences with reference [1] Achuthsankar S. Nair and T. Mahalakshmi " Are categorical periodograms and indicator sequences of genomes spectrally equivalent?, In Silico Biology, International Journal of Computational Molecular Biology , IOS Press, 6(2006), pp 215-222. [2] Achuthsankar S. Nair and Sivarama Pillai Sreenadhan, A coding measure scheme employing electron-ion interaction pseudopotential (EIIP), Bioinformation 1(6), 2006, pp. 197-202. [3] Achuthsankar. S. Nair and Sreenadhan.S, An improved digital filtering technique using nucleotide frequency indicators for locating exons. Journal of the Computer Society of India, Vol. 36, No.1 , 2006, pp 60-66. [4] Achuthsankar S Nair, Combatting Diseases with Computer-Aided Drug Design, IEEE Potentials, Vol 25, No. 6 Nov/Dec 2006, pp 39-41, [5] Gopikrishnan, Achuthsankar S. Nair and S. Sivakumar, "Optimization in DNA Microarray Manufacture", Conference proceedings, NCTT 2006, Thiruvananthapuram, Volume II, pp. M23-M28, November 2006. [6] Achuthsankar S Nair , Amjesh R, Sugunan V.S , Homology Modeling as a tool for Drug Action Analysis – A study on HCV NS3 Protease, Proceedings of the Kerala Science Congress, 2007.

485 [7] Achuthsankar S. Nair, Koshy P. Vaidyan, "Homology Modeling of Myoglobin using Adaptive Neurofuzzy Systems", Proceedings of International Conference on Bioinformatics and Computational Biology ( BIOCOMP 2006), Las Vegas, USA, June 26 – 29, 2006, pp. 24-30. [8] Koshy P. Vaidyan, Achuthsankar S. Nair, "Applying Nonlinear Control system Principles to Structural Bioinformatics", National Seminar on Bioinformatics and Computational Biology at Banaras Hindu University, Varanasi, March, 2006. [9] Koshy P. Vaidyan, Achuthsankar S. Nair, "Protein Sequence to Structure Mapping as a Causal, Non-linear System: A Study Using Adaptive Neuro Fuzzy Techniques", Proceedings of Kerala Science Congress, January 29 – 31, 2006, Thiruvananthapuram, pp. 288 – 290. [10] Achuthsankar S. Nair and Sreenadhan S., "Design of an anti-notch digital filter for exon identification from genomic signals", Paper presented at the National Seminar and Workshop on Bioinformatics and Computational Biology Benarus Hindu University, Varanasi, March 2006 22-24, [11] Achuthsankar S Nair & T Mahalakshmi, Visualisation of Genomic Data Using Inter- neucleotide Distance Signals, Paper presented in the IEEE International Workshop on Genomic Signal Processing, Bucharest, July 2005. [12] Achuthsankar S Nair & T Mahalakshmi, GSP Using Bi-neucleotide Distance Signals, Paper presented in the 13th International Conference on Advanced Computing and Communications, Coimbatore, December 2005. [13] T Mahalakshmi & Achuthsankar S Nair, Digital Signal Processing of Categorical Series Data in Bioinformatics, Proceedings of the Kerala Science Congress, January 2006. [14] Aneesha M. S, Vidhya R. V, Sugunan V. S, Achuthsankar S. Nair. Comparative study of genomes of Hepatitis C virus and Chikungunya virus. Proceedings of Bioinformatica Indica’08, Jan17-19. p: 76. [15] Anu James, Sukanta Mondal, Suryanarayanarao Ramakumar. A comparative sequence- structure-function analysis of molluscivorous and piscivorous δ-conotoxins. Proceedings of Bioinformatica Indica’08, Jan17-19. p: 69. [16] Sreenadhan S, Mahalekshmi T, Koshy Vaidyan, Betsy Sheena Cherian, Achuthsankar S. Nair. Genomic signal processing-contributions of Kerala University computational biology research group-a brief overview. Proceedings of Bioinformatica Indica’08, Jan17-19. pp: 35-42. [17] Vinod Chandra S. S, Betsy Sheena Cherian. Exploring features of RNA sequences. Proceedings of Bioinformatica Indica’08, Jan17-19. p: 72. [18] Subesh M. P, Umesh P, Gopakumar G, Achuthsankar S. Nair. Computational Approach to the study of the significance of mitochondrial DNA mutations causing diseases and identification of haplogroups. Proceedings of Bioinformatica Indica’08, Jan17-19. p: 66. [19] Sithara S, Gopakumar G, Achuthsankar S. Nair. Fractal analysis of genomic sequences. Proceedings of Bioinformatica Indica’08, Jan17-19. p: 75. [20] Keerthy A. S, J. S. (Pat) Heslop-Harrison, Achuthsankar S. Nair. Heterozygosity and allelic variation within and between Musa accessions. Proceedings of Bioinformatica Indica’08, Jan17-19. p: 71. [21] Renu S, Manoj Kumar, TejP. Singh, Achuthsankar S. Nair, Punit Kaur. In silico design of peptide inhibitors for Mycobacterium tuberculosis based on the structure of dihydrodipicolinaste reductase. . Proceedings of Bioinformatica Indica’08, Jan17-19. p: 54. [22] Suma L. S, Smitha Dharan, Abdul Nazeer K. A, Microarrary data analysis using non negative matrix factorization with sparseness constraint. Proceedings of Bioinformatica Indica’08, Jan17-19. p: 44. [23] Smitha Dharan and Achuth Sankar S. Nair, Non- Negative Matrix Factorization for Clustering Gene Expression Data from Microarray Digital Images, In National Conference on Recent Trends in Optoelectronics and Laser Technology, p.44-45, Apr 9-11, 2007.

12. Initiation of R&D activities in Bioinformatics. The Centre has 6 Full Time research students working in the areas mentioned in Section 2. Also one DIT funded project on Development of one open Source software – CGREx (Chaos Game Representation Explorer)

13. Details of Training / Workshop organized and total no. of user trained.

486 The Centre organized a series of training programmes / Workshops in the field of Bioinformatics.

• Workshop on Biosequence Analysis on 15th of June 2007. (40 participants). • One day Seminar on Scilab on 20th July, 2007 (65 participants). • A Seminar cum workshop on Molecular Visualization Softwares on 17th August, 2007(45 participants). • The Centre in association with Sree Chithira Thirunal Engineering College, Trivandrum, organized a seminar cum workshop in Bioinformatics on 6–7 November, 2007 and was attended by over 300 delegates. • A seminar cum workshop on Perl on 30 Nov (50 participants) • A seminar cum workshop on Hidden Markov Models on 1st Dec (20 participants) • Bioinformatica Indica 08: International Symposium on Computational Biology, Bioinformatics and Synthetic Biology. This was a major event with about 40 institutions from India and abroad represented:

14. Impact shown by your centre on the growth of biotechnology and allied areas. In this you may highlight the details like number of paper published/ number of papers published with the help of your centre, how your centre is promoting various activities of your organization and neighboring institutions, manpower trained, tools developed, patents & copyrights acquired and other services offered etc.

Already noted in Sections 4, 5C, 11 and 13.

15. Future activities. • To continue routine training activities. • To organize Bioinformatica Indica on a yearly basis* • To launch an open-source e-content on Bioinformatics* • Organize a International workshop on E-cell. • To launch a 3-6 month training programme for students*, whereby students will be given stipend and trained to work on chosen research/industry problem. (*subject to DBT support)

Additional Details: Name of the Coordinator: Dr.Achuthsankar S. Nair Postal Address: Centre for Bioinformatics, University of Kerala, Karyavattom Campus, Thiruvananthapuram 695581, Kerala Phone Number: +914712412759 Email: [email protected] Website: www.achu.keraluniversity.edu

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