The Biotechnology Information System Network in India PROCEEDINGS OF THE XXTH ANNUAL COORDINATORS’ MEETING
FOCAL THEME: ONLINE RESOURCES IN BIOINFORMATICS February 03-04, 2009
Bioinformatics Centre North-Eastern Hill University Shillong 793 022
Department of Biotechnology Ministry of Science and Technology Government of India The Biotechnology Information System Network in India Proceedings of the XXth All India BTISnet Coordinators’ Meeting February 03-04, 2009
Venue
Bioinformatics Centre North-Eastern Hill University Shillong 793 022
Department of Biotechnology Ministry of Sience and Technology Government of India Venue: Multi Use Convention Centre, NEHU North Eastern Hill University, Shillong Date: 3rd & 4th February 2009 PROGRAMME TUESDAY 03th FEBRURARY 2009
09:00-9:30 hrs Registration:
9:30-10:32 hrs Inaugural Session:
9:30 Arrival of the Chief Guest 9:30-9:32 National Anthem 9:32-9:35 Presentation of Bouquet 9:35-9:40 Welcome : Prof. Pramod Tandon, Vice Chancellor, NEHU 9:40-9:50 About BTISNet Programme & Brief Report of Activities during 2008-’09 : Dr. T. Madhan Mohan, Advisor, DBT, New Delhi 9:50-10:05 Keynote Address : Prof M. Vijayan, Chairman, Task Force 10:05-10:25 Inaugural Address by the Chief Guest : His Excellency, The Governor of Meghalaya, Shri. R.S. Mooshahary 10:25-10:30 Vote of Thanks : Prof. Veena Tandon, Deputy Coordinator, Bioinformatics Centre, NEHU, Shillong 10:30-10:32 National Anthem
10:32-11:00 hrs Tea Break
Session I
11:00-13:30 hrs Online Resources in Bioinformatics
Chair : Prof. M. Vijayan, IISc, Bangalore Rappoteur : Dr. Gulshan Wadhwa, PSO, DBT
Speakers (10 Minutes each)
1. Dr. P. Balasubramaian - TNAU, Coimbatore. 2. Dr. P. Gautam - Anna University, Chennai 3. Dr. Sanjay Londhe - Pune University, Pune 4. Dr. P. Chakravarti - Bose Institute, Kolkatta 5. Dr. P. P. Mathur - Pondicherry University, Puducherry 6. Dr. D. Mohanty - NII, New Delhi 7. Dr. K. Sekar - IISc, Bangalore 8. Dr. B. C. Harinath. - MGIMS, Sevagram 9. Dr. Subhasis Mukhopadhyay - University of Calcutta, Kolkatta 10. Dr. R. Keshavchandran - KAU, Thrissur 11. Dr. Prasad A. Wadegaonkar - SGBAU, Amravati 12. Dr. P N Krishnan - TBGRI, Thiruvanthapuram 13. Mr. Devendra K. Biswal - NEHU, Shillong 14. Dr. M. Balakrishnan - CARI, Portblair 15. Dr. Sudershan Kumar - NBRI, Lucknow 16. Dr. George V. Thomas - CPCRI Kasaragod. 17. Dr. Gitanjali Yadav - NIPGR, New Delhi.
13:30-14:30 hrs LUNCH
Session II
14:30-15:30 hrs Online Resource in Bioinformatics Presentation by Coordinators (Contd. …..)
Chairperson : Prof. Pramod Tandon, VC, NEHU, Shillong Rappoteur : Dr. Peyush Goyal, SSO-II, DBT
Speakers (10 Minutes each)
18. Dr. S. M. H. Qadri - CSRTI, Mysore. 19. Dr. Santhosh J. Eapen - IISR, Calicut 20. Dr. L. Uma - BU, Tiruchirappalli 21. Dr. Soma Marla - GBPUAT, Pantnagar 22. Dr. Desh Deepak Singh - IIAR, Gandhinagar 23. Dr. Sathish Mundayoor - RGCB, Thiruvananthapuram 24. Dr. Devendra S. Chauhan - JALMA, Agra 25. Dr. Probodh Borah - CVS, AAU, Guwahati 26. Dr. S. Karutha Pandian - Alagappa University, Karaikudi 27. Dr. D.K. Sharma - Gauhati University, Guwahati 28. Mrs. Kavitha B. - M. S. C., Bangalore. 29. Dr. S. Rajarajan - Presidency College, Chennai. 30. Dr. Alpana Seal - Kalyani University, Kalyani 31. Dr. C. S. Kumar - Sri KU, Anantpur 32. Dr. Sunil Thorat - IBSD, Imphal
16:30-17:00 hrs TEA
Session III
17:00-17:30 hrs Panel Discussion on Networking of Online Bioinformatics Resources Dr. M. Vijayan Dr. Pramod Tandon Dr. M. R. N. Murthy Dr. Alok Bhattacharya Dr. B. Jayaram Dr. T. Madhan Mohan 17:30-18:00 hrs A Report on the Bioinformatics Publications from India - Dr. S. Mallick, CDRI, Lucknow Bioinformatics Application & Resource Facility - Dr. Rajendra Joshi, C-DAC, Pune
WEDNESDAY 04th FEBRUARY 2009
10:00-12:00 hrs Session IV
Felicitation Ceremony
Special Lectures
Chairman : Dr. V. M. Katoch, Secretary, MoH & DG, ICMR Rappoteur: Dr. Arnab Sen, NBU, Siliguri
1. Dr. V. M. Katoch (Plenary Lecture ) 2. Dr. Akhilesh Tyagi, UDSC, New Delhi 3. Dr. Alok Bhattacharya, JNU, New Delhi 4. Dr. G. P. S. Ragahava, IMTECH, Chandigarh 5. Dr. B. Jayaraman, IIT Delhi 6. Dr. S. Ramakumar, IISc. Bangalore 7. Dr. M.R.N. Murty, IISc, Bangalore
11:00-11:30 hrs Tea Break
8. Dr. D. Velumurgan, Madras University, Chennai 9. Dr. K. Veluraja, M.S. U., Tirunelvelli 10. Dr. D. Sundar, IIT, Delhi
12:00-13:30 hrs Concluding Session
Presentations of the Chairperson of each sessions
Concluding Remarks and recommendations
Vote of Thanks, Sh. Nand Kishore, Deputy Secretary, DBT
LUNCH
North-Eastern Hill University Shillong 793 022 Professor Pramod Tandon Vice Chancellor Work: +91 364 255 0101, 272 1001-4 Home: +91 364 2550 0100, 255 0074 Fax: +91 364 255 0076 Email: [email protected]/[email protected]
January 28, 2009
Message
It gives me immense pleasure to note that the Department of Biotechnology (DBT), Govt. of India sponsored XXth All India Biotechnology Information System Network (BTISnet) Coordinators’ Meeting is being organized by the Bioinformatics Centre (BIC), NEHU during February 3-4, 2009 at Shillong. Moreover, it has been a year of many forward-thinking and positive changes at NEHU and I am quite delighted to learn that our BIC is organizing this event after the successful completion of the mega event of Indian Science Congress just a month ago. Outstanding advances in genetic science and technology have been made in the last five decades since the landmark discovery of DNA double helix in April 1953. The completion of the Human Genome Project (HGP) marked the dawn of a bold new era—the era of the genome in biology and medicine. The historic sequencing of the human genome was a scientific and technical achievement unrivaled in molecular biology – a feat made possible with the aid of a new biology with application of Information Technology namely “In Silico Biology”. Though surprising, the HGP traces its roots to a 1986 initiative at the US Department of Energy and the same year DBT, Govt. of India initiated the BTIS net with a view to providing state-of-the-art facilities and high throughput technologies in the area of biological sciences by establishing COEs, DICs, Sub DICs and BIFs and thereby providing skilled manpower, cutting edge techniques and technologies, and networking with professional researchers across the country. The newly constituted North-East Bioinformatics network (NEBInet) with some 25 odd centres in the north-eastern states is again a milestone achieved by DBT and a welcome opportunity for budding researchers in this part of the country. Not only this BTIS net promotes a scientific temperament among the researchers of the country but also plays a major role in promoting kinship and connections in our profession and strengthening the sense of community among BTISnet members. Everyone’s participation in and support of BTISnet is highly valued. The Coordinators’ meeting has been examining the results of this network and is using it as a basis for strategic planning and decision-making for the future. I wish to thank everyone involved in this important event and also wish the organizers all the very best for their enduring efforts to make the event a grand success.
(Pramod Tandon) XXth All India BTISnet Coordinators’ Meeting February 03-04, 2009 Contents
Centres of Excellence (COE) Bose Institute, Kolkata ...... 1 Indian Institute of Science, Bangalore ...... 3 Jawaharlal Nehru University ...... 4 Madurai Kamraj University, Madurai ...... 6 University of Pune ...... 9 Distributed Information Centres (DICs) Anna University, Chennai ...... 12 Centre for Cellular & Molecular Biology, Hyderabad ...... 14 Indian Agricultural Research Institute, New Delhi...... 16 Institute of Molecular Technology, Chandigarh ...... 18 Kerela Agriculture University...... 22 M.S. University of Baroda ...... 24 National Brain Research Centre, Manesar ...... 26 National Institute of Immunology, New Delhi ...... 30 Pondicherry University, Pondicherry ...... 32 University of Calcutta, Kolkata ...... 34 Sub-Distributed Information Centres (Sub-DICs) Advance Centre for Treatment Research and Education in Cancer, Mumbai ...... 34 All India Institute of Medical Sciences, New Delhi ...... 39 Assam Agricultural University, Jorhat ...... 41 Banaras Hindu University, Varanasi ...... 43 Banasthali Vidyapith, Banasthali ...... 45 Barkatullah University, Bhopal ...... 47 Bharathidasan University, Tiruchirapalli ...... 50 Biotech Consortium India Limited, New Delhi ...... 52 Biotech Park in Biotechnology City, Lucknow ...... 55 Birla Institute of Scientific Research, Jaipur...... 57 Birla Institute of Tehnology, Ranchi ...... 59 Central Agricultural Research Institute, Port Blair ...... 61 Central Drug Research Institute, Lucknow ...... 64 Central Institute of Fresh Water, Bhubaneshwar ...... 66 Central Institute of Medicinal and Aromatic Plants, Lucknow ...... 69 Central Plantation Crops Research Institute, Kasaragod ...... 72 Central Sericultural Research and Training Institute, Mysore ...... 73 CSK Himachal Pradesh Krishi Vishvavidyalaya, Palampur ...... 76 Dr. Y. S. Parmar University of Horticulture and Forestry, Solan...... 78 Devi Ahilya Vishvavidyalaya, Indore ...... 80 Engineering College, Raipur ...... 82 G. B. Pant University of Agriculture and Technology, Pant Nagar ...... 84 Guru Nanak Dev University, Amritsar ...... 85 Himachal Pradesh University, Shimla ...... 86 Indian Intitute of Spices Research, Calicut ...... 88 Indian Institute of Technology, Delhi ...... 90 Indian Institute of Technology, Kharagpur ...... 94 Indian Veterinary Research Institute, Izatnagar ...... 96 Institute of Life Sciences, Bhubaneshwar...... 99 Institute of Bioresources & Sustainable Development, Imphal ...... 100 Indian Institute of of Advance Research, Gandhinagar ...... 102 Indian Institute of Integrative Medicine, Jammu ...... 104 Karnataka Vetirinary, Animal & Fisheries Sciences, Mangalore ...... 106 Mahatma Gandhi Institute of Medical Sciences, Wardha ...... 108 National Botanical Research Institute, Lucknow ...... 110 National Dairy Research Institute, Karnal ...... 112 National Institute of Plant Genome Research, New Delhi ...... 114 National Institute of Oceanography, Goa ...... 116 National Institute Of Technology, Raipur...... 118 North-Eastern Hill University, Shillong...... 120 Punjab Agricultural University, Ludhiana ...... 123 Rajiv Gandhi Centre for Biotechnology, Trivandrum ...... 125 Sikkim State Council of Science and Technology, Sikkim ...... 127 T.M. Bhagalpur University, Bhagalpur ...... 129 Tamil Nadu Agricultural University, Coimbatore ...... 131 Tamilnadu Veterinary and Animal Science University, Chennai ...... 133 Tropical Botanical Garden and Research Institute, Thiruvananthapuram ...... 136 University of Kashmir, Kashmir ...... 138 Bioinformatics Infrastructure Facility (BIF) for Biology Teaching Through Bioinformatics (BTBI) Alagappa University, Karaikudi ...... 138 Assam Agricultural University, Guwahati ...... 142 Assam University, Silchar ...... 145 Berhampur University, Berhampur...... 147 Bharathiar University, Coimbatore ...... 148 CCS Haryana Agricultural University, Hisar ...... 151 Cotton College, Guwahati ...... 153 College of Veterinary Sciences & Animal Huabandry, CAU, Aizawl ...... 154 Dhanamanjari College of Science, Imphal ...... 156 Dibrugarh University, Dibrugarh...... 157 Dr. B. R. Ambedkar Center for Biomedical Research, Delhi ...... 158 Fakir Mohan University, Balasore...... 161 Forest Research Institute, Dehradun ...... 163 Gauhati University, Guwahati ...... 166 Guru Jambheshwar University of Science & Technology, Hisar...... 167 HNB Garhwal University, Garhwal...... 168 Indian Institute of Technology, Madras ...... 171 Indira Gandhi Krishi Vishwavidyalaya, Raipur ...... 173 National JALMA Institute for Leprosy & other Mycobacterial Diseases, Agra ...... 175 Jamia Hamdard University, Hamdard Nagar...... 176 Jamia Millia Islamia University, New Delhi ...... 177 Jiwaji University, Gwalior ...... 179 Kakatiya University, Warangal ...... 181 Kannur University, Kannur ...... 183 Karnataka State Women University, Bijapur ...... 186 XXth All India BTISnet Coordinators’ Meeting February 03-04, 2009
Karnataka University, Dharwad ...... 187 Kumaun University, Nainital ...... 189 Lady Doak College, Madurai ...... 191 Madras Christian College, Chennai ...... 193 Maharani Lakshmi Ammanni College for women, Bangalore ...... 195 Maharani's Science College for Women, Bangalore ...... 197 Maharashtra Animal & Fishery Science University, Nagpur...... 199 Manipur University, Imphal ...... 200 Manonmaniam Sundaranar University, Tirunelveli ...... 201 Maulana Azad National Institute of Technology, Bhopal ...... 203 Mizoram University, Aizawl ...... 206 Narendra Deva University of Agriculture & Technology, Faizabad ...... 207 National Institute of Pharmaceutical Education and Research, Chandigarh ...... 208 National Institute of Technology (NIT), Rourkela ...... 210 North-East Institute of Science and Technology, Jorhat ...... 212 North Eastern Regional Institute of Science & Technology, Nirjuli ...... 213 North Orissa University, Baripada ...... 214 Orissa University of Agriculture & Technology, Bhubaneshwar ...... 215 Presidency College, Chennai ...... 218 Rajiv Gandhi University, Itanagar ...... 219 St. Anthony’s College, Shillong ...... 221 St. Aloysius College, Mangalore...... 223 St. Edmund’s College, Shillong ...... 224 Sant Gadge Baba Amravati University, Amravati ...... 225 Sardar Vallabh Bhai Patel University of Agriculture and Technology, Meerut ...... 227 Sri Krishnadevaraya University, Anantapur ...... 229 S. Kula Women’s College, Manipur ...... 232 Sher-e-Kashmir University of Agricultural Sciences & Technology of Kashmir ...... 233 Sri Padmavati Mahila Visvavidyalayam, Tirtupati...... 235 Shri Mata Vaishno Vevi University, Katra (J&K) ...... 237 Sri Sathya Sai University, Prasanthi Nilayam...... 238 Sri Venkateswara Institute of Medical Science, Tirupati ...... 239 Tezpur University, Tezpur ...... 242 Tripura University, Tripura ...... 244 University of Allahabad, Allahabad ...... 245 University of Calicut, Kerela ...... 248 University of Hyderabad ...... 250 University of Jammu, Jammu ...... 252 University of Kalyani, Kalyani ...... 255 University of North Bengal, Siliguri ...... 258 University of Rajasthan, Jaipur...... 261 Vidyasagar University, Midnapur ...... 263 West Bengal University of Technology, Kolkata ...... 267 XXth All India BTISnet Coordinators’ Meeting February 03-04, 2009 Bose Institute, Kolkata Coordinator: Professor Pinak Chakrabarti The Bioinformatics Centre of Bose institute, established in 1988 as one of the ten nodal centres under the programme, BTIS of the Department of Biotechnology, has been recognized in 2004 as a “Centre of Excellence” in Bioinformatics to under- take research in the following areas: modeling of proteins structures; molecular interaction and docking; drug design; chromosomal dynamics; stress biology of plants; functional genomics and host-pathogen interactions.
Major activities of the Centre during 2008 During 2008 one student of the Centre, Tanya Banerjee was awarded the PhD degree of Jadavpur University. Dr. S. Basak received the Nilratan Sirkar Award of the Institute, 2007 for his work in bioinformatics The Centre organized a National Workshop on Protein folding and Bioinformatics (March 4-5, 2008). Eight students were trained for six months under the traineeship programme. Based on the work carried out at the Centre sixteen papers have been published in reputed inter- national journals. A number of webservers (such as ProFace, IntGeom, ConfPlot, ContPlot) have been developed and are available at: http://www.boseinst.ernet.in/resources/bioinfo/stag.html. To develop awareness in the subject, scientists from the Centre have delivered lectures at different institutes in the eastern region of the country. Presently, one Research Scientist, one Research Associate, nine JRFs/SRFs and six trainees are working in the COE in Bioinformatics.
Papers published in international journals in 2008 1. Evolutionary constraints on hub and non-hub proteins in human protein interaction network: insight from protein connectivity and intrinsic disorder. 2008 B. Manna, T. Bhattacharya, B. Kahali and T. C. Ghosh Gene (in press). 2. Differential Selective Constraints Shaping Codon Usage Pattern of Housekeeping and Tissue Specific Homolo gous Genes of rice and Arabidopsis. 2008. Mukhopadhyay, P., S. Basak and T. C. Ghosh. DNA Research 15: 347-356. 3. Exploring the evolutionary rate differences of party hub and date hub proteins in Saccharomyces cerevisiae protein-protein interaction network 2008. B. Kahali, S. Ahmad and T. C. Ghosh. Gene 429: 18-22. 4. Nucleotide Triplet Based Molecular Phylogeny of class-I and class II Aminoacyl t-RNA Synthetase in three Do- main of Life Process: Bacteria, Archaea and Eukarya. 2008. Mandal, U.K., B. Das, T.C. Ghosh, A. Sen and A.K. Bothra. J Biomol Struct & Dynamics 26: 321-328. 5. Delving deeper into the unexpected correlation between gene expressivity and codon usage bias of Escherichia coli genome. 2008. Kahali, B., S. Basak., and T.C. Ghosh. J Biomol Struct & Dynamics 25: 655-662. 6. Demethylation of (Cytosine-5-C-methyl) DNA and regulation of transcription in the epigenetic pathways of cancer development. 2008. Patra, S.K., A. Patra, F. Rizzi, T. C. Ghosh, S. Bettuzzi. Cancer Metastasis Rev. 27: 315-334. 7. Structural interaction between DsrE, DsrF and DsrH in Dsr operon. 2008. Bagchi, A., and T.C. Ghosh. A. Bagchi and T.C. Ghosh. J Biomol Struct & Dynamics 25: 517-524. 8. Cavities and atomic packing in protein structures and interfaces.(2008). Sonavane, S. and Chakrabarti, P. PLoS Comput. Biol. 4(9): e1000188 9. pi-Turns: types, systematics and the context of their occurrence in protein structures. (2008). Dasgupta, B. and Chakrabarti, P. BMC Structural Biology 8: 39 10. Dissection, residue conservation, and structural classification of protein-DNA interfaces. Biswas S, Guharoy, M and Chakrabarti P. Proteins (in press). 11. Structural segments and residue propensities in protein-RNA interfaces: comparison with protein-protein and protein-DNA complexes. (2008). Biswas S, Guharoy, M and Chakrabarti P. Bioinformation 2(10), 422-427 12. Protein-protein interaction and quaternary structure. (2008). Janin, J., Bahadur, R.P. and Chakrabarti, P. Q. Rev. Biophys. 41: 133-180. 13. Temperature-induced unfolding pathway of a type III antifreeze protein: insight from molecular dynamics simulation. 2008. Kundu S, Roy D. J Mol Graph Model. 27: 88-94.
1 Centres of Excellence (COEs)
14. Conformational preferences of a short Aib/Ala-based water-soluble peptide as a function of temperature. (2009). Proteins (in press). Banerjee, R., Chattaopdhyay, S., Basu, G. 15. Coulomb energies of protein-protein complexes with monopole-free charge distributions. (2009). Das, M., Basu, G. J Mol Graph Model. (in press). 16. Three-dimensional Models of NB-ARC Domains of Disease Resistance Proteins in Tomato, (2008). Journal of Biomolecular Structure & Dynamics, 25: 357-372. Chattopadhyaya R and Pal A Arabidopsis, and Flax.
Future activities On-going research on understanding protein-protein interactions, the code relating protein sequence to its native fold, evolutionary systems biology, etc. would continue in the coming year. Webservers are being planned for displaying evolu- tionary conservation of protein interfaces. An international collaborative work has been initiated with Universite Paris-Sud, Orsay, France and the one between T.C. Ghosh and G. D’Onofrio of Stazione Zoologica, Italy would continue.
Contact 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], or [email protected] Website: www.boseinst.ernet.in/bic Name of Contact Person(s): Prof. Pinak Chakrabarti (Email: [email protected])
2 XXth All India BTISnet Coordinators’ Meeting February 03-04, 2009 Indian Institute of Science, Bangalore Coordinator: Prof. S. Ramakumar Research Activities An area of focus at the Centre is in systems biology. Towards this systems–level modelling and simulation of mycobacterial metabolism has been carried out which has provided insights into key reactions and critical proteins in the bacterium. Protein-protein interactions at a genome scale have been identified and abstracted as a network, which has then been used for simulating knock-outs through systematic node and edge deletions. This analysis has provided information about criti- cal nodes to maintain the complex network and consequently helped significantly in identifying critical points of possible therapeutic intervention. Besides obtaining a birds’ eye-view of mycobacterial metabolism and the roles played by the components individually, the analyses have been applied to gain fundamental insights into various aspects of drug discov- ery such as target identification and target validation, which is believed to aid significantly in discovering new rational drugs. A second area of focus is development of algorithms for sequence and structural bioinformatics. An algorithm (FAIR) has been developed to find all distant repeats in a protein sequence, which will be useful for establishing correlations of the repeats with respect to their function and three-dimensional structure during the evolutionary process. Further, algorithms are being developed for finding distant repeats in a single and a pair of protein sequences. Also, web based internet computing servers are developed (PSAP: Protein Structure Analysis Package and CSSP: Consensus Secondary Structure Prediction) for analyzing the three-dimensional protein sequences and structures. In addition, the focus of the centre lies in solving and analyzing protein structures of biological relevance. A geometric clustering algorithm using backbone phi,psi angles to group conformationally similar peptide fragments of any length, has also been developed. By labeling each fragment in the cluster with the level-specific Gene Ontology ‘molecular function’ term of its protein, we are able to compute statistics for molecular function-propensity and p-value of individual fragments in the cluster, which ultimately useful in inferring function from structure. Two new algorithms for detecting binding cavities in protein structures (POCKETDEPTH) and for comparing binding sites at the structural level (POCKETMATCH) have also been developed. Together they are useful in identifying all possible binding pockets in a protein structure and comparing thousands of such pockets in available structures to address a variety of questions related to ligand binding, ligand specificity, ligand design and inferring function from sequence and structure. Bioinformatics approaches have been used to elucidate the extent of specificity of conotoxins towards nicotinic acetylcholine receptor subtypes and Kv1.6 channel, which provides a rationale for the relatively high specificity and binding mode of the pl14a conotoxin to Kv1.6 channel, leading to a hypothesis that different selectivity profiles against subtypes of
the potassium channels exist for the conopeptides. A molecular dynamics study of phospholipase A2, explains crystallo- graphically observed role of active site residues and that of catalytically important calcium ion, providing insights into the mechanistic details of this protein.
Sekar, K. Ph.D. Bioinformatics Centre (Centre of Excellence in Structural Biology and Biocomputing) Raman Building Indian Institute of Science Bangalore 560 012 INDIA
3 Centres of Excellence (COEs) Jawaharlal Nehru University Coordinator: Prof. Indira Ghosh 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 Infor- mation 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 are 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 objec- tive of human resource development activities and research in frontier areas of computational biology 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. Last year we have been sanctioned a UOPE project from UGC and built another facility Center at our school , High Performance Computing Center (HPCC) which will support the need of large scale data analysis , Systems Biology and simulation of large systems not only at JNU but also to northern Indian academia.
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. Joining of new professor since last year, center has started focusing development of the Chemoinformatics based drug designing tools.
Area of Specialization of the Centre • Computational Comparative genomics • Large scale data analysis • Systems biology • Evolutionary mechanisms • Computer based drug discovery • Computational Genomics • Development of Tools in Bioinformatics Major activities of the centre during the year 2008-09 • Faculty recruitment: 1 professor, 1 Asst. Professor and 1 Teaching Assistance joined makes total 12 faculties for 2 courses, M.Tech in Computational and system Biology and Ph.D/Pre-Ph.D in Computational Biology and Bioinformatics. • Setting up of a high performance computing facility : High Performance Computing Center (HPCC) as part of the UPOE, JNU has been established at our School during last year with joint collaboration with CDAC, Pune. The facility has been designed for the usage of the computational biology and large scale system level simulation community at JNU, New Delhi and other North Indian states. UPOE HPC Cluster has been installed and maintained by C-DAC. It has 64 nodes with 4 (dual core +dual socket) processors each having 2.6GHz. Its peak performance is 1.3 Teraflops and the technology which is used to build this cluster is ROCKS version 4.3 and the scheduler used is Sun Grid Engine. In order to provide the low latency, the separate switches for MPI, Storage and IPMI has been used in this cluster, also the total available storage is 4TB. Already exte:nsively used by Bioinformaticians, Biotechnologist and Physicist at JNU and at other Universities of Allahabad, Rajasthan etc. • First batch of six students h:ave passed out in our M.Tech program in Computational and Systems Biology. • Seven Ph.D students have submitted thesis and 5 have received their Ph.D degree in Computational Biology and Bioinformatics run by the center. • Hosting a number of visitors (1 fulbright visiting faculty), holding training programs(2), workshops( 4) and lectures(10). 4 XXth All India BTISnet Coordinators’ Meeting February 03-04, 2009
• Research in Bioinformatics in the fields like finding new molecules as potential drugs for Entamoeba histolytica, MD Simulation on Viral Proteins and inhibitor designing, Prediction of miRNAs , Dynamics of intracellular oscillators etc. are highlighted in this year. • In 2008 17 publications in reputed journals and 1 book was contributed by the faculties. • In addition to UOPE and 2 major existing projects (1 DBT and 1 CSIR), three more projects (2 MCIT and 1 European Commission) have been sanctioned to our school. • During 2008 one faculty received Indo-US research fellowship , 2 faculties received J.C.Bose Awards and 1 faculty awarded with membership of Third world Academy of Science, Italy.
Infrastructure facilities in the Bioinformatics Centre • High Performance Computing Center (HPCC) 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 node 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 is part of the BIO-GRID project of DBT with a ERNET connection of 2 Mbps connecting all major Bioinformatics Centre, and a shared internet bandwidth of 4Mpbs. • Implemented Video Conferencing as a method to share teaching and other resources and the EDUSAT Education facilities program cater to JNU and other institute regularly. • 2 M.Tech labs each equipped with 25 PC are organized for the teaching and training in addition to 2 research fellows laboratory has been reorganized. • 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, SYBYL 6.5,Chem Office, SigmaStat 2.0.3, SigmaPlot, MATLAB – Unix & Windows, AMBER 7, Chamm32, Scrodinger, FLEXx, DRAGON, Mathematica, Open Eye and Biobase. • Number of SW like ADF , GROMACS and OpenEye which could also be parallelized have been procured and installed on the HPC cluster • In house developed Databases, websites & Software packages are: √ Lunched web site : 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. √ ELAN: http://nldps.jnu.ac.in/bioit/ccbb/elan.html , a server based tools for genome wide analysis of mobile genetic elements have been developed. √ SRF : http://www.imtech.res.in/raghava/srf a Spectral Repeat Finder, Software for finding repeat structures in genomic DNA. √ MGDD : http://mirna.jnu.ac.in/mgdd .The database contains divergent regions present in members of tuberculosis complex. SNPs, repeats causing indels are also included in the database
5 Centres of Excellence (COEs) Madurai Kamraj University, Madurai Coordinator: Prof. S. Krishnaswamy 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. The National High Resolution Graphics Facility started to cater the need of structural biologist and molecular modelers from 1993. The centre initiated the one year Advanced Diploma Course in Bioinformatics in 1996. Now, the centre has got approval from DBT to upgrade the Advance Diploma course in Bioinformatics to an M.Sc program in Computational Biology as a network programme with Anna University and Pondicherry University.
Major research activities in Biotechnology and its related fields at the institution Structural bioinformatics of membrane proteins, Structural Genomics of prophage proteins, Protein aggregation and rela- tion to disease, Genome analysis for non coding RNAs, Computational biology of macromolecular interactions, Molecular Modeling and Drug design, Data mining and text mining, Proteomics and biomarkers discovery, Genetic Engineering and Strain Manipulation of industrially imp ortant microorganisms, Genomics of antibiotic biosynthesis, Plant genetic engineering for disease resistance and stress tolerance, Structural virology, Computer Aided Drug design, QSAR and Virtual Screening, Fungal biotechnology, Xenobiotics
Area of Specialization of the centre: Structural Bioinformatics and Genetic Engineering Major activities of the centre during the year 2007-08 Manpower development: · Ten students completed Advanced Diploma in Bioinformatics (2007-08). · Six PhD students completed till 2007. Eight new students registered. · Participation in local workshops and academic staff training. · In house seminars and workshops related to Bioinformatics. Infrastructure facilities in the Bioinformatics Centre A. Computers and Communication Facility Systems-PCs, SGI systems, Sun workstations, Multiprocessor cluster and server Dedicated 100Mbps RF VSNL connectivity, structured intranet network connecting entire School of Biotechnology 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, CCDC, GOLD etc. All databases and mirrors are available through (http://bicmku.in:8081, http://bicmku.in:8082, http://bicmku.in:8083, http://bicmku.in:8084).
Details about staff members working in the centre: Except for Dr. Sanjeev K. Singh in the teaching staff and Database Admin, Programmer and JRFs, are hired under CoE, rest of the staff have been taken over by the Govt. of Tamil Nadu. Teaching Staff
Educational activities with details of placement Ninety seven students have successfully completed the ADCB till 2008. Eighty percent of the students are placed in differ- ent 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 Connec-
6 XXth All India BTISnet Coordinators’ Meeting February 03-04, 2009 tions, Meta Helix, CCMB, and also in UK, US, Canada, Germany and Switzerland. As part of the CBCS, an elective in Pro- gramming for Computational Biology with a revised syllabus to include perl programming has been introduced for the post- graduate and M.Phil courses.
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.
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. Addis Ababa University, Ethiopia
Papers published or presented in the conferences with reference in 2008 G. 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 6: 3669-3679. Sridhar, J., and Rafi, Z.A. (2008). Functional annotations in bacterial genomes based on small RNA signatures. Bioinformation. 2, 284–295. Sridhar, J., Sathesh-Kumar, S., and Rafi, Z.A. (2008). Small RNA identification in Enterobacteriaceae using synteny and genomic backbone retention II. OMICS. An integrative journal of biology, (in press) An ab initio quantum mechanical drug designing procedure: Applications to design of balanced dual ACE/NEP inhibi- tors Nishi K Rao, Sanjeev Kumar Singh, Arpita Yadav Journal of Molecular Modelling 2008 (in press) 3D-QSAR CoMFA and CoMSIA study on Benzodipyrazoles as CDK2 Inhibitors. Nigus Dessalew and Sanjeev Kumar Singh Medicinal Chemistry, 4, 2008, 313-323. Functional insights by comparison of modeled structures of 18kDa small heat shock protein and it’s Mutant in Mycobacterium leprae E. A Rehna, Sanjeev K. Singh and K. Dharmalingam BIOINFORMATION, 3(5), 2008, 230-234. P.J. Eswari Pandaranayaka, J. Kanagavalli, S R Krishnadas, P. Sundaresan and S. Krishnaswamy. (2008) Over expression and purification of recombinant human myocilin World J. Microbiology and Biotechnology 24: 903-907 DOI: 10.1007/s11274-007-9549-6 S. Manicka, Y. Peleg, T. Unger, S. Albeck, O. Dym, HM Greenblatt, G Bourenkov, V. Lamzin, S. Krishnaswamy, J.L. Sussman (2008) Crystal structure of YagE, a putative DHDPS-like protein from Escherichia coli K12. Proteins 71: 2102-2108. Jeyabalan Nallathambi, Paul Laissue, Frank Batista, Bérénice A. Benayoun, Corinne Lesaffre, Lara Moumné, PJ Eswari Pandaranayaka, Kim Usha, S. Krishnaswamy, Periasamy Sundaresan, Reiner A. Veitia (2008) Differential Functional Effects of Novel Mutations of the Transcription Factor FOXL2 in BPES Patients. Human Mutation 29:E123-E131.
Initiation of R&D activities in Bioinformatics Comparison of Proteome Profile with Transcriptome Profile in E.coli Growing under Oxygen Stress (K. Dharmalingam) Secretome Analysis of Aspergillus niger – a computational approach (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 Sanjeev K. Singh) Structural genomics of prophage proteins (S. Krishnaswamy) Sub classification of HNH domain proteins (S. Krishnaswamy) Structural 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) Pharmacophoric studies on CYP51 inhibitors (Sanjeev K. Singh) Theoretical Studies on Cyclin Dependent Kinase Inhibitors (Sanjeev K. Singh) Modeling Studies on HIV-RT, protease and integrase Inhibitors (Sanjeev K. Singh)
7 Centres of Excellence (COEs)
Details of Training/ Workshop organized and total no. of user trained • Workshop on Data Mining and Structural Bioinformatics during March 17-19, 2008. Twenty participants at tended this workshop. • National workshop on Computer Aided Drug Design in association with Schrodinger, USA during 14-15 Oct., 2008 – Ten participants from all over the country attended the workshop. 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. disser- tations and project reports by the users. The centre has initiated research involving experimental and computational aspects in areas related to proteomics and structural biology.
Future activities Student skill enhancement programme; 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] Website: www.biotechmku.org , http://bicmku.in:8081
Name of Contact Person(s): Dr. Z. A. Rafi Email: [email protected], [email protected]
Dr. Sanjeev K. Singh Email: [email protected], [email protected]
8 XXth All India BTISnet Coordinators’ Meeting February 03-04, 2009 University of Pune Coordinator: Dr. Urmila Kulkarni Kale Review of activities during February 2008-Januray 2009 The Bioinformatics Centre at Pune University is actively involved in Human Resource Development as well as R&D in the area of Bioinformatics. With the help 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, Chemoinformatics and target based drug design. The Centre has also been granted ‘Centre of Excellence’ from MCIT, Govt of India. The centre has been awarded US and Vietnam patent for synthetic peptide vaccine against Japanese encephalitis virus jointly with National Institute of Virology. The conformational epitope prediction (CEP) server developed at the centre has received more than 42 citations in 3 years. It has also been independently evaluated by a group of crystallographers for prediction of epitopes of allergen proteins. Important activities of 2008-09 are revision of syllabus for M.Sc. Bioinformatics and strengthening of interactions with faculty/scientists from university departments/schools, national research laboratories and universities in India and abroad. As part of this initiative, Prof. Vasant Honavar, Professor Computer science & Bioinformatics, Iowa State University, USA has been invited to deliver seminar in the area of Bioinformatics and his long-term association with the centre as the honorary adjunct faculty is currently under process. M.Sc. students passed out from the center are placed in the academic institutions viz. CDAC, IISc, National Institute of Immunology etc. and industries. In fact, 14 students from our center have been employed by a single Bioinformatics company from Pune in 2008, which is a record in itself. The Bioinformatics centre has been serving as a nodal agency for conducting and coordinating the BINC examination insti- tuted by DBT in the year 2005. The centre has developed BINC examination online registration system (http://bioinfo.ernet.in/binc). Twelve students qualified BINC examination in the year 2008. They have been awarded cer- tificates and cash awards of Rs. 10,000 each at the hands of Prof. A.S. Kolaskar, Chairman BINC, Prof. P.B. Vidyasagar, Direc- tor, BCUD, UoP and Dr. Gulshan Wadhwa, Principal Scientific Officer, Department of Biotechnology, Government of India, on November 6, 2008. Out of the 20 candidates, who have cleared BINC examination from 2005-2008, 4 fellows have availed the DBT BINC JRF. This fellowship is given to the Indian nationals, who qualify the BINC examination and register for PhD in Bioinformatics in Indian institutes or Universities. Call for BINC 2009 examination has been published and the exami- nation is scheduled to take place on February 21-22, 2009. University of Hyderabad has been added as the examination centre for BINC 2009. The center has been interacting with various Biotechnology and Bioinformatics companies to provide R&D and other ser- vices. The center is also conducting a six-months certificate course in ‘Clinical Research & Clinical Data Management’ under academia-industry collaboration with Bioinnovat Research Services Pvt. Ltd. This course is being offered at 8 centers all over India and more than 550 students have been trained and certified so far. The successful candidates of CRCDM Jan- June 2008 batch were awarded certificates at the hands of Dr. Subhsh Kapre is the Executive Director of Serum Institute of India, Pune, Prof. A.S. Kolaskar, Former VC. UoP & Dr. C.L. Kaul, former Director of NIPER. The Internet connectivity at the centre was upgraded to 6Mbps (1:1) from 4Mbps since September 2008. Additional com- puter laboratory with 20 desktops was made available for students. Several eminent scientists and delegations from India and abroad viz. Ireland, Finland, Germany visited Bioinformatics centre, University of Pune during 2008. Prof. A. S. Kolaskar has been nominated as Chairman, Biotechnology board, MCCAI. Dr. Urmila Kulkarni-Kale visited the Eijkman Institute, Jakarta, Indonesia to participate as a faculty in the training course on Bioinformatics applied to emerging disease during April 7-18, 2008. Prof. Indira Ghosh, former Director moved to JNU, New Delhi as the Dean, SIT, JNU. Mr. Raghavendra Wadke, Ms. Vijaya Dhahiphale & Mr. V.R. Limbkar underwent training in office administration.
Plan of activities in 2009 • University of Pune would be celebrating Diamond jubilee during February 2009-2010. The centre plans to host a workshop/seminar and conference in the area of Bioinformatics during this period. • Steps have been initiated for induction of faculty and staff at various levels. As a result, one position of I nformation Scientist, which was vacant for several years, has been filled in the year 2008. Servers/databases @ Bioinformatics centre, University of Pune 1. Name of the Resource: Conformational Epitope Prediction (CEP)
9 Centres of Excellence (COEs)
2. Application: (Five Lines): CEP server provides a web interface to the algorithm developed in-house which predicts conformational epitope(s)/antibody binding sites on protein antigens. The epitopes are predicted using 3D structure data of protein antigens, which can be visualized graphically. The algorithm employs structure-based Bioinformatics approach and solvent accessibility of amino acids in an explicit manner. Accuracy of the algorithm was found to be 76. This is one of the first method available for the prediction of conformational epitopes, which is an attempt to map probable antibody-binding sites of protein antigens. The server is being extensively used by the scientific community and has received more than 42 citations during July 2005 to January 2009. The method has also been independently evaluated by the group of crystallographers for Ab-binding sites on allergen proteins and was found to predict the conformational epitopes/Ab-binding sites with high accuracy. 3. Target users: Scientists/Researchers working in the area of vaccine design & development; Bioinformatics com- munity involved in application development in the area of Immunoinformatics 4. Website/Portal address for such resource: http://bioinfo.ernet.in/cep.htm ——————————————————————————————————————— 1. Name of the Resource: VirGen: A Comprehensive Viral Genome Resource 2. Application: VirGen, a comprehensive viral genome resource, which organizes the ‘sequence space’ of viral ge- nomes in a structured fashion. It has been developed with an objective to serve as an annotated and curated data- base for complete viral genome sequences. VirGen employs the sequenced-based Bioinformatics approaches to annotate viral genome records and to identify the ‘alternative names’ of viral proteins, where available. It archives the results of comparisons of genomes, proteomes and individual proteins within and between viral species. VirGen is the first resource to provide phylogenetic trees of viral species computed using whole genome sequence data. The database also houses predicted B-cell epitopes of known viral antigenic proteins in an attempt to link the genome to its vaccinome. The comparative genome analyses would not only help in carrying out the basic research to study the evolution of various strains and species of viruses but would also facilitate and accelerate the applied research by identification of candidates for designing vaccines and anti-viral drugs. 3. Target users: Researchers working in the area of Virology, Biotechnology, Immunology and Bioinformatics 4. Website/Portal address for such resource: http://bioinfo.ernet.in/virgen.htm ——————————————————————————————————————— 1. Name of the Resource: PDB mirror and OCA browser 2. Application: Our Centre had installed the first Indian mirror site of PDB when PDB was housed at Brookhaven National Laboratory (BNL) USA. After the recent takeover of the operations of PDB from BNL to Research Collaboratory for Structural Bioinformatics (RCSB), Rutgers, the State University of New Jersey, we have the most updated version of PDB on our server. The complete RCSB PDB ftp structure is installed and updation is carried out automatically every week. Bioinformatics Centre, University of Pune is the only OCA mirror site in Asia. OCA browser is used for searching, browsing and retrieving PDB files and related data. 3. Target users: Scientists, teachers & students who wish to use PDB 4. Website/Portal address for such resource: http://bioinfo.ernet.in/mirrors/pdb.html ——————————————————————————————————————— 1. Name of the Resource: S-star alliance Bioinformatics educational 2. Application: Bioinformatics educational recourse that provides online education in Bioinformatics. The S* group of teaching institutions have formed a global alliance to provide a global, unified bioinformatics learning environ- ment (GLOBULE) made up of modular courses in the disciplines of genomics, bioinformatics, and medical informatics. Bioinformatics centre at University of Pune is hosting the mirror site. 3. Target users: All those who are interested to get trained in Bioinformatics 4. Website/Portal address for such resource: http://bioinfo.ernet.in/s-star/
10 XXth All India BTISnet Coordinators’ Meeting February 03-04, 2009
Contact Details
Name of the Coordinator: Dr. Urmila Kulkarni-Kale 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] Name of Contact Persons:Dr. Urmila Kulkarni-Kale Email: [email protected]
11 Distributed Information Centres (DICs) Anna University, Chennai Coordinator: Dr. P. Gautam 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 3 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.
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.
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.
Major activities of the centre during the year 2008-09 Research at the Centre is mainly focused in the areas of Molecular dynamics, Molecular modeling, Protein structural analyses, Genomics and Systems Biology.
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: SYBYL ,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 Details about staff members working in the centre:
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
12 Xth All India BTISnet Coordinators’ Meeting February 03-04, 2009
We are working on protein protein interaction networks. The results obtained in this study will be validated through single molecule studies using FRET. Papers published or presented in the conferences 1. Molecular Dynamics Simulations of Lipases Kaushik Ramakrishnan, Vinatha Krishna, Vinod KS, Lakshmi BS, Sharmila Anishetty, Pennathur Gautam. International Journal of Integrative Biology 2(3): 204. (2008). 2. Investigations on Domain Movements of N-Acetyltransferase in Nano Scale Vinatha Krishna, K. S. Vinod Kumar, Sharmila Anishetty, and Gautam Pennathur Journal of Nanoscience and Nanotechnology, Vol.9, 1–4, 2009 3. Protein Protein Interaction Studies : Applications in Nanotechnology Jayanthy J, Sharmila Anishetty, Gautam Pennathur (International Conference on Nano Science And Technology Feb, 2008) Initiation of R&D activities in Bioinformatics: Areas of Research: Molecular dynamics simulations of enzymes, Comparative Genomics, Protein protein interactions, Mutation studies. Ph.D. students: We have seven Ph.D. students in Computational Biology Details of Training/ Workshop organized and total no. of user trained: No. Workshop Title Period No.of Participants 1. Workshop on Sequence Analysis and Molecular Simulation Dec 10th – 13th, 2008 23 Impact shown by your centre on the growth of biotechnology and allied areas. We have published 11 papers in good impact international journals in the past four years. We have also developed an online knowledge base and a server for local structural deformation prediction in proteins. The server is freely available at http://www.annauniv.edu/biotech/tphome/tpindex.html 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]
13 Distributed Information Centres (DICs) Centre for Cellular & Molecular Biology, Hyderabad Coordinator: Dr. K. Guruprasad Work done during the year 2008-09 A model of RDE4, dsRNA binding protein in C.elegans was constructed using comparative protein modeling. The conformations corresponding to amino acid periodicities in protein structures have been analyzed. The environment of ~8000 zinc ions and ~9000 calcium ions in ~3000 proteins have been analyzed and classified according to the number and type of amino acid neighbourhood and solvent interactions in the protein and corresponding sequence templates have been generated. Some well-characterized structural motifs in proteins, such as, helix, strand, turn, beta-hairpin, sheet, beta-alpha-beta, disulfide, psi-loop, have been extracted from proteins in the PDB along with their sequence and other useful details and a beta-version of the database of structural motifs in proteins (DSMP-O) has been generated. We have updated the beta-propellers database (version 3.0). Certain enzymes in the non-mevalonate pathway in Plasmodium falciparum and Mycobacterium tuberculosis have been modeled and specificity pockets defined by interactions with certain small-molecules identified. A method is developed to predict boundary elements in Drosophila genome based on recognition motifs by proteins known to interact with boundary elements. Sequence analysis of defensins was carried out. A program BRM-Parser has been developed that combines the features of BLAST and RepeatMasker in order to study repeats with respect to their occurrence, periodicity and mutation frequency in genome. Detailed analysis of haplogroup R7 with a survey mtDNA sequences has been carried out. Sequence/structure analysis of WDR13 an X-chromosome- localized novel gene has been carried out. Sequence analysis of the activin type I receptor B in a dataset on Indian population has been carried out. A method for protein contact networks, in-silico modeling and analysis of signal transduction pathways in T-helper cells and spatiotemporal dynamics of 50 cells were carried out. Mathematical models for the population dynamics of Drosophila has been analyzed on a population data set of 49-generations for larvae and adult. Integrated analysis of transcriptome and protein expression data from mouse embryonic stem cell lines R1-9 and AB1 was carried out followed by pathway and gene ontology analysis. A comprehensive tool CompreSNPdb has been developed in order to retrieve information on genes, SNPs, diseases and pathways. Seventeen databases, including Entrez gene, GO, GOA, LSDBs, dbSNP, HapMap, Ensembl, ALFRED, SNP2nmd, SNP500cancer, SNPs3D, OMIM, GAD, GATACA, KEGG, HumanCYC and Inparanoid Eukaryotic Ortholog Groups have been integrated to allow retrieval of relevant information on disease related genes/SNPs. A computer program to scan complete genome sequences of prokaryotes and to predict protein-coding genes using Fourier transform was developed and applied to the E.coli genome. Phylogenetic studies in the Indian Deer species has been carried out using the cytochrome b, 16S and 12S DNA sequences. The phylogenetic relationships of Indian Scleratenians using mtDNA sequences was studied. 53 wildlife forensic services were provided using the pair of universal primers developed at CCMB and a computer program for subsequent analysis.
Publications 1. Settu Sridhar and Kunchur Guruprasad (2008) Conformational analysis corresponding to intra-chain disulfide bridged peptides in proteins of known three-dimensional structure. Protein and Peptide Letters. 15:160-87. 2. Settu Sridhar, A. V. N. Babu and Kunchur Guruprasad (2007) 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. 41:109-113. 3. Aggarwal, R.K., Kivisild, T., Ramadevi, J., and Singh, L. Mitochondrial DNA coding region sequences support the phylogenetic distinction of two Indian wolf species. (2007) Journal of Zoological Systematics and Evolutionary Research. 45:163-172. 4. Bajpai, A. Settu, S., Reddy, H.M. and Rachel, A.J. (2007) BRM-Parser: A tool for comprehensive analysis of BLAST and RepeatMasker results. In Silico Biology.7:27. 5. Rajesh, S., Sinha, S. and Somdatta Sinha. (2007) Synchronization in coupled cells with activator-inhibitor path ways. Physical Review E, 75:011906. 6. Bagler, G. and Sinha S. (2007) Assortative mixing in protein contact networks and protein folding kinetics. Bioinformatics. 15:1760-1767. 7. Bagler, G. and Sinha, S. (2007) Propogation of extrinsic perturbation in a negatively autoregulated pathway. Physical Biology 4:48-59.
14 Xth All India BTISnet Coordinators’ Meeting February 03-04, 2009
8. Banik, P., Pramanik, P., Sarkar, R.R., Bhattacharya, S. and Chattopadhayay, J. (2007) A mathematical model on the effect of M-denticulata weed on different winter crops. Biosystems 90:818-829. 9. Banerjee, S. and Sarkar, R. R. (2008) Delay-induced model for tumor-immune interaction and control of malignant tumor growth. Biosystems 91:268-288. 10.Bhaskar, L. V., Thangaraj, K., Shah, A. M., Pardhasaradhi, G., Kumar, K. P., Reddy, A. G., Rao, P. A., Mulligan, C. J., Singh, L. and Rao, V. R. (2007) Allelic variation in the NPY gene in 14 Indian populations. J. Hum Genet. 52:592-598. 11.Bhaskar, L.V., Thangaraj, K., Mulligan, C.J., Rao, A.P., Pardhasaradhi, G., Kumar, K.P., Shah, A.M., Sabeera, B., Reddy, A.G., Singh, L. and Rao, V.R. (2008) Allelic variation and haplotype structure of the Dopamine receptor gene DRD2 in 9 Indian populations. Genet. Testing 12: 153-160. 12. Maithreye, R. and Sinha, S. (2007) Synchronization in coupled cells with activator-inhibitor pathways. Physical Review E 75:011906. 13. Sarkar, R. R., Mukhopadhyay, S., Bhattacharyya, R. and Banerjee, S. (2007) Time lags can control algal bloom in two harmful phytoplankton-zooplankton system. Applied Mathematics and Computation 186: 445-459. 14. The Indian Genome Variation Database (2008) Genetic landscape of the people of India: a canvas for disease gene exploration. J. Genetics 87:3-20. Brief outline of ongoing work We are continuing to analyze data generated from microarray, proteomic & sequencing techniques. We are exploring certain aspects of sequence-structure relatedness in proteins. We are continuing to work on small-molecule inhibitor design and models of enzymes in the non-mevalonate pathway of certain microbial species. We are extending prediction of protein coding regions to eukaryotes and to analyze the non-coding regions. We are developing models for pathway and protein network analysis. We are continuing to analyze biodiversity from mtDNA sequences and study disease related genes.
Contact 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]
15 Distributed Information Centres (DICs) Indian Agricultural Research Institute, New Delhi Coordinator: Dr. H. Chandrasekharan 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. Biotechnological Abstract Information retrieval System (BAIRS) was developed by the Centre and extensively used by students and researchers. During the year under report, apart from Bioinformatics Studies, the Centre has initiated a quarterly News Letter titled “Agri-Bioinformatics” and the same is being circulated to various Institutes as well as Universities. So far three issues have been published and fourth is under process.
Major research activities in Biotechnology and its related fields at your institution • In-silico tRNA prediction and comparative analysis of Populus trichocarpa • Structure and Function prediction of Six Hypothetical Nuclear Proteins of Oryza sativa using in-silico approach • In Silico analysis of Hevein-like Protein (Arabidopsis) Area of Specialization of the centre: Agri-Bioinformatics Details about scientific staff members working in the Centre • Dr.H.Chandrasekharan, Head & Principal Scientist (Agricultural Physics/hydroinformatics) • Dr. P. S. Pandey, Principal Scientist (Biological data analysis and mathematical modeling • Dr. A. K. Mishra, Scientist (Biological data mining and Agri bioinformatics) Types of services provided • Software and Simulation Models development • Creation and update of databases (agri and bioinformatics) • Statistical analysis of research data (students and staff of the institute) • Human resources development Educational activities with details of placement 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.
Collaborative works/ initiatives Our Centre has collaboration with Department of Science and Technology (DST), Ministry of Information Technology (MIT) and other research and development organizations.
Databases/ Software packages developed and being updated so far: • Databases (Crop Production & Productivity, Area under High Yielding Varieties, Abstracts on Tissue Culture, Photosynthesis & Plant Molecular Biology etc.) • User-friendly information system software (Rice, Wheat, Maize, Chickpea) Papers published or presented in the conferences with reference 1. H. Chandrasekharan, A.K.Mishra, R.Sharma, S.kumar 2008 ICT based agro advisory and E-extension approach for sustainable agricultural development, Key Note lecture proceeding of 2nd National conference on computing for Nation development Indiacom-2008: 003-007 2. Samita Joshi, Rajendra Sharma, A. K. Mishra, H. Chandrasekaharan 2008 Insilco structural and functional prediction of hypothetical proteins in Arabidopsis thaliana in: Proceedings of National conference on Emerging trends in IT and its application in technical education at SBIT Alwar(Rajasthan) pp: 06-12 3. A. K. Mishra and D. K. Lobiyal 2008 Exploring dominating features from Apis mellifera pre-miRNA, IEEE Explorer: 363-367 4. A. K. Mishra, S. K. Bandopadhyay, and H. Chandrasekharan Information and Communication technology for technology development and dissemination for sustainable agriculture and livelihoods in proceedings of 96th Indian Science Congress (Agriculture and forestry science section): 17-18
16 Xth All India BTISnet Coordinators’ Meeting February 03-04, 2009
Details of Training/ Workshop organized and total no. of user trained A three days workshop cum training on “Application of Bioinformatics in Agricultural Research” was organized from 25-02-08 to 27-02-08. 30 Scientists and teachers from various R&D institutes and university have participated. Future activities • Strengthening research on bio- and agri-informatics aspects related to major crops. • To make IARI website as state of art for knowledge dissemination of Agri-Bioinformatics to various stakeholders. • To initiate M.Sc course in bioinformatics. 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, Email: [email protected] Dr. A.K.Mishra, Email: [email protected], [email protected]
17 Distributed Information Centres (DICs) Institute of Molecular Technology, Chandigarh Coordinator: Dr. G. P. S. Raghava
Bioinformatics centre at IMTECH has shown consistent growth in the different areas of bioinformatics. 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 100 research papers in reputed international journals and more than 50 abstract/poster/papers presented in national and international conferences (http://imtech.res.in/raghava/pub.html). Our servers are getting more than 25000 hits per day.
Major research activities in Biotechnology and its related fields • 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 nature with an equally overt leaning towards the finding of applications. Area of Specialization of the centre: Protein Modeling and Protein Engineering Major activities of the centre during the year 2008-09 This year our centre developed methods for - i) prediction of nuclear proteins ii) Subcellular localization of Eukaryotic proteins iii) Annotation of Plasmodium Falciparum and v) database for innate immunity.
Infrastructure facilities in the Bioinformatics Centre A. 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.
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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.
Details about staff members working in the Centre
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 Model-ing, 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: - Installing, implementing and maintaining software packages on computers. - Preventive maintenance of computers. - Updates the user with recent advances in computers/Internet. 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 150 per year) and others are heavily using facilities at BIC. BIC staff participates in the pre Ph.D. course in Bioinformatics at IMTECH.
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 25,000 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.
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. 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. 19 Distributed Information Centres (DICs)
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. Papers published or presented in the conferences with reference The BIC staff of this centre has published more than 100 research papers in reputed international journals. Following is list of papers published/accepted in year 2008, published by BIC staff. I) Garg, A. and Raghava, G. P. S. (2008) ESLpred2: Improved Method for Predicting Subcellular Localization of Eukaryotic Proteins BMC Bioinformatics 9:503. II) Raghava, G. P. S., Hwang, D.J. and Han, J.H. (2008) ECGpred: Correlation and Prediction of Gene Expression from Nucleotide Sequence The Open Bioinformatics Journal 2:64-71 III)Kalita MK, Nandal UK, Pattnaik A, Sivalingam A, Ramasamy G, Kumar M, Raghava, G. P. S. and Gupta, D. (2008) CyclinPred: a SVM-based method for predicting cyclin protein sequences. PLoS ONE 3(7):e2605. IV) Kush, A. and Raghava, G. P. S. (2008) AC2DGel: Analysis and Comparison of 2D Gels Journal of Proteomics & Bioinformatics 1:43-46. V) Lata, S. and Raghava, G. P. S. (2008) PRRDB: A comprehensive database of Pattern-Recognition Receptors and their ligands BMC Genomics 9:180. VI) Sethi D, Garg A and Raghava, G. P. S. (2008) DPROT: Prediction of Disordered Proteins using Evolutionary Information Amino Acids 35:599-605 VII)Verma R, Tiwari A, Kaur S, Varshney G.C. and Raghava, G. P. S. (2008) Identification of Proteins Secreted by Malaria Parasite into Erythrocyte using SVM and PSSM profiles . BMC Bioinformatics 9:201 VIII)Vivona, S., Gardy J.L., Ramachandran, S., Brinkman, F.S.L., Raghava, G. P. S., Flower, D.R. and Filippini, F. (2008) Computer aided biotechnology: from immunoinformatics to reverse vaccinology Trends in Biotechnology 26:190 IX) Garg, A. and Raghava, G. P. S. (2008) A machine learning based method for the prediction of secretory proteins using amino acid composition, their order and similarity-search In Silico Biology 8:12 X) Kumar, M., Thakur, V. and Raghava, G. P. S. (2008) COPid: composition based protein identification. In Silico Biology 8:11 XI) Lata, S. and Raghava, G. P. S.(2008) CytoPred: a server for prediction and classification of cytokines. Protein Engineering, Design and Selection 21:279-82
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.
Number of papers published/Number of papers published with help of the 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 1400 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.
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Patents/ Copyright obtained/ filed by your centre: More than 50 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, Director 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. Future activities The future activities will focus on research as mentioned above
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]
21 Distributed Information Centres (DICs) Kerela Agriculture University Coordinator: Dr. R. Keshavachandran About the Centre The Centre was established as the 23rd Distributed Information Sub Centre (DISC) in 1995 under the BTISnet programme and upgraded to DIC during 2004 to promote Bioinformatics research and education. We specialize in plant biotechnology research. The Centre is involved in research across a wide range of Bioinformatics disciplines, including gene & protein sequence analysis, protein structure prediction and interaction studies. In addition to this, the Centre offers [2+2] credit course in Bioinformatics to M.Sc Plant Biotechnology students, conducts routine training programmes in Bioinformatics and maintains various databases relevant to agriculture.
Major activities of the centre during the year 2007-08 • Conducted various training programme and trained more than 42 personnel. • Organized [2+2] credit course in Bioinformatics for M.Sc Plant Biotechnology students. • Established a leased line connectivity of 6Mbps speed. • Established well equipped infrastructural facilities to carry out R & D activities like gene analysis, structure prediction, interaction studies, evolutionary biology, data mining and Gel documentation for molecular marker data. • Creation and maintenance of website for the College of Horticulture and DIC. Infrastructure facilities in Bioinformatics Centre: A. Computer and Communication facility The Centre has one Dell Server with Microsoft Windows Vista, one IBM Server with Microsoft Windows Server 2003, ISA Server for networking, and 21 Personal Computers with Local Area Networking facility. Networking: The Centre has established a leased line connectivity of 4Mbps speed from AIRTEL and 2 Mbps from Reliance. B. Scientific software packages Accelrys Discovery Studio, Omiga 2.0, NTSYSpc 2.1, Rasmol , Cn3D , VMD , Chimera , Swiss PDB Viewer, Modeller 9v2 , Hex, Argus lab , Clustal X , Clustal W, Treemap , Tree Explorer , Phylip, Mega, Bioedit , Oligotes , Primer 3, Marvin Sketch, ISIS Draw. C. Databases and other information resources Derwent Biotechnology Abstracts, Biological and Agricultural Index, Agricola, Agrisearch. The Centre has a collection of over 192 Bioinformatics and Plant Biotechnology books. 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. • Courses in Bioinformatics to PG students. • Support to R&D activities for PG projects in Biotechnology. Databases/Software packages developed: The databases that are being developed include Improved Crop varieties at KAU, Tissue culture protocols, Database on Indian Spices, Database on Rice Info, and Database on Spices & Herbs for Wellness.
Papers published or presented in the conference • Centre has published a book on Plant Biotechnology: Methods in Tissue Culture and Gene Transfer. 2008 – edited by R.Keshavachandran and K.V. Peter Published by Universities Press, Hyderabad. • Suma,B., Keshavachandran,R and Nybe E.V. 2008. Agrobacterium tumefaciens mediated transformation and regeneration of ginger (Zingiber officinale Rosc.). Journal of Tropical Agriculture. 46(1-2): 26-32. • Nazeem, P.A., Achuthan, C.R., Babu, T.D., Parab, G.V., Girija,D., Keshavachandran,R and Samiyappan, R. 2008.
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Expression of pathogenesis related proteins in black pepper (Piper nigrum L.) in relation to Phytophthora foot rot disease. Journal of Tropical Agriculture. 46(1-2): 33-39. • Alishya Joy, R.Keshavachandran, Reena N and Nancy Thomas. Study of plant proteolytic enzyme cysteine proteinase involved in programmed cell death of plants. Paper presented at International Symposium on Industrial Biotechnology held at Nov 15th -17th, 2008 at Kodakara, Thrissur. • Reena N, R.Keshavachandran, Alishya Joy and Nancy Thomas. Implications for plant peptides as antidiabetic compounds: a computational biology approach. Paper presented at International Symposium on Industrial Biotechnology held at Nov 15th -17th, 2008 at Kodakara, Thrissur. • Nancy Thomas, R.Keshavachandran, Reena N and Alishya Joy. In silico modeling and docking studies on Alzheimer disease Amyloid a4 protein. Paper presented at International Symposium on Industrial Biotechnology held at Nov 15th -17th, 2008 at Kodakara, Thrissur. Initiation of R&D activities in Bioinformatics Bioinformatics Centre is undertaking research work on important thrust areas like proteomics to study plant responses to biotic and abiotic stresses, plant metabolomics using systems biology approaches, plant-pathogen interaction studies, analysis of active compounds in medicinal plants, in silico approaches to manage agriculturally important plant diseases.
Details of Training organized Three DBT funded training programmes were conducted this Year. They include: 1. Bioinformatics Resources for Genome & Proteome Analysis. 2. Computational methods in Structural Bioinformatics. 3. Introduction to Computational Biology and Bioinformatics. Income Generation training programmes conducted: 1. Computational methods in Structural biology (One week) 2. Bioinformatics: Approaches and Applications (One month) Future activities • Offer new training courses in Bioinformatics. • Further improvement of infrastructural facilities. • 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 • Publish an E-newsletter from the 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 • Obtain copyrights and update the existing databases. 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: Dr R. Keshavachandran Email: [email protected]
23 Distributed Information Centres (DICs) M.S. University of Baroda Coordinator: Dr. B.B. Chattoo
Activities at M.S.University have continued with teaching and training of students at M.Sc level. All the students carry out a small project in the area of Bioinformatics, as a part of the practical training. This project carries marks and is evaluated. In addition, the Bioinformatics resources have been used to supplement ongoing research projects. A brief summary is presented here.
Genomic Resources of Magnaporthe oryzae (GROMO): A comprehensive and integrated database on rice blast fungus Genomic Resources of Magnaporthe oyzae (GROMO), is a specialized, and comprehensive database for the rice blast fungus, integrating information from several resources. GROMO contains information on genomic sequence, mutants available, gene expression, localization of proteins, as primary data obtained from a variety of repositories. In addition, prediction of domains, pathways, protein-protein interactions, sumolyation sites and biochemical properties that were obtained after computational analysis of protein sequences have also been included as derived data. The database has an intuitive user interface that would prompt the user to explore various possible information resources available on a given gene or a protein, from a single source.
Development of MicroRNA Search Tool Several microRNAs are reported in different species of plants and animals. But till date there are no reports showing discovery of any microRNA family in fungal genome. In this project we made an attempt to develop a GUI (Graphical User Interface) based program for prediction of microRNA in the pathogenic fungus M. oryzae using available computational approaches. The MicroRNA Search Tool (MIST) designed incorporates features for both sequence based and structure based analyses required for prediction of novel microRNAs. The programs were written using Perl CGI (Common Gateway Interface) scripting language and interface were created using HTML. The program uses standalone BLAST package, Matcher program from EMBOSS package for sequence analysis and Web-based RNAfold and Mfold programs for structural analysis of probable microRNA sequences. The other part of the project involved prediction of probable target genes for predicted microRNAs from M. oryzae using miRANDA microRNA target prediction program.
Comparative analysis of microRNA in pathogenic and non-pathogenic fungi MicroRNAs are reported to be evolutionary conserved in closely related species which is one of the important parameters taken under consideration during prediction of novel microRNA in any species. In this project, study was carried out to analyze the conservation of microRNA sequences among pathogenic and non-pathogenic fungi. All available genome sequence of pathogenic fungi such as Aspergillus fumigatus, Aspergillus flavus, Aspergillus terreus, Candida albicans, Ustilago maydis, Rhizopus oryzae etc. and non-pathogenic fungi such as Aspergillus nidulans, Aspergillus niger, Aspergillus oryzae, Saccharomyces cerevisiae, Neurospora crassa, Saccharomyces bayanus etc. was collected and microRNA prediction analysis was performed for each genome sequence in both the groups using MIST. Target gene prediction for predicted microRNA from different species of fungi was also performed using miRANDA target prediction program. The predicted microRNA sequences were phylogenetically analyzed to show the conservation of microRNA in pathogenic and non-pathogenic fungi which may provide information on evolution of microRNAs in pathogenic and non-pathogenic species.
Analysis of serine-threonine protein kinases from rice blast fungus The lipid inducible protein kinase (LIPK) protein sequence from Colletotrichunm trifolii has been used to pick up the homologues from M. oryzae using BROAD MIT & Harvard database (http://www.broad.mit.edu/). Only Ser/Thr protein kinases showing relatively high level of homology to C. trifolii LIPK have been taken for further analysis. EMBL-EBI ClustalW2 software has been used for multiple sequence alignment and making of a phylogenetic tree. The Ser/Thr protein kinases falling in the same clade as C. trifolii LIPK have been finally selected for functional analysis in the wet lab. A detailed domain analysis has also been done using the following resources: Pfam (http://www.sanger.ac.uk/Software/Pfam/), Prosite (http://www.expasy.ch/prosite/), and ProDom (http://prodom.prabi.fr/prodom/current/html/home.php).
Online Bioinformatics Resources Name of the Resource: GROMO; Genomic Resources of Magnaporthe oryzae Application: Many scientists are working actively on functional characterization of blast fungal genes, expression profiling during host-pathogen interactions and also in the field of proteomics. The GROMO database provides researcher
24 Xth All India BTISnet Coordinators’ Meeting February 03-04, 2009 the information not only on gene and protein sequences but also on possible domains present in a protein, predicted pathways, probable interacting partners, sub-cellular localization, protein sumoylation sites and even biochemical properties of the protein. In addition to a common blast search, GROMO provides the user with the scope of doing a keyword search using the options like locus tag, domain name, pathway, localization, Signal P prediction, SAGE tag, MPSS tag, EST ID and mutants. Moreover, some of the experimental data obtained from external resources are represented in more interpretable form which can provide researchers with a better understanding about the fungus and help design critical experiments to gain deep insights into fungal biology in general and rice blast in particular. Target users: Researchers working on filamentous fungi, especially those are working on pathogenic fungi and rice blast fungus Website/Portal address: http://210.212.136.28/GROMO/main%20page%20program
25 Distributed Information Centres (DICs) National Brain Research Centre, Manesar Coordinator: Dr. Nandini C. Singh Summary of the progress made by the centre from its inception In order to keep up with the computing requirements at NBRC, high speed network computing has been set up by the Distributed Information Centre at NBRC. High-end multiprocessor SUN and IBM servers function as Web Servers (www.nbrc.ac.in), (www.nbrc.res.in), (www.neuroscienceacademy.org.in) Mailserver (http://webmail.nbrc.ac.in), DNS Server, FTP server and Application servers. Centralized Network Attached storage of 11 TB capacity has been provided for data storage and high end computing. Linux and Windows Application servers for computing requirements are connected with thin clients for working in a multi-user environment. In order to access and share resources all knowledge-based systems are connected to these servers through LAN. Several desktops/workstations loaded with heterogeneous operating systems have been added to the internal network. Interconnectivity been buildings has also been established by using fiber-optic backbone. Wi-Fi connection has been implemented within the campus along with enhanced Internet bandwidth to 5 Mbps. The DIC staff works as a team and focuses on in-house development, assists in technical problem solving, in addition to helping scientists, handling the servers and the network. Major research activities in Biotechnology and its related fields at your institution NBRC has spearheaded an effort to build awareness in computational neuroscience and neuroinformatics, a new challenging area which deals with the analysis, characterization and modeling of neural data. NBRC is has initiated 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 Imaging and Image analysis: This laboratory, set-up by Prof. Prasun Roy, is developing novel techniques of image acquisition and image analysis for more efficient application of diagnostic and therapeutic neuroimaging methodology. The laboratory utilizes MRI based strain analysis to estimate the stress in flowing blood to estimate cerebrovascular deficits, as also to delineate elastoplastic deformation of brain for early diagnosis and differentiation of Mild Cognitive Impairment and Alzheimer’s disease. Speech analysis – The speech and language laboratory headed by Nandini C Singh has developed new methods of spectral analysis to analyze speech signals from children and those with different speech disorders. interested in studying the phonological organization of different Indian languages. More recently this laboratory has initiated functional imaging paradigms to study reading in bilingual populations. Whilst, many bilinguals acquire reading abilities distinct scripts, there is little information regarding the neural mechanisms underlying this remarkable skill. This laboratory is currently investigating neural reading mechanisms in early and late Hindi-English bilinguals using functional neuroimaging.
Area of Specialization of the centre: NEUROINFORMATICS Major activities of the centre during the year 2008-09 The Computing facility of the center has been constantly upgraded with more computing power in the form of addition of high-end servers and workstations. The capacity of Storage servers (NAS) has been upgraded to 11 TB and are attached with high capacity Ultirim LTO-4/3 Tape drives for online data archival and backup. The Internet connectivity of the centre has been upgraded to 4 Mbps 1:1 leased line with another 1 Mbps 1:1 RF connectivity for redundancy. The centre has also acquired state-of-art video conferencing facility in the form of Polycom VSX-7000. Campus LAN and Wi-Fi network has been further strengthened with the addition of additional CISCO manageable switches and D-Link Access points. The centre also hosts and maintains website of Indian Academy of Neurosciences apart from official NBRC website.
Infrastructure facilities in the Bioinformatics Centre A. Computer & Communication facility 1. Sun Fire X 4100 servers 2. IBM x346 servers 3. IBM x3650 servers 4. IBM x 235 and 220 servers 5. NAS (Network Attached Storage) Servers with 11 TB Storage 6. IBM Desktops and Workstations 7. HP Thin Clients 8. Laptops , LCD Projectors and 42" LCD TV 9. HP Laserjets , Colour Laserjet, Designjet (42" plotter) etc. 10. Cisco Routers , Managed (L2/L3) and unmanaged Switches (CISCO / D-Link / 3 Com), wireless access points
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11. Nokia-Checkpoint Firewall cluster ( IP390 ) with content filtering. 12. 4 Mbps 1:1 Leased line from BSNL with 1 Mbps RF Link 13. Polycom Video Conferencing (VSX 7000) setup B. Scientific Software packages Matlab 7.3, SPSS, E-Prime, SPM, FSL, Brain Voyager, Neurolucida MriCro, Spot Fire (Micro Array), Silicocyte, Instrument Control Manager, Sequence Analyzer, Phred Phrap, Consensus (Sequencer), DS Modeling Software etc. C. Databases & other information resources Chemical Management System, Cell Lines Status in Lab’s Leave Management System, Speech Corpus Details about staff members working in the centre
Types of services provided DIC is providing diversified services like software development, Internet, intranet, mailing facilities, web-hosting, maintenance of servers and network.
Educational activities with details of placement NBRC is a deemed University and has two training programmes in Neuroscience namely a PhD programme and Integrated PhD programme in Neuroscience.
Collaborative works/ initiatives · 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 · MRI Vector field Imaging in Cerebrovascular conditions and Image Guided Radiotherapy of Brain Tumours, Utrecht University & Philips Electronics, Holland. · Four-dimensional Multimodal Imaging technique development: MRI, MRS & PET, Montreal Neurological Institute, McGill University, Montreal · EEG-fMRI Diagnostic Algorithm for substrate-negative Epilepsy, All-India Institute of Medical Sciences, New Delhi. · Tensor Morphometric Analysis for early neuroradiological diagnosis. University of California, Los Angeles. · Neural Information Analysis and Connectivity, University of Modena, Italy Databases/ Software packages developed Chemical Management System, Cell Lines Status in different laboratories in NBRC. Leave Management System, Speech Corpus
27 Distributed Information Centres (DICs)
Papers published or presented in the conferences with reference List Publications and patent applications: Computational Neuro-science and Neuroimaging laboratory · Subramanyam, V.P., Upadhyay, A., Budhachandra, Kh. and Roy, P.K. (2008) The Self and Its Brain: A Symbiotic Integration of Functional Mapping and Tensor Imaging Strategy for a Neuroinformatics initiative, Computer Society of India Communications. 32(3), 27-31. · Budhachandra, Kh. and Roy, P.K. Informational Tracking of Epileptic Focus in the Brain. Developmental Neurobiology and Neuroimaging (edited volume) (In Press). · Subramanyam, V.P. and Roy, P.K. (2008). Stochastic Resonance-based Tomographic Transform for Image Enhancement of Brain Lesions, J. Computer Assisted Tomography, 32(5), 675-683. Patents · Rapid Automated Screening for Diagnosis and Classification of Alzheimer’s Disease using Magnetic Resonance Imaging signal (Filed). · A Medical Image Enhancement Device based on Image Transform Resonance, using an Embedded System (filed). · A Technique to Enhance the Clinical Efficiency of Radiotherapy and Radiosurgery using Perturbative Beaming and Tissue-specific Radiobiology (Accepted). Speech and Language Laboratory · Singh, L. and Singh, N.C. (2008) The development of articulatory signatures in children, Developmental Science, Vol.11 (4):467-73. · T., Padma, Das, T., and Singh, N.C. (2008), Speech rhythms in children learning two languages: From Heart to Brain, Life Sciences Series, Springer (In Press). Initiation of R&D activities in Neuroinformatics As described above NBRC has initiated research in the area of the image analysis, speech processing and functional neuroimaging. By organizing annually a workshop on computational neuroscience, NBRC has introduced and trained more than 300 students to the field of computational neuroscience in different parts of the country. With the setting up of the 3T fMRI scanner at NBRC, research has been in neuroimaging and the data analysis of data acquired during various neuroimaging paradigms. We hope in the near future we will able to conduct workshop to train students in the exciting field of neuroimaging too.
Details of Training/ Workshop organized and total no. of user trained 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.
Impact shown by your centre on the growth of biotechnology and allied areas The computational neuroscience group at NBRC has published/submitted around 8 publications and patent applications in 2007-08 The NBRC is co-ordinating the DBT Biotech Consortia for digital library access throughout the country. This would not only create a model for networking of research libraries around the country but would also ensure resource sharing and networking. NBRC conducts Summer Training Programme every year for students from different academic backgrounds and varied academic Institutions, 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 21 students were trained in 2008. The DIC personnel play a significant role in non only ensuring maintenance smooth functioning of all the digital network and ensuring weekly backup in contributing to the developments of new signal processing tools to study speech and image analysis. More recently, DIVC personnel have been actively involved in developing paradigms for fMRI data acquisition and analysis.
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Future activities · High end cluster computing for Functional MRI analysis · Advancing the analysis of stress tensor imaging Additional Details
Name of the Coordinator: Dr. Nandini C.Singh Postal Address: National Brain Research Centre, Manesar-122050, Gurgaon Dist., Haryana Phone Number: 0124-2338921 Extn: 333 Email: [email protected] Website: www.nbrc.ac.in
Name of Contact Person(s): Mahender Kumar Singh, Email : [email protected]
29 Distributed Information Centres (DICs) National Institute of Immunology, New Delhi Coordinator: Dr. Dinakar M. Salunke Summary of the progress made by the centre from its inception The usage of the facilities provided by the Bioinformatics Center (BIC) at NII is reflected in large number of publications from various research groups at NII. The center is also engaged in advanced research in the area of computational and structural biology.
Major research activities in Biotechnology and its related fields at your institution 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.
Area of Specialization of the centre: Structural Biology & Molecular Modelling Major activities of the centre during the year 2008-09 During the year 2008-2009, the center has upgraded its computational resources by setting up high performance computing facility. The research work from the center has been published in several high impact journals.
Details about staff members working in the centre: All staff members are absorbed by NII
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.
Educational activities with details of placement Four students have completed Ph.D. in Bioinformatics from BIC, NII and a number of students are currently enrolled.
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.
Collaborative works/ initiatives The center is associated with several collaborative projects involving work on Mycobacterium tuberculosis and various other aspects of immunity and infection.
Databases/ Software packages developed Analysis of PKS/NRPS http://www.nii.ac.in/sbspks.html Motif Discovery http://www.nii.ac.in/~deepak/RegAnalyst 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 Papers published or presented in the conferences with reference 1. Yadav G, Gokhale RS and Mohanty D* (2009) PLoS Comput. Biol. (in press). 2. Arora P, Goyal A, Natarajan V, Rajakumara E, Verma P, Gupta R, Malikmohamed Y, Trivedi O, Mohanty D, Tyagi A, Sankaranarayanan R and Gokhale RS (2009) Nature Chemical Biology (in press). 3. Kaushik S, Mohanty D* and Surolia A* (2009) Biophys J. 96: 21-34. 4. Ansari MZ, Sharma J, Gokhale RS and Mohanty D* (2008) BMC Bioinformatics 9:454. 5. Chopra T, Banerjee S, Gupta S, Yadav G, Anand S, Surolia A, Roy RP, Mohanty D and Gokhale RS (2008) PLoS Biology 6: e163. 6. Ghosh R, Chhabra A, Phatale PA, Samrat SK, Sharma J, Gosain A, Mohanty D, Saran S, Gokhale RS (2008) J Biol Chem. 283:11348-54. 7. Krishnan L, Sahni G, Kaur KJ, Salunke DM* (2008) Biophys J. 94:1367-76. 8. Kaur KJ, Sarkar P, Nagpal S, Khan T, Salunke DM* (2008) Protein Sci. 17:545-54.
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9. Dutta RC, Nagpal S, Salunke DM* (2008) Int J Biochem Cell Biol. 40:1005-15. 10.Gupta P, Gaur V, Salunke DM* (2008) Acta Crystallogr Sect F Struct Biol Cryst Commun. 64:733-6. 11.Gaur V, Sethi DK, Salunke DM* (2008) Acta Crystallogr Sect F Struct Biol Cryst Commun. 64:32-5. 12.Gupta V, Gupta RK, Khare G, Surolia A, Salunke DM, Tyagi AK (2008) Acta Crystallogr Sect F Struct Biol Cryst Commun. 64:524-7. 13.Gupta V, Gupta RK, Khare G, Salunke DM, Tyagi AK (2008) Acta Crystallogr Sect F Struct Biol Cryst Commun. 64:398-401. 14.Ganguly N, Giang PH, Gupta C, Basu SK, Siddiqui I, Salunke DM, Sharma P (2008) Immunol Cell Biol. 86: 98-106. 12.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. Details of Training/ Workshop organized and total no. of user trained During the current reporting year, the center has arranged hands-on bioinformatics laboratory sessions for students and teachers of different degree colleges.
Impact shown by your centre on the growth of biotechnology and allied areas The impact of the center on the research at NII is reflected in about 50 publications every year in peer reviewed journals.
Future activities The center plans to expand the scope of the existing research projects to analyze regulation of secondary metabolite biosynthesis and drug target identification using protein structure similarity clustering.
Additional Details:
Name of the Coordinators: Dr. Dinakar M. Salunke/ Dr. D. Mohanty Postal Address: NII, Aruna Asaf Ali Marg, New Delhi-67 Phone : 011-26717108 E-mail: deb@nii.res.in Website: http://www.nii.res.in `
31 Distributed Information Centres (DICs) Pondicherry University, Pondicherry Coordinator: Dr. P.P. Mathur Educational activities with details of placement The Centre is offering a Masters’ program in Bioinformatics (M.Sc.,) since 2007 which is funded by the University Grants Commission (UGC) under its scheme of Innovative Programme in Emerging Areas. The Centre also offers a Ph.D programme in Bioinformatics. The Centre has been offering Advanced PG Diploma course in Bioinformatics with financial support from Department of Biotechnology (DBT), Govt., of India from 2001 which is now being upgraded to Network M.Sc., Programme in Computational Biology. 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: I. Industry Placements HCL Info systems, Pondicherry, Tata Consultancy Services, Molecular Connections, Bangalore, Institute of Bioinformatics, Bangalore, Protein Lounge, Bhubaneswar, Genemines, Chennai, BIOBASE Databases Indian Pvt. Ltd., Bangalore, Computational Reseach Lab, Pune
II. 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, Madurai, Indian Institute of Technology, Chennai, Jawaharlal Nehru University, New Delhi, Kumaun University, Nainital
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 Biotech- nology. 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 Major activities of the centre during the year 2008-09 Faculty and non teaching positions have been advertised and two lecturers have joined. The Centre has started offering a M.Sc. and Ph.D program in Bioinformatics. 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 Tutorials in Bioinformatics. The Centre has conducted various training programmes in Bioinformatics and arranged several invited lectures. The Centre is in a process of setting up a wet lab facility. The lab is functional with the following equipments: Quartz Distillation Unit, pH meter, Vertical Gel apparatus, Horizontal Gel apparatus, Western blot apparatus, -20ÚC Freezer, UV illuminator, Cooling Centrifuge, Eppendorf PCR, Eppendorf microfuge, Gel Documentation System, UV- Visible Spectrophotometer, -80ÚC Deep Freezer Databases/ Software packages developed • Bind-PredictdB : A Database for DNA Binding Proteins • Bind-PredictTool : A Tool for finding Zinc Finger Protein Binding Site • DrugMetZ DB - A Database on human drug Metabolizing Cytochromes available at www.bicpu.edu.in/databases.htm • HuMet DB - A Database on collection of Metabolites available at www.bicpu.edu.in/databases.htm • A CD on free software on Internet has been prepared and is available for distribution Papers published or presented in the conferences with references · Journal Papers - 9 · Conference Papers - 8 Details of Training/ Workshop organized and total no. of user trained (2006-2007) • National Seminar on “Applications of Bioinformatics in Genome Research”, February 13-15, 2008. No. participants : 130 • National Seminar on “Molecular Modeling and Drug Design”, October 14-16, 2008. No. of participants : 100 • National Seminar on “Current Trends in Bioinformatics Teaching and Research”, February 16-18, 2009. No. of participants : 100 (Proposed)
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Impact shown by your centre on the growth of biotechnology and allied areas • The Centre has created a big impact in Pondicherry University and surrounding in institutions towards teaching and research in Bioinformatics. The Centre has helped various Universities/ Colleges for curriculum development & training • 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. Future activities • Strengthening of teaching and R&D activities in the areas of comparative genomics, homology modeling, molecular docking, development of Databases • Identification and characterization of novel inhibitors of west nile virus • Development of Immune Epitope Database • Development of teaching aids in Bioinformatics • Starting of Network teaching programme in Computational Biology
Other details 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 Website : www.bicpu.edu.in
Name of Contact Person(s): Dr. P.P. Mathur Email: [email protected], [email protected]
33 Distributed Information Centres (DICs) University of Calcutta, Kolkata Coordinator: Subhasis Mukhopadhyay The Distributed Information Centre, Calcutta University has completed its 15th year in 2008. The center had taken off as a modest Sub-DIC since 1993 and had been upgraded to a full DIC in 2003. DBT had granted the One Year Advanced Diploma Course in Bioinformatics which has been running since 1999-2000 academic session. The activities of the Centre and the One Year Diploma Course had a synergistic effect and one is supplementing the other. Over the last one and a half decade, the efforts of theis center has been recognized by the host institute and as a result, this center has been made an integral part of the host institute.This center plays a cardinal role in providing both extra-mural as well as intra-mural support to the appropriate institutions and departmentand as well as in all allied activities of this region. Area of specialization of the center has been chosen to be Human resource development. This department has been in the forefront of starting new courses in the area of bioinformatics. The One Year Diploma Programme as well as the Two Year Masters course in Bioinformatics and Biophysics are the pioneer in this respect. The quality of the students passing out from both he two courses are recognized in the country and abroad. We have been able to retain most of the trained students in the One Year Diploma programme within the country ( in academics, industry and in the R & D sector of the country and are fairly distributed over these sectors). We are also using the infrastructure and the software resources of the Diploma Programme to buttress the Masters course which has also been accepted by the academic community of this country and abroad. The Centre is a small one but is into diverse research areas of Computational Biology and Computational Linguistics. Systems Biology has been taken up as an area of activity and the center has been able to publish a few papers in this area.
The following research programmes are being handled by the group: • Study of the sequence characteristics of leucine-rich repeat proteins - a class of proteins that participate in protein-protein interactions - and relate that to their function. • Study of the conformational consequences of post-transcriptional modifications of RNA bases and their role in tRNA structure and function • Study of the regulatory role of ABA in controlling gene expression in model plants such as A. thaliana and O. sativa. • Studying Single protein network to understand the sequence-structure-function relationship of proteins • Backup machinery of Regulatory network Reconstruction, characterization and analysis of genome scale meta bolic network of Oryza sativa • Use the FBA-like approach to understand and to identify potential pathways. • Clustering techniques are being used to identify metabolic pathways. • String Variable Grammar, Push-down automata is applied to large DNA sequences for predicting de Nuevo certain important features of the biological sequences. Software / Database: We reported in the last year the early version of two database/ webserver -
Arabidopsis thaliana regulatory element analyzer (AtREA) server and amino acid network webserver (AminoNet) to analyze and visulaze protein contact map. One of them has already been published ( Bioinformatics 2008, 24(19):22632264) and another manuscrpt would be submitted after revision. The weblinks are given below: 1. http://www. bioinformatics .org/grn/atrea.html . 2. http://www.bioinformatics.org/ aminonet / AminoNet .html In addition to those, TRABAS: A Database for Transcription Regulation by ABA Signaling has been developed and published (In silico Biology, Volume 8, 56, 2008). The link is given below. http://www.bioinformatics.org/trabas/
We have the following publications in the reported year. TRABAS: A Database for Transcription Regulation by ABA Signaling, In Silico Biology, Issue Volume 8, Number 56/ 2008, Ananyo Choudhury1, Ansuman Lahiri1
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Arabidopsis thaliana regulatory element analyzer, Bioinformatics 2008 24(19):2263-2264, Ananyo Choudhury * and Ansuman Lahiri Incorporation of enzyme concentrations into FBA and identification of optimal metabolic pathways, Rajat K De, Mouli Das and Subhasis Mukhopadhyay, BMC Systems Biology 2008, 2:65 (18 Jul 2008) Condition specific interregulations in yeast transcriptional regulatory networks Dhriti Sengupta and Sudip Kundu (Under review in Bioinformatics Journal (2008))
The group has eight PhD students, of which one is awaiting degree and is about to submit his thesis. The center routinely trains about 20 project students in a year One of the group member had visited Prof. David Fell’s group (Oxford Brookes University, UK) as an academic visitor (July 08 to Sept 08)-to work on “ Reconstruction and characterization of the rice metabolic network”. Apart from the on-going collaboration, the following new collaborations had been initiated: Safarik University, Kosice, Slovakia., Prof. David Fell – Oxford Brookes University, UK ,Dr. Shukla Ghosh and Dr. Swapan K Datta – University of Calcutta, Dr. Ramnrup Sarkar – CCMB, ICMR Bioinformatics Centre, NICED, Kolkata
35 Sub - Distributed Information Centres Advance Centre for Treatment Research and Education in Cancer, Mumbai Coordinator: Dr. Robin Mukhopadhayaya 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 to provide basic knowledge of applications in bioinformatics using data/information on cancer biology and proteomics, gene expres- sion analysis, structural bioinformatics 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.
Major research activities in Biotechnology and its related fields at your institution The major focus of the institute is on basic and translational research in cancer biology. The details of the scientist working on different aspects of cancer are available at http://www.actrec.gov.in/basic_main.htm. Bioinformatics related activities are on genomics, proteomics and structural biology of breast cancer, oral cancer, and cervical cancer.
Area of Specialization of the centre. Cancer Biology: Basic and Translational. Major activities of the centre during the year 2008-09 Significant addition of computational infrastructure contributed by the institute; Organization of training course; Training new JRF/Ph.D. students to use the bioinformatics tools for their research; Uploading of a new database developed in-house.
Infrastructure facilities in the Bioinformatics Centre A. Computer & Communication facility: As stated earlier last year we have very good Two Linux based IBM servers, purchased on DBT grant, and are used as the Internet and mail servers. Computational details are already given last year. B. Scientific Software packages: None C. Databases & other information resources: Database on oral cancer genes and chromatin (See 11 below)
Details about staff members working in the centre 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.
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.
Educational activities with details of placement: Nil 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.
Databases/ Software packages developed The Oral cancer database was updated by data mining of genes involved in oral cancer. The new markers (genes) were iden- tified by comparing the gene lists from 16 published articles by proteomics and autoantibody studies. Interactome maps have been generated for the genes that are categorized into important biological processes and molecular functions based on Gene-Ontology.A new database was developed here and uploaded on our website. (URL-http://www.actrec.gov.in/oralcancer/GeneHome.htm). A new Histone database was uploaded on our website
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Papers published or presented in the conferences with reference Santhosh CV, Tamhane MC, Mukhopadhyaya Rita, Mukhopadhyaya R. Full length genome characterization of an HIV-2 isolate from India. AIDS Res Human Retroviruses 2008; 24:1315-1317.
Initiation of R&D activities in Bioinformatics Bioinformatics based approaches to validate data, retrieval of scientific information, protein-protein interactions, molecular modeling and structure based drug design is an integrated approach of this centre. It is required for analysis of the genomics and proteomics related programs on oral cancer, cervical cancer, brain cancer and hematological malignancies. Since 2007, new area of science i.e Structural Biology has been introduced at this Centre. The scientist in this thrust field of science also has the expertise in interdisciplinary area include proteosomal, dynamics, structure activity relationships, apoptotic proteins and X-ray crystallography of cancer- associated proteins, Structure-based drug design and molecular modeling.
Details of Training/ Workshop organized and total no. of user trained A DBT-BTIS sponsored workshop on Bioinformatics was held on January 17-18, 2008 in seminar room at ACTREC. The main focus of the workshop was to teach basic concepts of bioinformatics to lecturers/ research scholars. There were total 13 participants from different institutes. The workshop covered most of the basic concepts of bioinformatics, biological databases and protein structure analysis; All participants were very enthusiastic to know about the practical applica- tion of data - base that was covered by Mr. Nikhil during hands on session. Other speakers were Mrs Sadhana Kannan, Dr. V. Prasanna, Dr. Kakoli Bose (ACTREC), Mrs Ojaswini Upasani (ACTREC). Dr. Robin Mukhopadhyaya coordinator DBT-BTIS briefly introduced the participants about the aim of DBT. The final lecture of the workshop was delivered by Dr. Ashok Varma (ACTREC). During the hands on session of Dr. Varma, participants learned a number of softwares for protein structure modeling, secondary and tertiary structure prediction and structure validation. Five students were provided six months training on Database development, protein modeling and structure activity relationship.
Impact shown by your centre on the growth of biotechnology and allied areas. Papers published from the center-51; Invited lectures by the staff of BTIS in neighboring institutes. There is a growing de- mand from many city colleges/institutes to hold the bioinformatics workshop twice in a year.
Future activities Infrastructure and expertise development in molecular modeling.
Additional Details
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]
35 Sub - Distributed Information Centres Aligargh Muslim University, Aligarh Coordinator: Dr. M. Saleemuddin 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. 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.
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 be- ing 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 intermedi- ate 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 process- ing machinery. Transcription regulation and gene silencing versus histone methylation .
Area of Specialization of the centre: Basic Biotechnology Major activities of the centre during the year 2008-09 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). 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 “In Silico molecular modeling and drug design” held during March 18-19, 2008 in which 25 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.
Infrastructure facilities in the Bioinformatics Centre (A) 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,
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one photocopier and a fax machine. (B) Scientific Software packages (C) Databases & other information resources: Medline, Biotechnology Abstracts, Agricola, and Life Science Collection (D) Journals: European Journal of Biochemistry, Science, New Scientist, Trends in Biochemical Sciences and Trends in Biotechnology, Nature, New Scientist, Nature Biotechnology etc. Details about staff members working in the centre (1) S. Faisal Maqbool, Sr. Scientific Officer, 19 years (2) Parveen Salahuddin, Sr. Res. Assistant, 18 years (3) S. Aqtedar Husain, Data Entry Operator, 18 years. All above have already absorbed by the University Types of services provided: (i) Workshops on Bioinformatics, (ii) E-Mail and Internet Facility, (iii) CD-ROM Databases Facility, (Iv) Scientific Software Facility (v) In-house Databases.
Educational activities with details of placement (i) Bioinformatics teaching (ii) Multimedia and E-learning initiatives:
Initiative to validate the outcome of bioinformatics resources Organizing workshop in bioinformatics for manpower development. (ii) Providing online services through BSNL dedicated 512 kbps leased line and BSNL 2 mbps Broad Band Connection for literature search etc. (iii) Providing offline services using CD-ROM database (Medline, Life Science Collection and Biotechnology Abstracts). (iv) 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.
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. Papers published or presented in the conferences with reference During the year (2008-2009 years more than 21 papers were published using bioinformatics facilities. 1. Gull N, Sen P, Khan RH, Kabir-Ud-Din. (2009) “ Spectroscopic studies on the comparative interaction of cationic single-chain and gemini surfactants with human serum albumin” Biochem. 145(1):67-77. 2. Dwivedi V, Vasco A, Vedi S, Dangi A, Arif K, Bhattacharya SM, Owais M. (2009) “Adjuvanticity and protective immunity of Plasmodium yoelii nigeriensis blood-stage soluble antigens encapsulated in fusogenic liposome” Vaccine. 14;27(3):473-82. 3. Fatima S, Jairajpuri DS, Saleemuddin M. (2008) “A procedure for the rapid screening of Maillard reaction inhibitors” J Biochem Biophys Methods.24;70, 958-65. 4. Sen P, Fatima S, Khan JM, Khan RH. (2008) “ How methyl cyanide induces aggregation in all-alpha proteins: A case study in four albumins.” Int J Biol Macromol. (In press) 5. Naseem F, Khan RH. (2008) “Pea lectin in alkaline conditions: formation of molten globule-like intermediate and its structural and thermal studies under the influence of hexafluoroisopropanol “Protein Pept Lett. 15(6): 606- 11. 6. Fatima S, Mishra A, Sen P, Khan RH. (2008) “Characterization of fluoroalcohols-induced intermediates of Mucor miehei lipase at low pH.” Protein Pept Lett. 15(4):346-52. 7. Sen P, Ahmad B, Khan RH. (2008) “Formation of a molten globule like state in bovine serum albumin at alkaline pH” Eur Biophys J. 37(8):1303-8. 8. Varshney A, Ahmad B, Khan RH. (2008) “Comparative studies of unfolding and binding of ligands to human serum albumin in the presence of fatty acid: spectroscopic approach” Int J Biol Macromol. 1;42(5):483-90. 9. Naseem F, Khan RH. (2008) “Structural intermediates of acid unfolded Con-A in different co-solvents: fluoroalcoholsand 37 Sub - Distributed Information Centres
polyethylene glycols. Int J Biol Macromol. 1;42(2):158-65. 10. Atif SM, Salam N, Ahmad N, Hasan IM, Jamal HS, Sudhanshu A, Azevedo V, Owais M. (2008) “Sperm membrane lipid liposomes can evoke an effective immune response against encapsulated antigen in BALB/c mice.” Vaccine. 29;26(46):5874-82. 11. Dwivedi V, Khan A, Vasco A, Fatima N, Soni VK, Dangi A, Misra-Bhattacharya S, Owais M. (2008) Immunomodulator effect of picroliv and its potential in treatment against resistant Plasmodium yoelii (MDR) infection in mice” Pharm Res. 25(10):2312-9. 12. Khan SN, Islam B, Yennamalli R, Zia Q, Subbarao N, Khan AU. (2008) “Characterization of doxorubicin binding site and drug induced alteration in the functionally important structural state of oxyhemoglobin.” J Pharm Biomed Anal. (In press) 13. Khan SN, Islam B, Yennamalli R, Sultan A, Subbarao N, Khan AU. (2008) “Interaction of mitoxantrone with human serum albumin: Spectroscopic and molecular modeling studies” Eur J Pharm Sci. 18;35(5):371-82. 14. Shakir M, Azam M, Parveen S, Khan AU, Firdaus F. (2008) “Synthesis and spectroscopic studies on complexes of N,N’-bis-(2-pyridinecarboxaldimine)-1,8-diaminonaphthalene (L); DNA binding studies on Cu(II) complex” Spectrochim Acta A Mol Biomol Spectrosc. 31;71(5):1851-6. 15. Shakil S, Akram M, Khan AU. (2008) “Tigecycline: a critical update” J Chemother. 20(4):411-9. Review. 16. Islam B, Khan SN, Haque I, Alam M, Mushfiq M, Khan AU. (2008) “Novel anti-adherence activity of mulberry leaves: inhibition of Streptococcus mutans biofilm by 1-deoxynojirimycin isolated from Morus alba “ J Antimicrob Chemother. 62 (4):751-7. 17. Khan SN, Islam B, Rajeswari MR, Usmani H, Khan AU. (2008) “Interaction of anesthetic supplement thiopental with human serum albumin” Acta Biochim Pol. 55(2):399-409. 18. Shahid M, Malik A, Akram M, Agrawal LM, Khan AU, Agrawal M. (2008) “Prevalent phenotypes and antibiotic resistance in Escherichia coli and Klebsiella pneumoniae at an Indian tertiary care hospital: plasmid-mediated cefoxitin resistance” Int J Infect Dis. 12(3):256-64. 19. Shakil S, Khan R, Zarrilli R, Khan AU. (2008) “Aminoglycosides versus bacteria—a description of the action, resistance mechanism, and nosocomial battleground” J Biomed Sci. 15(1):5-14. 20. Asad U Khan Ayesha Sultan, Anju Tyagi, Mohd Akram, Mohd Shahid, Shazia Zahoor, Sukhminderjit Kaur, Chetana V Vaishnavi, (2008) “Amplification ofmec A gene in some of the multidrug resistant strains ofStaphylococcus aureus isolated from hospital workers in India”. J Infection Dev Countries (In press) 21. Farha Firdaus, Kaniz Fatima, Hohd Azam, Shahper N Khan and Asad U Khan (2008) Template synthesis and physico-chemical studies on 14 membered hexaazino crocyclic complexes of Co (II, Ni(II), Co (II and Zn (II): A comparative approach in binding studies of DNA with Cu (II) and Ni (II) complex” Trans. Met. Chem (in press) Details of Training/ Workshop organized and total no. of user trained: The centre has organized 15 workshops since 1994 and has trained more than 350 users so far.
Impact shown by your centre on the growth of biotechnology and allied areas 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 hexam- ers) 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).
Future activities (i) Analysis of eukaryotic genomic DNA and its organization using gene finder program. (ii) Development of databases in the areas actively investigated at this University such as on vaccines against human diseases, chemokines, Enzyme immo- bilisation. etc. (iii) Organising workshops on bioinformatics. (iv) Organising seminar lecture programmes in the areas of bioinformatics and biotechnology (v) Online access to E-journals, softwares etc.
Additional details Name of Coordinator: Professor M. Saleemuddin, Distributed Information Sub-Centre, Interdisciplinary Biotechnology Unit, Aligarh Muslim University,
38 XXth All India BTISnet Coordinators’ Meeting February 03-04, 2009 All India Institute of Medical Sciences, New Delhi Coordinator: Dr. Y. D. Sharma Major activities of the centre during the year 2008-09 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 car- ried out in the field of infectious diseases including malaria & tuberculosis, cancer and cardiac diseases culminating in (iii) Publications, diagnostics and patents.
Infrastructure & Scientific software packages We have procured one Sun server with Xenon processor and GcG software to streamline research and teaching in Bioinformatics. Students, research scholars and faculty are using various scientific software like Labwork for Gel Analysis, GraphPad Prism for data analysis and End Note etc. 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 is being provided.
Teaching of Bioinformatics A 3.0 credit point course module in bioinformatics is being run for M,Biotechnology students. The students are imparted with hands on training in the use of various bioinformatics tools and packages. Experts are invited from various aca- demic 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, Computer Facility, AIIMS and Deptt. Of NMR, AIIMS.
Software developed The two-software packagesSpectral Repeat Finder and My Pattern Finder developed by us are being used by students for in silico analysis of research hypotheses and are finding support in experimental results.
Initiation of R&D activities in Bioinformatics 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.
Manpower trained BTIS is providing support to the M.Biotech. Teaching Programme, PhD scholars, MD/MS trainees, WHO fellows, DBT Associ- ates and summer trainees. The total strength of manpower trained is, therefore, greater than 387.
Impact shown by centre on the growth of biotechnology and allied areas No. of M.Biotech students trained: : 179 No. of PhD scholars passed out : 32 No. of PhD scholars enrolled currently : 16 No. of Post MD/MS professionals trained : 17 No. of summer trainees : 96 No. of WHO fellows trained : 17 No. of papers published in 2008 : 19 No. of patents : 15 Papers communicated In 2008 19 papers have been published in peer-reviewed (Pub-Med indexed) journals. 1. Siddiqui, A. A., H. Bora, N. Singh, A. P. Dash, and Y. D. Sharma. 2008. Expression, purification, and characterization of the immunological response to a 40-kilodalton Plasmodium vivax tryptophan-rich antigen. Infect Immun 76: 2576-86. 2. Garg, S., S. S. Chauhan, N. Singh, and Y. D. Sharma. 2008. Immunological responses to a 39.8kDa Plasmodium vivax tryptophan-rich antigen (PvTRAg39.8) among humans. Microbes Infect 10:1097-105. 3. Alam, M. T., H. Bora, N. Singh, and Y. D. Sharma. 2008. High immunogenecity and erythrocyte-binding activity in the tryptophan-rich domain (TRD) of the 74-kDa Plasmodium vivax alanine-tryptophan-rich antigen (PvATRAg74). Vaccine 26:3787-94.
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4. Alam, M. T., H. Bora, M. K. Das, and Y. D. Sharma. 2008. The type and mysorensis forms of the Anopheles stephensi (Diptera: Culicidae) in India exhibit identical ribosomal DNA ITS2 and domain-3 sequences. Parasitol Res 103:75-80. 5. Mehlotra, R.K., G. Mattera, M.J. Bockarie, J.D. Maguire, J.K. Baird, Y.D. Sharma, M. Alifrangis, G. Dorsey, P. J. Rosenthal, D.J. Fryauff, J.W. Kazura, M. Stoneking, and Peter A. Zimmerman. 2008. Discordant patterns of genetic variation at two chloroquine-resistant loci in worldwide populations of malaria parasite Plasmodium falciparum. Antimicrob Agents Chemother 52:2212-22. 6. Ahmed, A., and Y. D. Sharma. 2008. Ribozyme cleavage of Plasmodium falciparum gyrase A gene transcript affects the parasite growth. Parasitol Res 103:751-63. 7. Thakur, A., M. T. Alam, H. Bora, P. Kaur, and Y. D. Sharma. 2008. Plasmodium vivax: sequence polymorphism and effect of natural selection at apical membrane antigen 1 (PvAMA1) among Indian population. Gene 419:35-42. 8. Thakur, A., M. T. Alam, and Y. D. Sharma. 2008. Genetic diversity in the C-terminal 42 kDa region of merozoite surface protein-1 of Plasmodium vivax (PvMSP-1(42)) among Indian isolates. Acta Trop 108:58-63. 9. Alam, M. T., H. Bora, P. Mittra, N. Singh, and Y. D. Sharma. 2008. Cellular immune responses to recombinant Plasmodium vivax tryptophan-rich antigen (PvTRAg) among individuals exposed to vivax malaria. Parasite Immunol 30:379-83. 10. Choudhary, V., and Y. D. Sharma. 2008. Extensive heterozygosity in flanking microsatellites of Plasmodium falciparum Na(+)/H(+) exchanger (pfnhe-1) gene among Indian isolates. Acta Trop. (In press) 11. Chauhan, S., and J.S. Tyagi. 2008. Cooperative binding of phosphorylated DevR to upstream sites is necessary and sufficient for activation of the Rv3134c-devRS operon in Mycobacterium tuberculosis: Implication in the induction of DevR target genes. J. Bacteriol 190:4301-12. 12. Chauhan, S. and J.S. Tyagi. 2008. Interaction of DevR with multiple binding sites synergistically activates divergent transcription of narK2-Rv1738 genes in Mycobacterium tuberculosis. J. Bacteriol 190:5394-403. 13. Kumar, P., N. P. Shah, A. Singhal, D. S. Chauhan, V. M. Katoch, S. Mittal, S. Kumar, M.K. Singh, S. Datta Gupta, and H. K. Prasad. 2008. Association of Tuberculous Endometritis with Infertility and Other Gynecological Complaints of Women in Indian. J Clin Microbiol 46: 4068-70. 14. Kumar, P., M. V. P. Srivatsava, S. Singh, and H. K. Prasad. 2008. Filtration of Cerebrospinal Fluid Improves Isolation of Mycobacteria. J Clin Microbiol 46:2824-5. 15. Srivastava, K., D.S. Chauhan, P. Gupta, H.B. Singh, V.D. Sharma, V.S. Yadav, Sreekumaran*, S.S. Thakral* J.S. Dharamdheeran*, P. Nigam*, H.K. Prasad** and V.M. Katoch. 2008. Isolation of Mycobacterium bovis & M. tuberculosis from cattle of some farms in north India - Possible relevance in human health. Indian J Med Res 128:26-31. 16. Gupta, R., V. Kapuria and S.N. Das. 2008. Single Nucleotide Polymorphisms inTNF-á, TNFR2 gene and TNF-á production in Asian Indians. Immunol Invest. (In press) 17. Baniasadi, V., and S.N. Das. 2008. No evidence for association ofPTPN22 R620W functional variant C1858T with type 1 diabetes in Asian Indians. J Cell Mol Med 12:1061-2. 18. Somvanshi, R.K., R. Subashini, V. Dhanasekaran, G. Arulprakash, S.N. Das and S. Dey. 2008. Synthesis, Crystal Structure Cytotoxic and apoptotic activity of 2, 4-Dichloro-6-Methyl Quinoline on human oral carcinoma cell line. J Chem Crystallogr 38: 381-6. 19. Gupta, R., S.C. Sharma and S.N. Das. 2008: Association ofTNF-á and TNFR1 promoters and 3’ UTR region of TNFR2 gene polymorphisms with genetic susceptibility to tobacco related Oral Carcinoma in Asian Indians. Oral Oncol 44: 445-63. 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 of Infrastructure Facility shall be carried out for teaching purposes. Refurbishing of the website will be carried out.
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]
40 XXth All India BTISnet Coordinators’ Meeting February 03-04, 2009 Assam Agricultural University, Jorhat Coordinator: Dr. Mahendra Kumar Modi The Assam Agricultural University, Jorhat Center of BTISNet is functioning since 1990. At present the university has four faculties viz. Agriculture, Veterinary, Home Science and Fisheries with six constituent colleges. The main activity of the center is providing IT support to the students and scientistsvia Reference Retrieval system and facilities like computational analysis of the research data, Internet/Email facilities and imparting teaching and organizing training programmes on Bioinformatics. The facility is available for the teachers and researchers from 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 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 is actively engaged in 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 northeast India along with their detailed morphological and biochemical characteristics. We are also in the process of preparing a database on rice germplasm of North-East India
Major activities of the centre during the year 2008-09 1. Ministry of Information and Communication, Govt. of India, New Delhi has sanctioned a research project entitled “Agriculture Bioinformatics Promotion Project”. This project has three sub project entitled:
a) Bioinformatics Analysis of ADP Glucose Pyrophosphorylase
b) Computational Mining and Survey of Simple Sequence Repeats (SSR) and Single Nucleotide Sequence (SNP) in Expressed sequence tags of commercially important plants
c) Bioinformatics approaches for identification and characterization of R gene in crops and Avr gene in fungal pathogen with an aim to increase disease resistance.
2. 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. 3. The centre 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. 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, Titabor of Assam Agricul- tural 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, and 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.
Industry Relations Tea being the major agro-based industry of this region, the Scientists, manager, research workers from tea industry and Tocklai Tea Research Station has been supported by this Centre.
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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. The existing databases will be converted to web-accessible format so that these can be made available online.
42 XXth All India BTISnet Coordinators’ Meeting February 03-04, 2009 Banaras Hindu University, Varanasi Coordinator: Prof. Ashok Kumar Summary of the progress made by the Centre from its inception The Bioinformatics Centre was setup at the School of Biotechnology, Faculty of Science, Banaras Hindu University, Varanasi in 1989. The Centre has got three rooms with a total floor area of 740 sq ft. The posts of Data Entry Operator (grade II) and Programmer (grade II) were filled up in 1995 and and made permanent in 2005. The University has also provided the fiber optics connectivity. The Centre has acquired a number of software and databases for the use of researchers. It 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 Bioinformatics component of the M.Sc. Biotechnology course. The centre has been organizing training courses for manpower development in the area of Bioinformatics.
Major research activities in Biotechnology and its related fields Comparative and Functional genomics: Genome of Azospirillum brasilense is being analyzed for the regulatory cascades and networks that control signal perception, transduction and change in gene expression. Homology modeling, protein-protein interaction and protein-drug interaction: Structures of enzymes such as a-amylase, asparaginase, b-galactosidase,b-lactamase etc are generated by homology modeling. Molecular Microbial Diversity: Using methods based on nucleotide sequence of 16S rRNA genes microbial diversity has been characterized from human tissues samples, aquatic and desert plants, coalbeds and from contaminated sites. Bioprospecting novel genes by metagenomics: Clone library from the DNA from the metagenome of the coalbed microbes is being prepared and sequenced to find novel genes that might produce industrially important enzymes.
Area of Specialization of the Centre: Bioinformatics & Agriculture Major activities of the centre during 2007-2008 1. Activation of research in the areas dependent on Bioinformatics. 2. Executive Committee meeting held on 3. Participated in the teaching to the M.Sc. Biotechnology students on “Computer Applications, Bioinformatics and Biostatistics” course. Infrastructure facilities in the Bioinformatics Centre: A. Computer and Communication facility: Sl. NO. Particulars Quantity 1. HP Proliant ML 350 Server 1 No. 2. Optical Fiber Internet Connection (University) 1.No. 3. Xeon based 2.4 GHz Server with color monitor 1 No. 4. Pentium IV Computer System with color monitor 13 Nos. 5. HP Laser Jet Color/BW Printer 4 No. B. Scientific Software packages: The Centre has acquired software packages viz., “Exome” Version 1.3, Accelerys Gene 2.5.
Details about staff members working in the centre
Types of services provided: 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 Centre provides database accessibility online and through CD to all the interested users. c. Communication Services: The Centre provides the communication facilities to all the interested persons in the university.
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Educational activities with details of placement A course on Computer Applications, Bioinformatics and Biostatistics is offered to M.Sc. Biotechnology students. The facility is also used by M.Sc. Bioinformatics students of the university.
Collaborative works/initiative The Centre is providing support to the M. Sc. Bioinformatics program of Mahila Mahavidyalaya, BHU. It is also closely interacting with the Structural Biology group of CDRI, Lucknow; Centre for Bioinformatics, Pondicherry University, Biotechnology Unit, Aligarh Muslim University and Hyderabad Central University.
Papers published or presented in conferences with reference: 1. Nagarajan, T., Mishra, M. N., Spaepen, S., Vanderleyden, J., Gross, C.A. and Tripathi, A.K. (2008) Microbiology 154: 2096-2105 2. Kumar S, Kumar A, Dixit VK. (2008) Diagnostic Microbiolology & Infectious Diseases. 62:366-373 3. Jha, P.N. and Kumar, A. (2007) Journal of Applied Microbiology 103:1311-1320 4. Nagarajan, T., Vanderleyden, J. and Tripathi, A.K. (2007). Molecular Genetics and Genomics 278: 43-51. 5. Tripathi, P., Leggio, L.L., Mansfeld, J., Ulbrich-Hofmann, R., and Kayastha, A.M. (2007). Phytochemistry 68:1623-1631. 6. S Unlu, Kumar A, W. R. Waterman, J. Tsukada, K. Z. Q. Wang, D. L Galson, P. E. Auron (2007) Molecular Immunology 44: 3364-3379. Initiation of R&D activities in Bioinformatics The School has an Automated DNA Sequencer, which is linked to the Bioinformatics centre. This has facilitated and speeded 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). Genome of A. brasilense is being analyzed to identify the genes and their promoters related to abiotic stress tolerance.
Details of Training workshop organized and total no. of users trained: Organized a Short Training Course on LATEX for Ph.D. students in January 2009. Total No. of participants: 20.
Impact shown by your centre on the growth of biotechnology and allied areas. The centre has provided facilities in literature survey, sequence homology search, primer designing etc. More than 20 re- search papers have been published in Journals of repute with the tools available in the Centre.
Future activities The Centre proposes to organize two short training courses annually for the benefits of researchers involved in bioscience. The Centre also plans to develop its expertise in bacterial genomics.
Additional Details
Name of the Coordinator: Prof. A. K. Tripathi 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): Mr Dinesh Chaudhary Email: [email protected], [email protected]
44 XXth All India BTISnet Coordinators’ Meeting February 03-04, 2009 Banasthali Vidyapith, Banasthali Coordinator: Dr. Vinay Sharma Most significant achievements To cater the regional and national needs, the Centre has completed the database on “Flora of Indian Desert”. The following databases and software of biological and general importance were acquired by the Centre. A. Software packages Specialized Software Exome-An advanced sequence analysis tool General Software MS Windows Vista MS Office2007 Adobe creative suite 3.0 Adobe dream weaver Oracle 10G std. (for linux /unix, windows) B. Databases Agris Infrastructure facilities Sony DCR-SR 62 E Digital Video recording camera DVD Writer external (2 nos.) HP Laptop (HP Compaq 2210 b ,Intel 1.8 GHz,2 GB RAM, 160 GB HDD) (1 no.) HP Computer E-4500 (Intel-D 2.2 GHz, 2GB DDR RAM, 160 GB HDD) (4 nos.) HP Computer (Intel-D 3.0 GHz, 4GB DDR RAM, 160 GB HDD) (4 nos.) Photocopier machine Konica Minolta Model (1 no.) UPS 10 KVA Publications of Year 2008 Kumari, N. and Sharma,V. 2008. V-PPase in Plants: An Overview. Research J. of Biotechnology, 3:57-63. Verma, K., Shekhawat, G.S., Sharma, A., Mehta, S.K. and Sharma, V. 2008. Cadmium induced oxidative stress and changes in soluble and ionically bound cell wall peroxidase activities in roots of seedling and 3–4 leaf stage plants of Brassica juncea (L.) czern. Plant Cell Reports, 27: 1261-1269. Tripathi A., Sharma, N. and Sharma, V. 2008. In vitro efficacy of Hyptis suaveolens L. (Poit) essential oil on growth and morphogenesis of Fusarium oxysporum f.sp. gladioli (Massey) Synder & Hansen. World Journal of Microbiology and Biotechnology (in press). Sharma, V., Kumari, N. and Tripathi, B.N. 2008. V-ATPase in plants: An overview. Int. J. Biotechnol. & Biochem. (accepted) Vaishali, Khan, S. and Sharma, V. 2008. RAPD based assessment of genetic diversity ofButea monosperma from different agro-ecological regions of India. Indian J. Biotechnology, 7:320-327. Singh, A., Mishra, S., Raghav, D., Shanker, A. and Sharma, V. 2008. In silico method for the identification of Mycobacterial sp. Potential drug targets. ICCES, 174: 1-5. Tripathi, A., Sharma, N. and Sharma, V. 2008. Hyptis suaveolens (L.) Poit: A source of potential fungitoxic essential oil against post-harvest pathogens. Biochemical and Cellular Archives 8: 1-6. Sharma C.K., Saxena M. and Sharma V. 2008. Effect of different concentrations of sucrose on Picrol IV from Hairy root culture of picrorhiza Kurrooa. Biochem. Cell Arch. 8:255-259.
Books Published Sharma V., Munjal A. and Shanker A. (2008). Textbook of Bioinformatics. Rastogi Publications, Meerut.
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Proposed activities of year 2009-10 The centre is actively working on following projects: a) Bioinformatics analysis of Chloroplast Genomes b) Database of “Plant Host-Pathogen Interaction”. The centre proposes to organize specialized workshops in Bioinformatics.
46 XXth All India BTISnet Coordinators’ Meeting February 03-04, 2009 Barkatullah University, Bhopal Coordinator: Dr. Anil Prakash Summary of the Progress made by the centers from its inception Center has published one paper and one article in Bioinformatics and 4 papers in Biotechnology with the acknowledgment of Bioinformatics center. Center has also published 3 abstracts on Bioinformatics research in 49th AMI conference and In- ternational Symposium on “Microbial Biotechnology: Diversity, Genomics and Metagenomics” organized by University of Delhi during 18-20 Nov 2008. One abstract is also published by Dr. Anil Prakash in 12th ISME international conference Cairns, Australia. 5 more abstract are also published. Department organized 6 days training program for students IEHE College, Bhopal in Bioinformatics. Center has provided the teaching and training facility to Students of colleges and departments affiliated to the Barkatullah University.
Major research activities in Biotechnology and its related fields at your institution Biotechnology: a) Rhizobacterial diversity, Field evaluation of PGPR in association with the indigenous AMF in soybean and wheat cropping system b) Mycorrhiza Biofertilisers c) Mass propagation of Biofuel plant d) Inventorization of Medicinal plant e) Bioactive Compound from Medicinal Plant Bioinformatics: a) Microbial Genomics
Area of Specialization of the Centers Biotechnology: a) Micorhizal diversity b) Secondary metabolites produced by rhizobial bacteria c) Micorhizal AS Biofertilisers d) Mass propagation of Biofuel plant e) Medicinal Plant diversity of Madhya Pradesh Bioinformatics: a) Microbial Genomics Major Activities of the Center during the year 2005-2006 • 3 students did their Training in Bioinformatics • Organized 6 days training program for the students of IEHE college Bhopal. • Participated one international and 2 National Level Conferences and presented 9 posters (4 in Bioinformatics and 5 in Biotechnology) Infrastructure facilities in the Bioinformatics Center A. Computer & Communication facility Computer and Peripherals: 2 Servers (DNA- Windows Server 2003 & RNA – Linux Fedora Core 4) of Intel Xeon Processor 400 GB, 4 GB SDRAM 10 Clients Desktop: - Compaq – P IV, 40 GB and 256 DDRAM and 18 from Biotechnology grant: Wipro, P-IV, 20 GB, 128 RAM Printer: 5 in No. (HP Laser Color 1, Laser HP 1200 series – 2, Dot-matrix Wipro– 2) Scanner: 3 No. Networking Equipments Internet Facility: Router Cisco 1751 series, Switches: 4 Internet Connection: 512 kbps leased line connection Power Supply: UPS: 5 in no. (Working condition 2), B. Scientific Software Packages: 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
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(1 user), SQL Server 2000(1 server & 5 client) Licensed Bioinformatics Software: Hyperchem Release 7.5 (1 user) and ExomED research (1 user) C. Database & Other information resources: Details about staff members working in the center
Types of services provided • Training in Bioinformatics • Guideline in online reference and material searching and retrieval. • Solving the Hardware & Software related problems • Providing the Internet facility • Providing the Computational facility Collaborative Work/initiatives Biotechnology: MPCST, Bhopal Bioinformatics: Department of Limnology, Barkatullah University, Bhopal for FISH Biodiversity database of Madhya Pradesh Paper published or personated in the conferences with references: Nil Paper Publications: 6 Paper and Article in Bioinformatics 1. Anil Prakash and Kishor Shende, 2008; Bioinformatics and Personalized Medicine; proc. MEDBIO-2008 meet, BMHRC pub., 99-105 2. Neha Garg1, Sachin Pundhir, Anil Prakash and Anil Kumar; 2008, Primer Designing for Dreb1A, A Cold Induced Gene, Jou. Prot. Bioinfo., Vol.1:1-10. Publications with the Acknowledgement of Bioinformatics Center 3. D. K. Chaudhary and B. N. Johri, Anil Prakash; 2008; Volatiles as priming agents that induce plant growth and defense response; Current Science, Vol 94, No. 5:1-10. 4. Ragini Gothalwal; 2008; Anti Leishmanial drug therapy and Immunomodulation; proc. MEDBIO-2008 meet BMHRC publ. 5. Bhavdish N Johri and Ankit Kumar,2008; Rhamnolipids and their Potential applications; proc. MEDBIO-2008 meet, BMHRC pub.,65-72 6. Mishra, J, Agnihotri, RK, Nandi, SK, Palni, LMS & Prakash, A (2008) Characterization and clonal identification of selected tea Camellia sinensis (L.) O. Kuntze clones for plantation in Indian central Himalaya, using RAPD and ISSR markers (Submitted). Abstracts Published and Poster Presented: 9 Bioinformatics: 1. Kishor Shende, Anil Prakash, Ragini Gothalwal and Praniti Patidar, 2008, Codon usage pattern, in replication, transcription and translational genes of Lactobacillus acidophilus and Lactobacillus brevisATCC367, Proc. 49th AMI conf. Delhi, MB12:9 2. Kishor Shende, Tanushri Roy, Durgesh Gupta, Anil Prakash and Ragini Gothalwal, 2008, Diversity of Microcystin synthetase gene cluster among the cyanobacteria, Proc. 49th AMI conf. Delhi, MB 13:10. 3. Kishor Shende, Ragini Gothalwal, Kamalraj Pardasani and Anil Prakash, 2008, Codon usage pattern in protein
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coding genes of Staphylococcus aureus MSSA476, Proc. 49th AMI conf. Delhi, MB 29:18. 4. Kishor Shende; Anil Prakash, Ragini Gothalwal; Durgesh Gupta, Leena Agarwal and Prinyanka MAthur; 2008; Compositional bias in codon usage preferences among the 4152 genes ofBacillus licheniformis ATCC 14580; Proc. of 1st TEFBP, GGU, CG. FP-66:117. Posters published with Acknowledgment of Bioinformatics 5. Anil Prakash, Rubina Begum and B. N. Johri, 2008, Diversity of endophytic fungi in leaves of Stevia rebaudiana Bertoni, Proc. 12th ISME Cairns, Australia, 6. Ragini Gothalwal, & Sweta Rao; 2008; Comparative study of plant growth parameters ofArchis hypogea in fly ash and plant growth hormone supplemented Matsai soil; Proc. TEFBP, GGU, CG; FP-29:80 7. Mishra, J, Joshi, SC, Nandi, SK, Palni, LMS & Prakash, A., 2008, Characterization and clonal identification of tea clones selected from different agroclimatic zones of India using RAPD and ISSR markers, Proc. Sec. Int. Conf. “Trends in Cellular and Molecular Biology” JNU New Delhi. 8. Mishra, J, Nandi, SK, Palni, LMS & Prakash, A., 2008, Characterization and identification of tea clones using morphological, physiological and molecular markers, Int. Conf. “Biotechnology” Vellore Institute of Technology, Vellore. 9. Mamata Joshi, Abdul Khalid, Rashmi Srivastav, Ashish Kumar, Anil Prakash and Anil Kumar Sharma, 2008, Management of Fusarial wilt using antagonistic Fusaria., Proc. IPS-MEZ Ann. Meet. & Nat. Symp., P-115:162.
Details of Training/Workshop organized and total no. of user trained
Impact shown by your center on the growth of Biotechnology and allied areas i. Paper Published in Bioinformatics: 2 ii. Paper published with the help of Bioinformatics center: 4 iii. 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. iv. Through the Departmental website and the organizing workshop and Training in Bioinformatics Future activities i. To Start M.Sc. Course in Bioinformatics ii. To organize 3 workshops iii. To organize 3 months and 6 months training programs for the students Other Details
Name of the Coordinator: Dr. Anil Prakash Postal Address: Department of Biotechnology & Bioinformatics Center, Barkatullah University, Bhopal – 462 026 (Madhya Pradesh) India Phone Number: 91-755-2491848, 2491849 Fax No.: 91-755-2491850 E-Mail: [email protected] Website: www.bioinfobubpl.nic.in
Name of Contact person(s): Dr. Anil Prakash (Coordinator) Email: [email protected]
49 Sub - Distributed Information Centres Bharathidasan University, Tiruchirapalli Coordinator: Dr. L. Uma 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. Training workshops on the basics of bioinformatics are being conducted every year during the month of February / March. The Centre assists the National Facility for Marine Cyanobacteria (DBT, Sponsored Facility) and the Department of Marine Biotechnology faculty scholars and students by providing infrastructural facilities like internet, email, printing and also conducts bioinformatics theory and laboratory courses for M.Sc. and M.Phil programmes and project students. The Bioinformatics Centre at this institute, supported by DBT, has created awareness in cyanobacteria, the primordial organism. The Centre focuses on da- tabase generation, data mining and its application in wet lab research.
Major research activities in Biotechnology and its related fields at your institution The centre assists NFMC in the biotechnological exploitation of marine cyanobacteria through genome wide hunt in the areas of food, feed, fertilizer, fuel, fine chemicals, colourant, pharmaceuticals and waste treatment using marine cyanobac- terial Indian Isolates.
Area of specialization of the centre: Cyanobacteriology Major activities of the centre during the year 2008-2009 The leased line internet facility has been upgraded to 1mbps, and a pair of 1mbps 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 & WORTIC) is conducted every year and this year it is scheduled from March 2nd to 11th 2009). The wet lab hands on experiments are supported by insilico methods. The man power trained per year is @50 (students and researchers)
Research in Cyanobacterial bioinformatics: DATA MINING Identified keys to classify nitrilases, a novel enantiomeric/steriospecific non-protein C-N splitting superfamily of enzymes Predicted the unique putrescine synthesis (polyamine) pathway in cyanobacteria. The reverse putrescine synthesis pathway is also found to be absent. Development of database for cyanobacterial superoxide dismutases - the first line of defense antioxidant against oxidative damage (till dec 25th sequences categoreised 96)
Infrastructure facilities in the Bioinformatics Centre A. Computer & Communication facility Alpha Servers-2, Xeon Server-1, SGI FUEL Workstation-1,Pentium IV Computers-21 (2 Laptops), Scanner -1, Printers- 5 (4 + 1 Large format printer), 7.5 KVA UPS-1, LCD Projector- 1, Router-1, Leased Line Modems- One Pair, Lease line- 1mbps Leased-line internet connection is available round the clock. B. 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 260 books on bioinformatics and computer science is available for the researchers.
Details about staff members working in the centre Name Designation Specialization Period of working Whether absorbed Mrs.V.Sangeetha Technical Assistant Information Technology May 2008 No Mrs. R. Renganayagi Technical Assistant Computer Application 3.3 yrs. No Ms.Dhivya Jensi Technical Assistant Bioinformatics May 2008. No
Collaborative works / initiatives Collaboration with University of Calcutta and Apt Software Avenues Pvt Ltd, Kolkata on comparison and prediction of Cyto- chrome P450 superfamily the prime important detoxifying enzyme. is underway.
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Papers presented in conferences with reference In International Conference on Bioinformatics (InCoB 2008), organised by National Yang-Ming University, Taipei, Taiwan, Oct 20 – 22, 2008 1. Comparative analysis of cyanobacterial superoxide dismutases to discriminate canonical forms 2. Nitrilase superfamily in cyanobacteria – a concise study” 3. Biodecolourization mechanism of textile dye by marine cyanobacteria in National Conference on Environment Science and Technology, Bharathidasan University, Tiruchirappalli & Society for Science & Technology, Jalgoan. Nov 28 – 29, 2008
Initiation of R&D activities in bioinformatics Comparison of azoreducatses, cytochrome P450, important decolourizing /detoxifying enzymes Tools developed Online database on cyanobacteriology – available at www.nfmc.res.in A database booklet for workshop Almanac. Additional Detials
Name of Coordinator: Dr. L. UMA Postal Address: Bioinformatics Centre, NFMC Bharathidasan University Tiruchirappalli – 620 024 E mail: [email protected] Phone/Fax. : 0431 2407084
51 Sub - Distributed Information Centres Biotech Consortium India Limited, New Delhi Coordinator: Dr. Purnima Sharma 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 publica- tions and periodicals, databases and status reports and has organized several seminars/workshops, events, entrepre- neurs’ 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.
Major activities in biotechnology and its related fields at DISC BCIL’s main objective is to provide linkages to facilitate commercialization of biotechnology. BCIL has been en- gaged in technology transfer, consultancy, project management, fund syndication, certification services, information dissemination, and manpower training related to biotechnology. In these areas, it has assisted over 200 clients includ- ing scientists, technologists, research institutions, universities, first generation entrepreneurs, the corporate sector, government, banks and financial institutions.
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.
Major activities of the centre during the year 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: 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. II. Maintenance of following websites: The following websites were developed during the previous year and are being continuously updated by DISC: a) Indian Biosafety Clearing House (BCH) website (http://indbch.nic.in) b) Updation & Maintenance of DBT Biosafety website (http://dbtbiosafety.nic.in) 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 considering the immediate need for creating awareness on Management of IPR, a workshop on “Management of IPR in 52 XXth All India BTISnet Coordinators’ Meeting February 03-04, 2009
Biotechnology” was organized in the context of emerging global challenges. The workshop was attended by students, scientists and entrepreneurs in biotechnology. Eminent speakers from industry, institutions and patent office made presentations in the workshop. b) Entrepreneurship Development Programme (EDP) in Biotechnology: DISC at BCIL organized a series of Entrepreneurship Development Programmes (EDP) in Biotechnology under sponsorship from Department of Biotechnology (DBT) and Office of the Development Commissioner (MSME), Ministry of Micro, Small and Medium Enterprises were organized at Kolkata, Pune, Shimla, Indore, 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 such as medicinal and herbal plants, plant tissue culture, biofertilizers, biopesticides, probiotics, enzyme production, bioremediation etc. Around 300 prospective entrepreneurs attended these programmes 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.
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 th(5 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.
Impact shown by centre on the growth of biotechnology The DISC at BCIL is promoting activities related to commercial biotechnology by organizing workshops on 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 640 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 bollwormHelicoverpa armigera
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was transferred to two leading companies 3) A PCR based TB diagnostics technology was transferred to Arbro Pharmaceuticals Ltd., New Delhi. 4) The Directory of Biotechnology Industries and Institutions in India-5th Edition covering more than 1000 records was updated and released. 5) 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.
Future activities The Distributed Information Sub Centre (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. Organizing workshop on Management of IPR in Biotechnology iv. Updation of technology profiles v. Establishment and maintenance of websites vi. 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 vii. Providing value added services to the members of Biotechnology Club of DISC at BCIL viii. IPR Facilitation services Additional Details
Name of the Coordinator : Dr. Purnima Sharma Postal Address : Biotech Consortium India Limited 5th Floor, Anuvrat Bhawan 210, Deen Dayal Upadhyaya Marg New Delhi – 110 002 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]
54 XXth All India BTISnet Coordinators’ Meeting February 03-04, 2009 Biotech Park in Biotechnology City, Lucknow Coordinator: Dr. P. K. Seth
Bioinformatics centre, a cardinal component of the Biobusiness centre of the Biotech Park, serves as nodal point for industry- academia-public institution interaction. The centre offers a unique fusion of informatics with biotechnology and related disciplines. With hands-on facilities available at the Bioinformatics centre, its training programs are extremely successful and popular amongst research fellows, industry entrants and professionals planning to diversify and develop knowledge - based bio-business. The major thrust during the current year was to develop databases relevant to the need of the industries and the researches in the local area , strengthen the bioinformatics centre with addition of eighteen new internet nodes and eight new com- puters for catering the increasing need of training in fields relevant to industry and academia and to encourage research activity among the trainees and provide support to local institutions. Major highlights of the work undertaken during the current year are given below:
Databases The centre developed twelve databases namely Bio Control Agents, Medicinal & Aromatic Plants, DNA Repair Genes in Human, Neurotoxicant Biomarkers, Anti-Asthma Plants, Virus & diseases In Human, Virus & Viral diseases in Hu- man, Bacterial Diseases in human, Protein Misfolding Diseases caused in Human, Antioxidants, Role of FABPs in Meta- bolic Diseases and Fatty Acid binding Proteins. Five existing databases on Organic Farming, Biofertilizers/ Biopesti- cides, hemophelia, Educational Institutes in Uttar Pradesh, Antidibetic plants based on clinical/experimental trial were updated. In addition, the centre developed and maintained website onJatropha (www.dbtjatropha.gov.in), under a DBT sponsored project National Database on Jatropha, , which was launched by Shri Kapil Sibal, Honorable Union Minister of Science and Technology and Earth Science, Government of India at DBT on July 14, 2008.
Research Activities The center iniaited collaboration with Chhatrapati Shahuji Maharaj Medical University Lucknow and a student working as Programmer has been registered for Ph.D. degree on the topic “In-silico: identification of novel drugs for antiviral therapy against delta hepatitis using genomic approaches”. Another student pursuing studies on dengue virus and dengue hemorrhagic fever using bioinformatics tools for her Ph.D. degree was awarded Senior Research Fellowship of ICMR. Research work is also being undertaken by assigning small research projects to trainees in area of molecular modeling, proteomics and genomics study of dengue and hepatitis virus, modeling of membrane bound protein of mycobacte- rium tuberculosis; in-silico drug designing; phylogenetic analysis of envelope glycoprotein gp160 of HIV1 virus in Asian Countries; structure prediction of mannose binding lectine protein of Convovolus arvensis; mechanism of action of anti- diabetic herbs; clinical and experimental trails of anti-diabetic herbs; and database on medicinal and aromatic plants. These activates have led to submission of twelve protein structures in Protein Data Bank, development of above referred twelve databases and nine research papers given below: 1. Somvanshi P, Singh V, Seth PK (2008). Prediction of epitopes in Hemagglutinin and Neuraminidase proteins of Influenza A virus H5N1 strain: A clue for diagnostic and vaccine development. Journal of Integrative Biology Vol 12 (1) 61-69 PMID: 18266559. 2. Somvanshi P Singh V and Seth PK (2008). Identification and analysis of putative promoter motifsFlavivirus of using in silico techniques. Bioinformation. Vol 3 (4) 162-167. 3. Somvanshi P, Singh V, Seth PK (2008). In silico prediction of epitopes in virulence proteins ofMycobacterium tuberculosis H37Rv for diagnostic and subunit vaccine design. Journal of Proteomics and Bioinformatics Vol 1 (3) 143-153. 4. Somvanshi P, Singh V, Seth PK (2008).Insilico subcellular localization of putative protein of Mycobacterium tuberculosis H37Rv strain. The Internet Journal of Health Vol 7(1). 5. Somvanshi P, Singh V, Seth PK (2008).Phylogenetic and computational proteome analysis of Influenza A virus subtype H5N1.Internet Journal of Genomics and Proteomics Vol 3(2).
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6. Somvanshi P, Singh V, Seth PK (2008). In silico prediction and mapping of IgE motif epitopes in allergens from genetically modified foods for Immunotherapy strategy. Internet Journal of Infectious diseases. Vol 6 (2). 7. Somvanshi P and Seth PK (2008). In silico primer designing of structural region of dengue virus for molecular diagnostic. Internet Journal of Genomics and Proteomics Vol 3 (2). 8. Somvanshi P, Singh V, Seth PK (2008). Assessing the precision of high throughput computational approaches for the genome wide subcellular localization of putative proteins fromVibrio cholerae. Internet Journal of Genomics and Proteomics. Vol 3(2). 9. Somvanshi P, Singh V, Seth PK (2008). Phylogenetic investigation of lin genes involved in degradation of Hexachlorocyclohexane (HCH) Internet Journal of Toxicology.Vol 4 (2). Training Three DBT sponsored training workshops on (1) In-Silico Analysis of Bio Molecules and Drug Designing (2) Bioinformatics in Molecular Modeling, Data Analysis and System Biology and (3) Computational Tools and Databases for Genomics & Pro- teomics were organized in which 36 persons: scientists, medical doctors, research scholars and students form Maharashtra, Dehardun, Delhi, Lucknow, Kanpur, Allahabad, and other places of the country participated. Further 145 persons undertaken short and long-term (I to 6 month) training programs at the centre. More than 200 persons form different educational institutions viz. Medical collages, Pharmaceutical institutes, Universities and colleges visited the centre and got acquainted with bioinformatics tools and their applications.
Proposed activities for the year 2009-2010 Retrieval and dissemination of information on availability of funds from public and private organizations for start up companies, public private partnerships, and researchers in all fields of biotechnology. Database on resource persons for consultancy and guidance to startup companies in field of biopharma- and agribiotechnology. Updating of the website of Biotech Park, Lucknow and National database of Jatropha curcas To organize three short-term Training programmes and one national workshop on bioinformatics. Additional details
Name of the Coordinator: Dr. P. K. Seth Chief Executive Officer Postal Address: Biotech Park, Lucknow Sector-G, Jankipuram, Kursi Road, Lucknow-226021 Phone Number: +91-522- 4053000-20, 4012076. Fax No: +91-522-4012081 Email: [email protected] [email protected] Website: www.biotechpark.org.in Name of the contact person(s): Dr. Pragya Gupta/ Mr. Sunil Kumar Gupta
56 XXth All India BTISnet Coordinators’ Meeting February 03-04, 2009 Birla Institute of Scientific Research, Jaipur Coordinator: Dr. M. Krishna Mohan Summary of the centre Birla Institute of Scientific Research, Jaipur is a leading 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. The BTIS-SubDIC at BISR was established in 1999. This is one of the core facility used by scientist for analysis of data using various Bioinformatics software application for their research work. This facility is also used by other nearby academic institutes and universities. Recently BISR has initiated research in the area of Proteomics, Genomics and Structural Bioinformatics. Besides, efforts are being made to develop various quality information resources in the form of databases and software for professionals in the area of biotechnology and Bioinfor- matics.
Major activities of the institute 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. Major activities of the centre during the year 2008 - 09 a) National workshop on advance areas of Bioinformatics Molecular Modeling and Drug Designing, 16-18 October 2008 Computational Genomics , 20-22 January 2009 b) Research training in Bioinformatics was imparted to 10 students in the form of their dissertation work. c) Initiation of development of a tool for understanding Interaction-Specificity in Protein-Ligand Complexes has been started. d) Development of a tool for theoretical prediction and analysis of proteomic data has been started.
Infrastructure and Scientific Software at Bioinformatics Centre The centre has procured the following scientific software packages: GCG Sequence Analysis Package from Wisconsin group, Exome Horizon from MASCON, Discovery Studio Package from Ac- celrys, Vector NTI, Reference Manager, Visual Studio, CLC workbench, PDQuest Image Analysis.
Types of services provided 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. The centre has leased line Internet connection as well latest Bioinformatics software for sequence and structure analysis. The center provides the following services: a) Bioinformatics supports to researchers b) Customized training in Bioinformatics for researchers and faculty members c) Support in Installing, implementing and maintaining software on computer. d) Create awareness for taking preventive measure against data security e) Organizing workshops in Bioinformatics f) Research Training to students of Biotechnology and Bioinformatics g) Email and communication facility Biotechnology Impact and Publication 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 2007-09 institutes has published 10 57 Sub - Distributed Information Centres research papers in peer reviewed journals in the area of Biotechnology and Bioinformatics. The recent publication is Amit N, OP Jangir, PS Solanki, Vijay S, M Krishnamohan (2008) In Silico and In Vivo Study of Lens Regeneration Under the Influence of Retinoid. J Proteomics Bioinform 1: 104-108. Name of Contact Persons
1. Dr M Krishnamohan Mobile: +91-9314509942 Email: [email protected] 2. Mr. P S Solanki Mobile: +91-9928365838
58 XXth All India BTISnet Coordinators’ Meeting February 03-04, 2009 Birla Institute of Tehnology, Ranchi Coordinator: Dr. A. S. Vidyarthi Summary about the Bioinformatics center 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. Organiza- tion of training programs, workshops and scientific meetings in order to create awareness of bioinformatics in the local community is among its regular activities.
Area of specialization of the center Medicinal and Aromatic Plants, Molecular Modeling, Database development, drug designing, Functional Genomics of Rice and Computational Bioinformatics.
Major activities of the center during the year 2008-09 • Projects for B. E. Biotechnology and M. Sc. Bioinformatics students were assigned and conducted in this lab. • Development and upgradation of database of medicinal and aromatic plants available at Jharkhand, Infectious disease, Economically Important microorganism, Target proteins are in progress. • Development of Protein Sequence Analyzing and motif finding Software. • Identification and modeling of Anti-sars drugs, NS3 protease and potential therapeutic targets. • Codon biasing and host radiation Study in H5N1 influenza viruses. • Rice Functional Genomics and Analysis. • Drug discovery by high through put screening against target molecules and known homologs from different medicinal plants. Infrastructure facilities in the Bioinformatics Center A. Scientific Software packages • GCG 11.0 (Sequence Analysis) • Insight II, HOMOLOGY, BIOPOLYMER (Molecular Modeling) • SYSTAT 11.0, SIGMAPLOT 9.0 (Statistical Analysis) • DS GENE STATIC (Sequence search on Internet) Details about staff working in the center
Educational activities with details of placement M. Sc. in Bioinformatics (2 years) and B.E. in Biotechnology (4 years). Placement of the students in the institute is more than 70%.
Databases/ Softwares packages developed • Database for aromatic and medicinal plants (AROMED) has been developed. • Infectious Disease Database is in progress. • Economically Important microorganism database is in progress. • Database of Target protein: Yersinia pestis – A case study. Papers published or presented in the conferences with references • Ashutosh Ranjan, A. S. Vidyarthi and Raju Poddar, Evaluation of Codon Bias Perspectives in Phage Therapy of Mycobacterium tuberculosis by Multivariate Analysis, In silico Biology, 2007, 7 (4-5), 423-431. • S. Sharma, A. S. Vidyarthi and R. Poddar. Analysis of Synonymous Codon Usage Bias in Pseudomonas Syringae Phages: Implication in Phage Therapy for Halo Blight Disease. Journal of Proteomics & Bioinformatics, 2008, 1(4), 206-18.
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• S. Srivastava, P. Shukla and Raju Poddar, In sillico study of sequence homology of family 11 Xylenases from Thermomyces lanuginosus, Journal of Applied Sciences in Environmental Sanitation. 2 (3): 70-76. • Kumar A, Smita S, Sahu N, Sharma V, Shankaracharya, Vidyarthi AS, Pandey DM (2009) In silico analysis of Motifs in Promoter of Differentially Expressed Genes in Rice (Oryza sativa L) under Anoxia” IJBRA (Accepted). • Kumar A, Barik A, Vidyarthi AS and Pandey DM (2008). In Silico prediction and identification of Anoxia Responsive Single Exon Genes in Rice (Oryza sativa L.). In: 6th International Symposium on Rice Functional Genomics at Jeju, Republic of Korea scheduled on 10-12 November, 2008. 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, in silico analysis of siRNA and miRNA in plants.
Details of training/ Workshop organized and total no. of user trained “National Workshop on Structural Bioinformatics” held on September 8-13, 2008. (Number of participants 20).
Future activities Research • Functional genomics of Rice • Molecular modeling and drug design • Systems Biology and pathway modeling • Workshop: A workshop will be conducted on systems biology and Pathways modeling. • Training: Students will be allotted under the scheme traineeship and studentship to accomplish the tasks in Bioinformatics. 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] Website: www.bitmesra.ac.in Name of the contact person: Dr. A. S. Vidyarthi Mr. Shankaracharya E-mail: [email protected] [email protected]
60 XXth All India BTISnet Coordinators’ Meeting February 03-04, 2009 Central Agricultural Research Institute, Port Blair Coordinator: Dr. M. Balakrishnan 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 developed with well equipped computer facility like hardware including computers, proxy server, mail server, database server and VSAT. The main aim Bioinformat- ics 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. This centre can serves as an ac- tive 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.
Major research activity in biotechnology, bioinformatics and its related fields at your institution Biotechnology Section of CARI, conceptualized and developed during 1992 and the projects on cell technology and molecular biology research including transgenic development and gene tagging for excess salt tolerance were started. The facilities like 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) 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.
Area of specialization of the centre. Development of database for the Biodiversity of A & N Islands.
Major activities of the centre during the year 2008-2009. The Centre during this year has been actively involving in the creation of databases for the biodiversity of A & N Islands, IFS and mango along with imparting training students of various universities in the field of molecular model- ing 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.
Infrastructure facility at the Bioinformatics centre A. Computer and Communication Facility The hardware includes Pentium desktop computer (12 nos), LAN, proxy server, mail server, database server and VSAT (Institutional Facility), digital photocopier, Network Printer, UPS 7.5 kw (2 nos), Scanner, LCD Projector.The Software includes windows NT, 2000 and 2003,Redhat-9, BioLinux, Java, Ms-Office, Adobe and Macro Media Collections, Oracle 9i, Ms SQL server 2005, MS.Net. B. Scientific & Software Packages Scientific software packages Molecular modeling (Modeller 9v2, JACKAL, ICM Pro, CAChe, Discover studio), Sequence analysis (GeneDoc, Accelrys gene, CLC work bench 2, Bioedit.), Protein Analysis(Cn 3D, Rasmol, Jmol, SPDB Vivwer, Pymol), Docking(Hex, Arguslab),Bio-Statistical Analysis(Spss, Matlab), 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), Bio perl, Bio Pythan, Bio java, Bio SQL are available. Details about staff members working in the centre. Name of the Staff Designation Specialization Period of working Absorption status Mr. Ramachandran RA M.Sc. Bioinformatics November 2008 nil Ms. Soma Mondal SRF M.Sc. Computer Science March 2007 nil Ms.AgeethaBibi JRF M.Sc. Biotechnology November 2008 nil Types of service provided. Bioinformatics Centre at Central Agricultural Research Institute, Port Blair is focused on providing qualify consul- tancy services in the field of website architect, database development, administration, Biological softwares and tools development and manpower training. Our team here at Bioinformatics centre can assist any progressive organization /
61 Sub - Distributed Information Centres institute in developing, integrating and maintaining valuable biological data so that it can be accessible in a safe and com- fortable manner.
Educational activity with details of placement. 5 M.Sc. (Biotechnology), 5 M.Sc. (Bioinformatics), 1 M.Sc. (Microbiology) final year students along with 4 summer training students from mainland universities Bharthidasan, Bharthiyar, Rajasthan, Durgapur University had successfully completed their dissertation work in field of molecular modeling, structure based drug designing and gene annotation. Currently a total of 15 students from Bharthidasan and Bharathiar University are undergoing their project work.
Initiative to validate the outcome of bioinformatics resources. N.A Collaborative works/initiatives. Collaboration with Pondichery University (Training), NIOT(Fish Genetic Resources), Presidency College(Drug Design), Chen- nai and ICMR’s (Genomic Sequencing) regional centre here in the islands and Anna university in the area of molecular modeling and database development.
Databases / Software package developed. The databases on medicinal plants, economically important plants, rice cultivars, orchids, Mangroves, fish genetic resources, etc, have been developed. Recently CARI, Sub-DIC has also developed 4 more databases which include database for Inte- grated farming system models in A & N Islands, database of Biodiversity of A & N Islands, animal genetic resources, fodder resources of A & N Islands and Internet tools & Database Resources for Plant Genetics.
Paper published or presented in the conference with references Balakrishnan, R.C.Srivastava and Mayank pokriyal(2008). Biodiversityn Of Andaman and Nicobar Islands, BioBytes Journal, ISSN 0971 3271: Vol (3)Oct - 2008: pp: 09 - 11. Balakrishnan, M., S.Jayakumar, R.C.Srivastava and Mayank Pokhiryal. Database for Animal Genetic Resources of A & N Islands. In Proc. of National Workshop on Molecular Modeling and Protein Docking organized by Department of Biotechnology, New Delhi. on 25- 28 February 2008, pp.67-70. Balakrishnan, M., R.C.Srivastava S.K.Zamir Ahmed and Subash Chand. Text Mining:Potential Application in Bioinformatics. In Proc. of National Workshop on Molecular Modeling and Protein Docking organized by Department of Biotechnology, New Delhi. on 25- 28 February 2008, pp.85-88. Balakrishnan, M., R.C.Srivastava. 2008. Internet tools & Database Resources for Plant Genetics, The Echo of India, Port Blair September -24(08) : pp.5. Balakrishnan, M., Ravisanjar, N., R.C.Srivastava and S.K.Zamir Ahmed. 2008. E Agriculture – Prospects and Retrospects, The Echo of India, Port Blair August - 4(08) : pp.5.
Initiation of R & D activities in bioinformatics Sub-DIC is actively involving in research activities like application of bioinformatics in nucleotide and protein sequence align- ment, 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.
Details of training / workshop organized and total no. of user trained. Sl.No Topic From To No. of Participants 1 One day workshop on bioinformatics and its application 27th Mar, 2008 30 2 Bioinformatics tools for gene and protein Analysis 4 days 26th -29th July, 2006 27 3 Database Development and its Application in Biodiversity 19th – 23rd Feb, 2007 27 4 National Conference on “Bioinformatics Tools for Gene and Protein Analysis” in collaboration with SIGC, Trichy 7th – 8th Sept, 2007 450 5 National workshop cum training on “Molecular Modelling and Protein Docking” 25th – 28th Feb, 2008 30
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Impact shown by your centre on the growth of biotechnology and allied areas. The centre is also providing training on bioinformatics tools for gene and protein sequence analysis, gene annotation, da- tabase designing, web technology to UG, PG students from mainland universities.
Future Activities Gene expression studies related to agricultural crops of prime importance in A & N Islands. Development of Protein Prediction models using the concept of Artificial Neural Network (ANN) and Data mining. Database for medicinal plants with anti-HIV activity in A & N Islands. Creation of database for stress responsive genes in agricultural crops . To design and develop database on plant genetic resources of Bay Islands.
Additional Details
Address: Central Agricultural Research Institute Coordinator: Dr. M. Balakrishnan Bioinformatics Centre Biotechnology Section Port Blair - 744101
63 Sub - Distributed Information Centres Central Drug Research Institute, Lucknow Coordinator: Dr. P. K. Roy Summary of the progress made by the centre from its inception BTIS centre has been catering to the information requirements of the users working in the area of Biomedical Research. 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 includes: 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 Area of Specialization of the Centre: Biomedical Research Major Activities Bioinformatics BTIS at CDRI extends hardware/software facilities and provides information resources for the Bioinformatics research work being carried out by CDRI as well as other visiting scientists/students working in the area of Bioinformatics. Information Services Being a National Information Centre on Drugs and Pharmaceuticals, our library caters to the information needs of the students, researchers of institutions/ universities involved in biomedical Research all over the country. Current Awareness services Current awareness service in the area of Drugs and Pharmaceuticals 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 are: Drugs & Pharmaceuticals - Industry Highlights (Monthly) Drugs & Pharmaceuticals - Current R&D Highlights (Quarterly) Infrastructure facilities in the Bioinformatics Centre Earlier, We had few computers attached to a server to cater to the users information needs. However, with the grant made available by the BTIS we have acquired more computers and latest version of server. The resources procured are: R&D Insight online Pharmacopoeias on CD About 3000 online journals of all major publishers More than 350 journals 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.
Papers published or presented in the conferences with reference K. Avasthi, S. Aswal, S. M. Farooq, R. Raghunandan, P. R. Maulik,: Unusual effect of bulky isopropyl group on robustness of the U-motif in pyrazolo[3,4-d]pyrimidine core based ‘Leonard linker’ compounds in comparison to methyl/ethyl group: A 1H NMR and X-ray crystallographic study. J. Mol. Structure, 888, 327–336. Kumar R, Bhakuni V.: Mycobacterium tuberculosis isocitrate lyase (MtbIcl): role of divalent cations in modulation of functional and structural properties. PROTEINS: STRUCT. FUNCT. BIOINFORMATICS (2008)72(3), 892-900. Kumar, A., Chaturvedi,V., Bhatnagar, S., Sinha, S., and Siddiqi, M.I.: Knowledge based identification of potent anti-tubercular compounds usingstructure based virtual screening and structure interaction fingerprints http://pubs.acs.org/doi/abs/10.1021/ci8003607) J. Chem. Info. and model. (Available online 9 Dec, 2008 Luthra A, Malik SS & Ravishankar Ramachandran: Comparative structural analysis of two hypothetical proteins from Mycobacterium tuberculosis found in the human granuloma during persistence and highly up-regulated under carbon-starvation conditions Prot. Exp. Purif. 62, 64-74, 2008
64 XXth All India BTISnet Coordinators’ Meeting February 03-04, 2009
Malik SS, Luthra A & Ravishankar Ramachandran: Interactions of theM. tuberculosis UsfX with the cognate sigma factor SigF and the anti-anti sigma factor RsfABBA:Proteins & Proteomics, 10.1016/j.bbapap.2008.11.007 Malik SS, Luthra A, Srivastava S & Ravishankar Ramachandran: The M. tuberculosis UsfX (Rv3287c) exhibits novel nucleotide binding and hydrolysis propertiesBiochem. Biophys. Res. Comm. 375, 465-470, 2008 Ritu Malik, Shailesh Tondwal, K S Venkatesh and Amit Misra: Nanoscaffold matrices for size-controlled, pulsatile transdermal testosterone delivery: nanosize effects on the time dimension, 2008, Nanotechnology 19 (43) 435101 Singh, K., Bhakuni, V.: Toxoplasma gondii Ferredoxin-NADP+ Reductase (TgFNR): Role of ionic interactions in stabilization of native conformation and structural cooperativity PROTEINS: STRUCT. FUNCT. BIOINFORMATICS (2008) 71(4):1879-88. Tripathi SM & Ravishankar Ramachandran: Crystal structures of the Mycobacterium tuberculosis secretory antigen Alanine dehydrogenase (Rv2780) in apo and ternary complex forms captures ‘open’ and ‘closed’ enzyme conformations PROTEINS 72, 1089-1095, 2008 Tripathi SM & Ravishankar Ramachandran: Over-expression, purification, crystallization and preliminary X-ray analysis of Rv2780 from Mycobacterium tuberculosis H37Rv Acta. Cryst. Sect. F 64, 367-370, 2008 Y.S. Prabhakar and M.K. Gupta: Chemical Structure Indices. In Silico Molecular Design, Sci Pharm. 76, 101-132 (2008);
Future activities With the funds 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 develop in-house databases in the areas hitherto untouched by others. Additional Details Name of the coordinator: Dr. ( Mrs) Sheela Tandon Dy. Director & Scientist-in-Charge Knowledge Resource Centre Central Drug Research Institute Lucknow-226001 Phone No.: 522-2613812 Fax. No.: 522-623405 Email: [email protected]
65 Sub - Distributed Information Centres Central Institute of Fresh Water, Bhubaneshwar Coordinator: Dr. A. K. Roy Important activities after last coordinators meeting 1. Up gradation and Maintenance of hardware and software The Bioinformatics centre (BIC) of CIFA is maintaining an excellent IT facilities in terms of the hardware and software. Since last coordinators meeting the Bioinformatics centre is further upgraded by installation of two window based server. In order to protect the system from virus and malwares, the centre is protected through gate way level of protection with cyberroam. The standalone antivirus is also provided to servers and all PCs connected to the BIC. The new software dealing with the analysis of statistic and econometrics like STATA, LIMDEP, JMULTI, GRETI and GPOWER are acquired and installed in the BIC. The existing software like SAS and SPSS are in operational and served continuously. 2. Creation of intranet The INTRANET of CIFA is being created and operated from the serves installed in the BIS. It is an window of information on circulars, internal documents, chat, blog etc for the staff of CIFA. 3. Data base All the relevant data on the agriculture, water and fisheries are being acquired and maintained by the BIC. The FAO data base on fisheries “Aquatic sciences and fisheries Abstract” ASFA online is maintained and used widely by researchers and students. Agricultural and fisheries journals made available by the Indian Council of Agricultural Research available through Bioinformatics centre. A total of 1181 journals are available through it. 4. National Workshop cum Training Programme A National Workshop-Cum-Training on Bioinformatics and Statistics in Aquaculture Research during 24th to 26th March 2007 was orgasnised. The workshop was inaugurated by Dr. Swadhin Pattanaik, Director, Institute of Mathematics & Application. Honorable Prof. S. C. De Sarkar, VC, KIIT University and Dr. P. Kumar, Ex- Professor & Head IARI, New Delhi were the Guest of Honour. Altogether 45 participants comprising officials from the states of Orissa, West Bengal, Chhattisgarh, Uttar Pradesh, Karnataka, Bihar and Andhra Pradesh attended the workshop. The Institutes represented by participants are IASE Off Campus Center, Dept. of Marine Living Resources, Andhra University, S.K. Mahila College, Indian Institute of Toxicology Research, University of Burdwan, Fakir Mohan University, TACT School of Biotech Sciences, CMFRI, Mangalore, Newton Science College, State Fisheries, Chattishgarh, Dept. of Bioinformatics, OUAT, Aquatic Resource Health Management Centre, SIFT, Kikinada, MITS, Sriram Bihar and CIFA. A total of 48 Resource Persons from various Organizations/ Institutes viz. Indian Agricultural Statistics Research Institute, New Delhi, Bose Institute, Kolkata, Indian Agricultural Research Institute, New Delhi, CARI, Portblair KIIT University, Bhubaneswar, Indira Gandhi Agriculture University, Orissa Community Task Project, Dept. of Water Resources, Knowedge Trust, Bhubaneswar, Dept. of Statistics, BCKV, Mohanpur, OUAT, Bhubaneswar, Dept. of Natural Resource Economics, WTCER, Bhubaneswar, Deshbandhu College, Delhi University, , Institute of Life Science, Bhubaneswar, PL Nayak Research Foundation, Cuttack, Regional Research Laboratory and CIFA, Bhubaneswar. The lectures were delivered by the resource persons in various areas like Relevance of Bioinformatics in Biotechnology, Cryoconservation, Knowledge Discovery Probiotics, Fundamentals of proteomics and Functional Genomes, Molecular Taxonomic Analysis using DNA Surveillance and DNA Barcoding, Soft Computing Techniques for Data Analysis and Modeling, Application of Software in molecular Modeling, Statistical Techniques in Bioinformatics, Nanotechnology, Data Warehousing, Recent trends in Artificial Neural Network and Fuzzy Logic and their application in Aquaculture, Present Scenariop of Ornamental fish farming and Trade, Multivariate Data Analysis, Institutional and Policy Dimension for Aquaculture Development, Genomic Data Analysis using Softwares, Construction of Phylogenetic Tree Using Clustal W & Phylip, Data mining and Databases, Extension in digital Era, Modeling and Forecasting and Genetic Statistics, Centrometric Studies on Fisheries Research, Econometric Analysis, IPR issues in Aquaculture, etc. 5. Research Works Correspondance Analysis (CoA) of Genomic Sequence of carps using SPSS (Statistical Package for Social Sciences): Correspondance Analysis on 38 nucleotide Sequences including est ( 24 expressed sequence tags) and cds (14 Coding Sequences) of Labeo rohita is carried out and it is found that most of the sequences are baised to GC ending codons . Correspondence Analysis of RSCU (Relative Synonymous Codon Usage) of 13 genes of Cyprinus carpio is carried out. From the biplot generated by SPSS it is revealed that The Genomic Sequence of Cyprinus carpio is rich in GC content. Stepwise demonstration of the Correspondence Analysis using SPSS is carried out to understand the intermediate
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steps of analysis. The correspondence map of symmetric Normalization reveling the association between nucleotide sequences and codons are plotted through a number of steps which includes generation of profiles and distances, active margins, Masses, singular values, inertia and finally the scores in various dimensions that are the coordinates for points in the plot. Comparative analysis of Codon Usage values of three species viz. Cyprinus carpio, Carassius auratus x Cyprinus carpio and Carassius auratus x Cyprinus carpio x Carassius cuvieri is being carried out. Microarray Analysis Different Statistical Methods used in the analysis of Microarray data are K-means clustering, Hierarchical Clustering, Self Organizing Map, Fuzzy C-Means Clustering, etc.
Proposed activities for 2009-10 · Continuation of the Bioinformatics centre: All the hardware, software, facilities etc created in the centre since last 18 years will be maintained. · Workshop on Bioinformatics in Aquaculture: A national level workshop and training on Bioinformatics in aquaculture will be organised during March. · Recruitment of staff: Two students in will be recruited in the project to support the project activities. · Publication of book on bioinformatics, statistics and economics: the edited book on the bioinformatics, statistics and economics covering new research themes will be published · Development of the websites: New website of the institute will be developed. · Connectivity: The speed of internet connectivity to the Bioinfmatics centres will be upgraded to 1 G from 512 MB through lease line connection. · Acquiring hardware and software: The four old computer will be replaced with new one in the BIC and new statistical software SYSTAT will be aquired. · Data base: The data on the socio-economics and biotechnology available from the government sources will be acquired and maintained particularly from National Sample Survey. List of publications published by the center in the area of Bioinofrmatics Books: • Roy, A.K. and N. Sarangi. 2008. Applied Bioinformatics, Statistics & Economics in Fisheries Research,New India Publication Publishing Agency, Pitam pura New Delhi.Pp. XXI + 605 • Roy, A.K., G S Saha, P. Kumaraiah, N. Sarangi, B. S. Giri and S. Ayappan. 2008. Socio & Techno-economic Aspects of Aquaculture in Kolleru Lake, AP, India. Central Institute of Freshwater Aquaculture (CIFA), Kausalyaganga, Bhubaneswar. Pp. XVI + 154. Research Articles: 1. Roy, A. K. and S. R. Martha 2007. Correspondence Analysis of Relative Synonymous Codon Usage values of L.rohita. SPSS Analyst. Oct-Dec:30-35. 2. Roy, A. K. and S. R. Martha. 2007. Multivariate Statistical Analysis of Codon Usage values L.of rohita. International Conference on Applied Bioengineering held at Chennai during 5th-7th December 2007(Abs.). 3. 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). 4. 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 (CCMB, Hyderabad, India). 9 -10 (Abs.). 5. Roy, A. K., H. K. De, G.P. Reddy and J.Goudo.2007.Status and Methodological Aspect of Impact Assessment in Aquaculture. Ibid., pp: 359-377. 6. Saxena, Ravi R and A. K. Roy. 2007. Analysis of Aquaculture Experiments using Statistical Packages. Ibid. pp 285-297. 7. Jena Nibedita and Nirupama Panda and D.P. Rath 2007. Linear Programming and its Applications. Ibid. pp: 503-509. 8. Saxena, Ravi R. and A. K. Roy. 2007. Statistical Methods for Assessment of Poverty Levels. Ibid. pp: 476-483.
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9. Rath, S.N., 2007. Application of .Net Platform in Designing Website.Ibid. 244-246. 10. Panda Nirupama and Nibedita Jena. 2007. Economic Order Quantity (EOQ) Model for Inventory Management in Fisheries. Ibid. pp: 527-530. 11. De, H. K. 2007. How to Conduct Evaluation of Extension Programmes. Ibid. 494-502.
68 XXth All India BTISnet Coordinators’ Meeting February 03-04, 2009 Central Institute of Medicinal and Aromatic Plants, Lucknow Coordinator: Dr. Ashok Sharma Summary of the Progress made by the centre from its inception Bioinformatics Centre, since its inception in 1998 is the backbone of bioinformatics/computational analysis in R&D activities of CIMAP. The major research activities undertaken include database/ tool development and computa- tional research analysis in the areas of Genomics, Transcriptomics, Proteomics, Metabolomics, Cheminformatics, Pharmacoinformatics, Virtual High Throughput Screening etc. Besides, microsatellite genetic markers identification, functional annotation of drug/biomolecules target identification, lead molecules identification & optimization R &Dare also pursued at the Bioinformatics Centre. Centre also continued to provide Human Resource Development through its summer and winter training programs.
Major research activities in Biotechnology and its related fields 1. Research Analysis/ novel in silico method development in Genomics Proteomics and Cheminformatics & Pharmacoinformatics 2. Development of Bioinformatics Databases/Tools:
Area of specialization Bioinformatics, Cheminformatics & Pharmacoinformatics studies related to biomolecules/bioactive compounds of Medicinal & Aromatic Plants (MAPs).
Major achievements made during 2008-09 Bioinformatics R&D activities- 1. Development of Bioinformatics Database: a. DbMDR: A Web-Accessible Relational Database for Multi Drug Resistance Genes 2. Development of Bioinformatics Tool: a. D-MATRIX: A tool for constructing transcription factor binding sites weight matrix. 3. Research analysis related to genomics, transcriptomics, proteomics and metabolomics: a. In silico metabolic pathway reconstruction of vanillin biosynthesis in Aspergillus sp. b. Weight matrix based genomic identification of SinR transcription factor binding sites in nitrogen fixing bacterium Bradyrhizobium japonicum. c. Performance evaluation of DNA Motif Discovery Programs. d. Prediction of MHC Class-I binders/non-binders peptides using probability distribution functions and artificial neural network e. Identification of SSR-ESTs corresponding to alkaloid, phenylpropanoid and terpenoid biosynthesis in MAP’s. 4. Research analysis related to cheminformatics & pharmacoinformatics: QSPR & docking based structure properties and docking based virtual high throughput screening for anti-cancer lead identification; Pharmacovigilance: Effects of Herbal components on human drugs interactions involving Cytochrome P450; Antifungal drug target identification for fungiCandida albicans; Functional assignment of hypothetical proteins in Candida albicans as potential anti-fungal drug targets. Infrastructure facilities in the Bioinformatics Centre Commercial Bioinformatics Softwares: 1. SYSTAT (For statistical analysis) 2. GENOCLUSTER (For Biological Sequence analysis) 3. Oscimum’s GenChek (For Biological Sequence analysis) 4. Scigress Explorer (CAChe) (For QSAR/QSPR and Docking analysis) 5. ADME_Work_Model_Builder (For QSAR/QSPR model building)
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Details about Staff members working in the centre
Papers/ published or presented in the conferences 1. Akansha Saxena, Kumar Parijat Tripathi, Sudeep Roy, Feroz Khan, Ashok Sharma. 2008. Pharmacovigilance: Effects of Herbal components on Human Drugs Interactions involving Cytochrome P450. Bioinformation, 3(5), 198- 204. 2. Kumar Parijat Tripathi, Sudeep Roy, Feroz Khan, Ajit Kumar Shasany, Ashok Sharma and S.P.S Khanuja. 2008. Identification of SSR-ESTs Corresponding to Alkaloid, Phenylpropanoid and Terpenoid Biosynthesis in MAP’s. Online Journal of Bioinformatics, Vol. 9 (1): 78-91. 3. Ashok Sharma, Sudeep Roy, Kumar Parijat Tripathi, Manoj Mishra, Pratibha Roy, Feroz Khan and Abha Meena. In silico Insight to Predict and Analyse Putative Metal Binding Sites for Phytoremediation in MAP’s. Proceeding of Asia Pacific Bioinformatics Network (APBioNet) 7th International Conference on Bioinformatics (InCoB2008), Taipei, Taiwan, 20–23 October, 2008. (Oral Presentation) (To be published in special issue of Bioinformation Journal). 4. Kumar Parijat tripathi, Sudeep Roy, Pakhi Khanna, Sanchita, Abha Meena, Feroz Khan, Ashok Sharma. Identification and modelling of proteins presents in Curcuma longa using splice alignment methodology: Comparative Genomics approach. Proceeding of Fourth National Interactive Meet on “Scope & Opportunities in Research & Business of Medicinal & Aromatic Plants: Meeting the Global Competition & Quality Standards (NIM- 2008), November 29-30, 2008, NIM-90, CIMAP, Lucknow (Won the Best Poster Prize). 5. Suchita Srivastava, Suaib Luqman, Feroz Khan, Chandan S. Chanotiya, Mahendra P. Darokar, Ashok Sharma. In silico Metabolic Pathway Reconstruction of Vanillin Biosynthesis in Aspergillus sp.Proceeding of 49th Annual Conference of Association of Microbiologists of India, International Symposium on ‘Microbial Biotechnology: Diversity, Genomics & Metagenomics’, organized by Dept. of Zoology, North Campus and Dept. of Microbiology, South Campus, University of Delhi, November 18-20, 2008. (Poster Presentation)
Initiation of R&D activities in Bioinformatics: i) Genomics & Proteomics: a) To analyze hypothetical genes, ESTs sequence assembly and functional annotation of genes. b) To identify potential genetic markers such as microsatellite (SSR) related to MAPs. ii) Cheminformatics & Pharmacoinformatics: a) To identify the active sites of the receptors/targets, binding pockets, interaction energies through docking studies. b) To identify potential leads & targets through in silico Virtual High Throughput Screening (VHTS). c) To study pharmacokinetics of chemical compound/biomolecules for Drug-likeness/Druggability through Lipinski’s Rule of Five filter, QSAR/QSPR and ADMET analysis. iii) Development of Bioinformatics Databases/Datawarehouses Related to Microsatellites and Primers, MAPs secondary metabolites & Metabolic Pathways Details of Training/Workshop organized and total no of user trained 1. CIMAP Winter Training on Techniques & Tools of Biotechnology & Bioinformatics (CWT-2008) – 25 students 2. CIMAP Summer Training on Techniques & Tools of Biotechnology & Bioinformatics (CST-2008) – 45 students 70 XXth All India BTISnet Coordinators’ Meeting February 03-04, 2009
3. School Science Teachers Training on Integrative science Approaches in Education(SSTT-2008) - 15 teachers 4. Research Project Work/ Dissertation in Medicinal & Aromatic Plant Bioinformatics. – 10 students 5. CSIR Programme for “Youth for Leadership in Science (CPYLS)”, sponsored by HRDG, CSIR, New Delhi.
Impact shown by the Centre Bioinformatics Centre of CIMAP, Lucknow is continuously progressing towards the centre of Exellence in the R&D of Plant Bioinformatics especially Medicinal & Aromatic Plants (MAPs). The extensive research is going on the secondary metabolism of MAPs, genomic sequence analysis such as ESTs for SSRs identification in MAPs. Beside this, Bioinformatics centre strengthen the ongoing In-house/Network/Sponsored research projects and successfully organized the Bioinfor- matics training & teaching, thus contributing to skilled manpower development. Some of the major impacts shown by the Bioinformatics Centre are: development of various specialized databases on medicinal plants e.g. databases on alka- loid genes (dbAlkaloid), alkaloid biosynthesis pathway information database (Aropath) & Monoterpene synthase genes database (MSGene), Terpene information database (dbterpene) and some others such as Multiple Drug Resistance genes (dbMDR).
Future activities To analyze structure activity relationship (SAR) of compound/biomolecules/leads; To analyze 2D & 3D Quantitative Structure-Activity Relationship (QSAR) models of leads by using different descriptors; To study docking and evaluate ligand-protein interactions with scoring functions; To employ robust and cross-validated Quantitative Structure Toxic- ity Relationship (QSTR) models for assessing various measures of Toxicity; To study predictive ADME/Toxicity models; To analyze pharmacophore, conformers/analog designing, docking based virtual high throughput screening of compound library; To analyze regulatory DNA motifs and genetic marker sequences (e.g. SSR) in genomic sequences; To analyze protein motifs at proteome level as active site for ligand binding; To analyze gene ontology of orphan genes as novel drug target; To develop Bioinformatics databases related to MAPs; To develop Bioinformatics tools based on machine learning algorithms; To develop a separate web portal of Bioinformatics resources related with MAPs.
Additional details
Name of the Coordinator: Dr. Ashok Sharma Postal Address: Central Institute of Medicinal & Aromatic Plants, P.O. CIMAP, Kukrail Picnic Spot Road, Lucknow-226015 Phone Number: 0522-2717626 Fax No.: 0522-2342666 Email: [email protected], [email protected] Website: www.cimap.res.in
71 Sub - Distributed Information Centres Central Plantation Crops Research Institute, Kasaragod Coordinator: Dr. George V. Thomas Area of Specialization of the centre: Bioinformatics applications in plantation crops (coconut, arecanut, cocoa)
Major activities of the centre during the year 2008-09 Databases of microsatellite markers in coconut & PGPR from coconut vermicompost were developed. Insect odorant binding (OBPs) genes were isolated from coconut red palm weevil. Molecular modeling of OBP from palm weevil & WRKY protein from Coconut were carried out. EST-SSRs were designed using in silico tools for cocoa & validated under wet lab conditions. All 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 five days training programme on “Bioinformatics and Biotechnology: Introduction and Applications in Plantation crops” from August 4th to 8th and “Principles and Applications of Bioinformatics” from November 3rd to 7th 2008. At present three bioinformatics students are doing their studentship project and four trainees are getting training under traineeship programme.
Educational activities with details of placement Under studentship program four students are doing their projects on following topics. a). Creation of Somatic Embryogenesis Receptor Kinase Database and its analysis using Bioinformatics software. b). In silico analysis of Eudrilus eugineae for its molecular identification c). Algorithm development for motif finding Databases/ Software packages developed during 2008 –09 • Molecular marker database for coconut accessions • Plant disease resistant gene data base • Developed Shannon Index • Literature Databases updated Papers published or presented in the conferences Rajesh, M.K., Subaharan, K., Sathish Kumar, K., Ritto Paul., Bobby Paul., Sreesmitha.V.and George.V. Thomas. 2008 A comparative study of insect odorant protein binding (OBP) genes and isolation of a partial OBP gene from coco- nut red palm weevil, Rhynchophorus ferrugineus F. Journal of Plantation Crops. 36(3): 418-424. Sreesmitha, V., Rajesh, M.K., Subaharan, K., Sathish Kumar, K. and George.V. Thomas. 2008. Homology modeling and docking studies in an odorant binding protein from palm weevil. Journal of Plantation Crops. 36(3): 430-434. Sreesmitha, V., Rajesh, M.K., Anitha Karun., Ramesh Kumar.M.P. and George.V. Thomas. 2008. In silico prediction of function and modeling of WRKY2 protein in coconut(Cocos nucifera L). Poster presented in National Symposium from chromosomes to genomes;challenges and prospects ,held at Kerala University, Thiruvanamthapuram 26-28,2008 P4-3. Details of Training/ Workshop organized and total no. of user trained 1. Bioinformatics and Biotechnology: Introduction and Applications in Plantation crops on 4th – 8th August 2008, 14 students participated in the training 2. Principles and Applications of Bioinformatics held on 3rd – 7th November 2008.Eight members participated in this training session
Future activities • Creation of database of SERK & MAP kinase gene • Sequence analysis of GST(Glutathione -S-transferse) genes using bioinformatics tool • miRNA detection in cocoa. • Gene expression studies and updating molecular markers databases on palms and cocoa. • Developing a program for detailed microsatellite analysis using excel macro • Creation of phytoplasma data base by analyzing motifs references. • Conducting training programmes.
72 XXth All India BTISnet Coordinators’ Meeting February 03-04, 2009 Central Sericultural Research and Training Institute, Mysore Coordinator: Dr. S. M. H. Qadri 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. Since inception, the center has conducted 14 workshops in which 489 personnel were trained.
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 fa- cilities 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. Presently, 8 research projects funded by DBT/ DST and 14 projects funded by Central Silk Board are being carried out on the areas like, evaluation of transgenic mulberry for abiotic stress, identification of QTLs for root traits and water use efficiency, DNA markers associated with diseases and pest resistance in mulberry, detection of EST cDNA markers linked to cocoon and post cocoon traits in silkworm, identification of RAPD-SCAR markers associated with BmNPV resistance in silkworm, refinement of semi-synthetic diet suitable for mulberry and Vanya silkworms, development of silkworm byproducts for human health, characterization of botanicals involved in management of silkworm diseases etc.
Area of Specialization of the center The main thrust area of this center is Seri-biotechnology and Seri-bioinformatics.
Major activities of the center during the year 2008-09 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 hosted the 19th Annual All India Coordinators meeting of BTISnet during 3 - 4 February 2008.
Infrastructure facilities in the Bioinformatics Centre 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. Details of staff members working in the center Name of staffs Designation Specialization Period working 1. Dr. S. K. Ashwath Scientist C” M.Sc., Ph.D Since April 2007 2. Mr. Kantharaj H. M. Information Officer M.Sc. Biotechnology Since Sep. 2008 3. Mr. Anis Ahmed Shariff Technical Assistant B.Sc., PGDCA, PGDSM, Since Nov. 1999 Computer Applications; Sericulture & Sericulture Management 4. Mrs. Gousia Kauser Technical Assistant B.Sc., STC in Sericulture, Since Nov. 1999 Diploma in Computer Office Automation 5. Mrs. Sumathy R. Computer Operator M.Sc. Bioinformatics Since Aug. 2008 6. Ms. Vijina Chakkyarath ComputerOperator M.Sc. and M.Phil. in Bioinformatics Since Aug. 2008
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Type of Services provided The center is equipped with 512 kbps BSNL Leased Line Internet connectivity which provides internet facility 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.
Educational activities with details of placement: The center does not offer any course in bioinformatics.
Initiative to validate the outcome of bioinformatics resources The databases related to silkworm and mulberry biotechnology have been developed in consultation with the respective scientists who have validated the same and these databases have been made accessible through the website of the center for the use by scientists working in seribiotechnology.
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 project 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.
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 These databases are being hosted from the server installed at Bioinformatics Centre. The present databases are being updated and upgraded regularly.
Papers published or presented in the conferences with reference Sreekumar, S.; Chitra, S.; Ashwath, S.K. and Rajesh, G.K. (2007) Comparison of haemolymph protein profiles be- tween multivoltine and bivoltine silkworm breeds under temperature stress. Proc. Int.Conf. Sericulture chal- lenges in the 21st Century. Bulgaria, September 18-21,2007, pp 125-133. Kanika Trivedy ; Nirmal Kumar. S.; Mousumi Mondal and Anil Kumar Bhat. C. (2008) Protein banding pattern and major amino acids component in de-oiled pupal powder of silkworm, Bombyx mori. Journal of Entomology (USA), 5(1):10-16. Mousumi Mondal ; Kanika Trivedy and Nirmal Kumar, S. (2007) Silk proteins sericin and fibroin in silkworm, Bombyx mori Linn,-A review Caspian Journal of Environmental Sciences (Iran), 5 (2): 63-76. Mousumi Mondal, Kanika Trivedy and Nirmal Kumar, S. (2007) Extraction of liquid and powder fibroin from cocoon shell of silkworm Bombyx mori Linn. Journal of Entomological Research Society (Turkey)., 9(3): 15-22. 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.
Details of Training/Workshop organized and total no. of user trained 38 persons were trained during the year 2008 in Bioinformatics concepts and applications (B.Sc. Biotechnology from -Ma hajanas Collage, Mysore). Since establishment of the centre, 489 persons have been trained.
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Impact shown by your centre on the growth of biotechnology and allied areas A total of 228 Research papers were published by the scientists of the Institute & Nested units (International - 27; National – 44; Presented in Conferences – 79; and Popular articles – 78). The institute is publishing the Indian Journal of Sericulture ( Biannual), Seridoc (Biannual), Reshme Vahini ( Kannada, Bimonthly) and Pattu Vignanam (Telugu, 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 persons under different programmes. Major Sericulture states were covered to impart training in different disciplines of sericulture. During the year, patents have been obtained for Nursery guard ( Biofungicide), Nutrid ( semisynthetic diet for silkworm) and Seritorch ( sterilizing appliance). Further, Amruth, an eco-friendly bed disinfectant, machineries like High pressure seri sprayer, Seri humidifier-cum-heater have been commercialized.
Future Activities The existing databases will be updated with new features, which will be hosted from the present server. New databases, namely, Soilinfo - which provides the information like type of soil, physico-chemical properties, micro nutrients etc. of the given soil area and Silkdis – containing information about the symptoms, causative organism, seasonal occurrence of pests and diseases of mulberry and silkworm, Bioinfolib – which is a bioinformatics library that provides the information on the softwares, tools, databases etc., will be developed. Further, it has been planned to develop sequence analysis tools and local blast server in which blast features 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. S.M.H. Qadri 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]
Bioinformatics centre : [email protected] Website : www.btismysore.in, www.csrtimys.res.in
Name of Contact Person: Dr. S. K. Ashwath, Scientist ‘C’ Email : [email protected]
75 Sub - Distributed Information Centres CSK Himachal Pradesh Krishi Vishvavidyalaya, Palampur Coordinator: Dr. S. R. Thakur Summary of the progress made by the Centre from its inception Distributed Information Sub-Centre (DISC) at Advanced Centre for Hill Bioresources and Biotechnology, CSK HPKV, Palampur (HP) came into existence in October, 2002. Since its inception, the Centre has developed good infrastructure in the form of 32 Computers/laptops, two servers (one is used as web server and other is internal server), Communication equipments and Printers, one Photocopier, Fax machine, one interactive class room etc. All the computers are linked through Local Area Network (LAN) and internet with 256 kbps lease line. During the period under report, the Centre has procured softwares like LINUX, ORACLE, WINDOWS NET SERVER WINDOWS SERVER 2003, BIO-SYSTEMATICA, SQL SERVER, ADOBE ACROBATE PROFESSIONAL and VStudio.Net for normal bioinformatics work including analysis, software development, database cre- ation and management. The Centre has created 5 databases and one software. The Bioinformatics Center was formally inaugurated by Prof. M.K. Bhan, Secretary, Deptt. of Biotechnology, Govt. of India on 16th October, 2004.
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 Bio- technology: i. Molecular marker-assisted pyramiding of blast resistance genes in rice ii. Biofortification of maize for enhanced zinc and iron content in grains iii. Development of DNA-based diagnostics for Fusarium species iv. Understanding molecular genetics of bacterial wilt resistance in pepper with implications in solanaceae genomes v. Using molecular markers for diversity studies of different crop plants. Area of specialization of the Centre: Bioinformatics & Agricultural Biotechnology Major activities of the centre during the year 2008-09 A. Following databases/tools have been created by the Centre during 2008-09: 1. Data base on marker resources of crop plantsThe marker resources of crop plants database has been created to catalogue relevant information. It will be an unique database for marker resources of crop plants, covering RAPD, RFLP, AFLP, SSR, SNP etc. markers in different crop plants. However, huge efforts will be required to fully develop it. 2. DNA based composition analysis ToolThe tool is designed to help the scientists, students and researcher for counting the total number of nucleotides in a sequence and number of each nucleotide with percentage present in the sequence. B. Following databases have been upgraded by the Centre during 2008-08: 1. Database on Biological Wealth of Himalayas The biological wealth of Himalayas has been exploited recklessly both legally as well as illegally. The database has been created to catalogue relevant information of use to govt. and private institutions. 2. e-Extension network system The Bioinformatics Centre has created an internet-based e-Extension system in order to speed up the process of outreaching the processes and technologies of the university to end users i.e. farming community. 3. Library Management System The software is created using Visual Basic 6.0 as a front-end and Access 2000 as a back-end. The software has been created for easy and quick search, checking out and retrieval of Biotechnology books available in the Centre Search facility is available for books with either their name or author or Publisher etc.
Infrastructure facilities in the Bioinformatics Centre a. Computer & Communication facility 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(4)
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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 Details about staff members working in the Centre
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 Educational activities 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 hands on training on how to develop a database and what are the various components of a database, 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.
Initiative to validate the outcome of bioinformatics resources The Bioinformatics Centre is involved to teach and use the bioinformatics resources both online as well as various software like CLUSTAL W, NTSYS, BLAST, ExPASy, SOPMA, CDD database, molecular tool kit etc.
Initiation of R&D activities in Bioinformatics We have downloaded more than 500 NBS-LRR (nucleotide binding and leucine-rich repeat) genes of the rice genome. The NBS-LRR genes have been implicated in plant disease resistance in different crop plants. We are developing SNP markers using bioinformatics tools from these genes for use in marker-assisted selection of disease resistance in rice. Scripts are being written to analyze genome sequence data.
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. Efforts to start a PG Diploma in Bioinformatics & Information Technology. 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
77 Sub - Distributed Information Centres Dr. Y. S. Parmar University of Horticulture and Forestry, Solan Coordinator: Dr. S. V. Bhardwaj Area of Specialization of the Centre: Crop Biotechnology/Horticulture Major activities of the Centre during the year 2007-08 The Centre facilitates the research work of the department by providing bioinformatics softwares (Prism, Exome, Exome ED, Exome BLAST, Hyperchem professional 7.5, Geno cluster version 3.0) and databases (Biotechnology Abstracts, Directory of Biotechnology Institutes) in addition to the online databases and bioinformatics tools, email and online literature search facility and conducting workshops/trainings. i) Research
Project 1: Comparative genome analysis of cucumber mosaic virus (CMV) using bioinformatics tools Cucumber mosaic cucumovirus (CMV) belonging to genus cucumovirus of family bromoviridae has a wide range of hosts (as many as 191 host species in 40 families). It is widely known that coat protein (CP) of a plant virus is not only a determinant of its antigenic properties but also responsible for the virus-vector relationship and their mode of transmission. Thus, comparative analysis of coat protein region was conducted to deduce evolutionary status of the virus. Serological diagnosis through DAS-ELISA confirmed presence of CMV in various fields of Dr. Y.S. Parmar UHF Nauni, Solan. CP test sequence of Cucumber mosaic virus from India shared impressive homology of 43%-97% at nucleotide level and 43%- 96% at protein level with the rest 195 sequences scrutinized from around the world. Phylogenetic tree construction employing four techniques, namely, Neighbor-Joining (NJ), Unweighted Pair Group Method of Arithmetic Averages (UPGMA), Maximum Parsimony (MP), Maximum Likelihood (ML) and their analyses for all 12 countries along with the world trees was also pursued. Six motifs were identified in each sequence when scanned against PROSITE database. These were N-glycosylation site, cAMP- and cGMP- dependent protein kinase phosphorylation site, Protein kinase C phosphorylation site, Casein kinase II phosphorylation site, N-myristoylation site and Amidation site. Present analysis elucidated high evolutionary rates of cucumoviruses attesting their cosmopolitan nature and rampant spread. These changes are replicating in the protein sequences, though at a slower rate, thereby, helping them to evade their host defence mechanism. Project 2: Comparative genome analysis of apple mosaic and apple chlorotic leaf spot viruses infecting apples in H.P. The Apple chlorotic leaf spot virus and Apple mosaic virus is prevalent in H.P. as confirmed by serological detection using DAS-ELISA. These are positive sense RNA viruses and are major limiting factors for cultivation of apple and other stone fruits throughout the world. Sequence analysis was performed on the coat protein (CP) in order to determine the sequence variability of ACLSV and ApMV isolates which could be helpful in designing knowledge based strategies such as coat protein mediated resistance in these plants against these viruses. Studies on coat protein (CP) gene sequences of ACLSV isolates depicted that the test virus, ACLSV isolate of apple from Solan; AM494507 81%-100% and 88-100% homology at nucleotide and amino acid levels, respectively, with 39 other ACLSV isolates of members of family rosaceae from different countries downloaded from NCBI database. Phylogenetic analysis was performed with ACLSV isolates of CP gene sequences by UPGMA, Neighbor-joining, parsimony and Maximum likelihood methods. Analysis showed that the test ACLSV CP gene sequence was closely grouped with ACLSV CP gene sequence of apple from Nagri and shared its most recent common ancestries with four ACLSV isolates viz. Nagri-apple (AM494505), Nihari-apple (AM494508), Kala Amritsari plum (AM931534) and Salooni-cydonia (AM498049) and two of the ACLSV isolates viz. Palampur- Mdvda (AM409324) and Japan-GC10j (AB326230) were placed closely to the test sequence. Similarly, Sequence analysis was performed on the coat protein (CP) in order to determine the sequence variability ApMV isolates Studies on coat protein (CP) gene sequences of ApMV isolates depicted that the test virus partial sequence, ApMV isolate of apple from Shimla; FM178274 87%-96% and 83%-98% homology at nucleotide and amino acid levels, respectively, with 15 other ApMV isolates of members of family rosaceae from different countries downloaded from NCBI database. Phylogenetic analysis was performed with ApMV CP gene sequences by UPGMA, Neighbor-joining, parsimony and Maximum likelihood methods. NJ nucleotide sequence analysis showed that the test ApMV CP gene sequence was placed on separate branch in a cluster of four isolates from Czech Republic viz. pear Iv10 (AY542542), pear Kravare (AY542543), pear roz 144 (AY542545) & pear Cerin (AY542544) and one isolate pear It1, AY542546 from Italy. Project 3: Primer designing against apple chlorotic leaf spot virus infecting apples in Himachal Pradesh. After assuring the presence of Apple chlorotic leaf spot virus (ACLSV) by serological testing, primers were designed using different software viz: EXOME Horizon, Web Primer, Primer 3, Gene Fisher and Primer Blast and the properties of designed primers were checked by using oligonucleotide property calculator. These best primer pairs (Forward/Reverse) were
78 XXth All India BTISnet Coordinators’ Meeting February 03-04, 2009
selected on the basis of important parameneters like primer length, Tm, GC% and formation of secondary structures which are necessary for proper working of primers. Efficacy of these primers was tested using RT-PCR. Results of RT-PCR showed that Primer pair 1 (Forward SÈ AAGGTAGACGCAFGATTTGAAGG 3È; Reverse SÈ CACTCCATTAATACCACGACTC 3È showed amplification at 800 bp and Primer 2 Forward primer SÈ TCAGTTAAAGGTGGACGCAGA 3È Reverse primer SÈ CATGGGTTCAAGAGTTTGACG 3È showed amplification at 600 BP. Both primer pair amplified the coat protein gene of ACLSV. However, primer 3 (forward primer SÈ GATCAGAAGGAGGAGGATGG; REVERSE PRIMER SÈ TGGGTTCAAGAGTGGGATTC) showed non specific amplification at 500 bp as band was present in both healthy and diseased sample. So out of these three primers Primer 1 and 2 are recommended to use for detection of CP gene of ACLSV. These primers were small in size and thus coat effective. Project 4: Work on Effect of Asparagus adscendens Roxb. on target-receptor interactions is under progress. ii) Database Development: The database on various horticultural crops of HP viz,HimCrop is under preparation. iii) Trainings/workshops • The Centre has organized a 6 days trainings on “Creation and Management of Database” and a 2 days Patent Awareness Workshop” during 2008-09. • The Centre proposes to organize a 6 days training on, “Bioinformatics and its application in plant sciences” wef 19th to 24th Jan., 2009. • The Centre has started imparting 2 to 4 months training in bioinformatics to the MSc Biotechnology students of other universities/institutes. iv) Technologies transferred/commercialized The following technologies were identified by NRDC for commercialization through IPR cell under the Centre. • A process for in-vitro elimination of plant virus by preparing and using an extract ofAzadirachta indica plant. • Elimination of carnation latent virus from infected plants by extract ofAsparagus adscendens and Asparagus officinalis through supplemented tissue Culture medium. • Plant origin based pesticide formulation against fungal disease of plants. • Technology for the manufacture of quality strawberry, plum, and apricot wine. • A Process for the production of bittergourd hypoglycaemic drink for the control of diabetes mellitus (Type-2). • HIMFLORA- A computerized botanical database on wild ornamental plants of Himalayas v) Submission of Adhoc Project The centre has submitted an adhoc research project on “Studies on comparative genomics and proteomics of coat protein gene of some viruses infecting Lillium species” to DBT for financial assistance.
Proposed activities during 2009-2010 1. Research work in different aspects of Bioinformatics including ligand receptor interaction and drug designing to Ph.D/ M. Sc students in the department. 2. Development of information systems and databases on horticultural crops. 3. Atleast two short term trainings or workshops on Bioinformatics and / or IPR 4. Work on Crop databases, “HimCrop” will continue.
79 Sub - Distributed Information Centres Devi Ahilya Vishvavidyalaya, Indore Coordinator: Prof. Anil Kumar Summary of the progress made by the Centre from its inception: • The Distributed Information Sub-Centre was established in 1993. • Our center has BSNL 512 Kbps internet lease line connection. • The centre also setup a web server (http://www.davvbiotech.res.in) having all the software & database developed/ procured by the centre. • The development of a server for the identification and characterization of Genomic and Pathogenicity Islands has been completed and a research paper has been published in In-Silico Biology (Pundhir, S. Vijayvargiya, H. and Kumar, A. 2008 ,In Silico Biology 8, 0019.). PredictBias is available at http://www.davvbiotech.res.in/PredictBias. • We have designed primers for endo-1,4-â Xylanase gene.(Garg, S., Sohani, N., Pundhir, S. and Kumar, A. 2007, J. Cell Tissue Res. 7, 1147-1154) & also for DREB1A gene. (Garg, N., Pundhir, S., Prakash, A. and Kumar, A. 2008 J. Proteomics Bioinformatics 1, 37-46). Area of specialization of the Centre: Sequence analysis, Biological software & database development related to medical bioinformatics and human resource development.
Major activities in the year 2008-09: Database & Software Development
Human Resource Development • During 2008, one trainee-ship has been offered to a research scholar. • We also successfully organized workshop on “Machine learning techniques for Bioinformatics Data Analysis” from Nov 4-8, 2008, and trained nearly thirty participants. Infrastructure facilities in the Bioinformatics Sub-Centre: A. Computer & Communication facility: (i) Servers : Web Svr: HP Prolient ML 570 (Quad Proc. with 4 GB RAM); Proxy Svr: HP Prolient ML 150 with 1 GB RAM. (ii) Desktops Pc’s, Printers, Scanners & Communication facility
B. Scientific software packages: MATLAB, DNASIS, PROSIS, AMOS, SPSS, MOE, Reference Manager 11. C. Databases & other information resources: We have subscription for Journals like Nature & Journal of Bioscience & Bioengineering & Journal of Cell & Tissue Research. Collaborative works / initiatives: We have Collaboration with NCCS, Pune and Jain Hi-Tech Industry, Jalgaon.
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Databases / Software packages developed:
Full length research papers related to bioinformatics published in 2008 • Pundhir, S., Vijayvargiya, H. and Kumar, A. (2008) PredictBias: a Server for the identification of genomic and pathogenicity islands in prokaryotes.In Silico Biology 8, 0019. • Garg, N., Pundhir, S., Prakash, A. and Kumar, A. (2008) Primer designing for DREB1A, A cold induced gene. J. Proteomics Bioinformatics 1(1), 37-46. • Garg, N., Pundhir, S., Prakash, A. and Kumar, A. (2008) PCR Primer design: DREB Genes. J Comp Sci Syst Biol 1: 021-040. Research papers related to bioinformatics presented in various conferences during 2008: Pundhir, S. and Kumar, A. (2008) SSPred: A prediction server based on SVM for the identification & classification of proteins involved in bacterial secretion systems. Poster Presentation HUGO’s 13th Human Genome Meet at Hyderabad, Sept. 27-30, 2008. Pundhir, S., Vijayvargiya, H. and Kumar, A., (2008) PredictBias: a server for the identification of genomic and pathogenicity islands in prokaryotes. Oral Presentation. International Conference on Bioinformatics(Incob2008) at Taipei, Taiwan. Oct. 20-23, 2008. Pundhir, S. and Kumar, A. (2008) SSPred: A prediction server based on SVM for the identification & classification of proteins involved in bacterial secretion systems. Poster Presentation. International Conference on Bioinformatics(Incob2008) at Taipei, Taiwan. Oct. 20-23, 2008.
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. Future activities Our University plans to start M.Sc. Bioinformatics program. We are also doing research & development work related to the primer designing for á-Glucan Phosphorylase and many other enzymes of Carbohydrate metabolism. We also plan to design processes for enzymes.
Additional Details
Coordinator: Prof. Dr. Anil Kumar Postal Address: Head, School of Biotechnology, Devi Ahilya Univeristy Khandwa Road, INDORE - 452001, INDIA. Phone Number: +91-731-2470372, 2470373; Fax No.: +91-731-2470372. Email: [email protected], [email protected] Website: http://www.davvbiotech.res.in
81 Sub - Distributed Information Centres Engineering College, Raipur Coordinator: Prof. M. K. Verma Major activities of the centre during the year 2008-09 a. 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. Initiated & enriched the research environment which resulted in: i. One National Workshop/Training on “Introduction to Drug/vaccine Designing” imparted a total 1575 man-hour. ii. One National Symposium (In Progress) iii. Publications: National Journal: 1 International Conferences: 8 National Conferences: 1 iv. Projects Guided: UG -2, PG – 1, M. Phil - 1 v. International database enrichment: Two protein structures submitted to “La Sapienza” ‘Protein Model database ‘Rome. Major research activities in Biotechnology and its related fields at our institution a. Research work in Bioinformatics was carried by students of M.Phill./M.Sc./B.Tech Bioinformatics, Biomedical, Biotechnology, and Computer Technology. b. Research work initiated and carried in the Bioinformatics especially in Homology Modeling, Vaccine and Drug Designing and Evolutionary Analysis. c. Data base generation and Data mining were initiated by center. d. Research work carried in the field of Fuzzy Logic/ANN and Medical Bioinformatics.
Infrastructure facilities in the Bioinformatics Centre a. Computer & Communication facility with Internet. b. Scientific Software packages: MATLAB TOOL BOX, Genechek and Genowitch, IRNA. c. Databases & Library facilities. . Collaborative works/ initiatives Development of Decision Support System for Asthma disease is in progress with Integral University Lucknow.
Databases/ Software packages developed Database under process on Medicinal Plants for Arthritis, Epilepsy.
Papers published or presented in the conferences with reference: 1) “Computational approach for comparative analysis of in-silico 3D structures of Enolase [Bos Taurus]”, “National conference on Next generation computing & information system NGCIS 2009”, Kot Bhalwa, Jammu, India, Feb. 14-15, 2009. 2) “Bioinformatics tools based approach in identification and in-silico structure prediction of PRDX-2 protein involved in anti-oxidant activity in c.elegans”, ‘International conference Health Expo & Conference, 2008, Chandigarh, 3) “Application of artificial neural network approach for prediction of proteaosomal cleavage sites of Hepatitis D virus”, International conference Health Expo & Conference, 2008, Chandigarh, 4) “Parkinson disease pathway: Design a computational model for comparative study of c.elegans with homo-sapiens, mus musculus and cannis familiar International conference Health Expo & Conference, 2008, Chandigarh, 5) “In-silico 3D structure prediction of Enolase [Bos taurus]” has been accepted for poster presentation in the 7th InCOB-Seventh International Conference on Bioinformatics 2008 at Taipei, Taiwan
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6) “In silico designing of inhibitor against Tin2 for aging” HUGO’s 13th Human Genome Meeting Hyderabad. 7) “An artificial neural network approach for prediction of proteaosomal cleavage sites for large delta antigen (HDAg-L) containing small delta antigen (HDAg-S) of Hepatitis D virus,” “International symposium on newer frontiers in biomedical research” Regional Medical Research Centre, N.E. region (ICMR), Dibrugarh 8) “Insilico vaccine prediction against Herpes Simplex Virus1 (HSV1)” “International symposium on newer frontiers in biomedical research” Regional Medical Research Centre, N.E. region (ICMR), Dibrugarh, 9) Paper Published in IX International symposium on vector & vector borne diseases -”Insilico 3D structure prediction of matrix protein1 of influenza A virus responsible for bird flu disease” Indian Council of Medical Research at Puri, Orissa -2008.
Additional datails
Postal Address: Sub-DIC Bioinformatics Centre, N. I. T. Raipur, G. E. Road, Raipur (C.G.) Phone Number: 0771-4062385 Mobile: 9425203472 Email: [email protected] Website: www.nitrr.ac.in Name of Contact Person(s): Dr. M. K. Verma
83 Sub - Distributed Information Centres G. B. Pant University of Agriculture and Technology, Pant Nagar Coordinator: Dr. Soma Maria Major activities of the centre during the year 2005-06 1. Training Workshops: The centre has successfully conducted a DBT funded regional workshops – Protein structure Prediction and applications in Agriculture and Veterinary ( Oct, 12-14, 2008) and was attended by 44 participants from all over the country. 2. Research: The centre is also involved in conducting active research in in silico prediction and isolation of Blast disease resistant genes in rice crop using metabolic modeling and flux analysis. The PCR amplified & sequenced rice LOX genes were deposited in NCBI GenBank:EU032507, EU032508, EU146294, EU700314115. Analysis of role of MAP Kinase signaling work in Alternaria blight infection in Brassica Juncea ( 2006-20011), DBT funded Project In silico characterization of microflora capable to degrade Heavy metal polluted soil and water samples, (2008- 2010), DBT.
Research publications 1). P. K.Latha, R. Soni. M. Khan, SomaMarla and R. Goel, (2009), Exploration of Csp Genes from Temperate and Glacier soils of the Indian Himalayas and In silico Analyssi of Encoding Proteins, Current Microbiology (Springler) In Press. 2). Kishwaha, H., Gupta, N., Singh, V. K., and Yadav, D. ( 2008)In silico Analyssi of PCR amplified DOF (DNA binding with one finger) transcription factor domain and cloned genes from cereals and millets, Online Journal of Bioinformatics, .V. 9 (2): 130-143. 3). Soma Marla and Singh, V.K. (2009), Isolation & characterization of LOX genes imparting resistance to Rice blast disease (International Rice News letter, Manila, Philippines (In Press).
Educational Activities Teaching three courses- Bioinformatics and Molecular modeling (B.Tech, Biotech), Elements of Bioinformatics, Computer basics of Protein modeling ( at PG & Ph.D level).
Databases & Software developed Three software packages have been developed - A). In silico annotation and neural net classification of Rice seed storage Proteins (http://www.gbpuat.ac.in/acads/cbsh/Bioinformatics/ssp.html). B). Cry-Bt identifier- a biological database for detection and PCR identification of Cry genes present in Transgenic Plants., (http://www.gbpuat.ac.in/acads/cbsh/Bioinformatics/cry.htm ) C). A Java bases Pathogen Genome Display tool. http://www.gbpuat.ac.in/acads/cbsh/Bioinformatics/GenomViewer/bgv.htm)
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. Phone No.: 05944- 233287 Email: [email protected], Website: http://www.gbpuat.ac.in/acads/cbsh/Bioinformatics/home.htm
84 XXth All India BTISnet Coordinators’ Meeting February 03-04, 2009 Guru Nanak Dev University, Amritsar Coordinator: Dr. Gurcharan Kaur Facilities and services provided by the centre 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 available for facilitating literature search by students and faculty members. At present the hardware installed includes Computers Systems (42), Coloured Laser Printers (2), six Laser Printers (6), Deskjet Printers (2), one Line Matrix Printer, Scanners (two), Xerox machine, Multimedia Projector and one laptop computer. Recently, the Centre has purchased one more Panasonic multimedia projector (PT-LB60NTEA). These facilities are being extended to the students, research scholars, and faculty members of the University departments as well as neighbouring Institutes. DISC has facilitated faculty members/research scholars in strengthening their research publications.
Current events The department has established two new computer labs. for M.Sc. Bioinformatics students. A two day workshop on “Structural Bioinformatics towards Drug Design” was organized on 21st - 22nd March, 2008 by the Distributed Informatics Sub-Centre, Department of Biotechnology, Guru Nanak Dev University, Amritsar. The workshop was attended by fifteen participants from different University departments, affiliated colleges and Govt. medical college, Amritsar. Prof. P.V. Bharatam, Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Mohali, and Mr. Harpreet Singh, SQA Engineer, Pacific Square, Gurgaon were invited to deliver the lectures and to impart hands-on training to the participants. Besides this the department has organized lecturers from different visiting faculty from different institutes for M.Sc. Bio- technology and M.sc. Bioinformatics students. The department has filled the post of Lecturer (Bioinformatics) on regular basis. The post of Programmer is advertised and will be filled shortly.
Proposed activities during the year 2009-2010 1. Currently we are working on tools for development of biologicaldatabase management and integration and in future we plan to work on structure based drug designing and genome analysis. 2. The department plans to purchase new softwares for Molecular Modelling and simulations studies (Hyperchem/ Discovery studio) and Docking and drug designing (Discovery studio/sybyl/Gold) to facilitate research activity in this area and also for strengthening of M.Sc. Bioinformatics and M.Sc. Biotechnology course. 3. Efforts will be made to procure workstations to carry out in silico drug designing and genome analysis. 4. Upgradation of leased line connectivity from 512 kbps to 2Mbps. 5. More computers systems will be procured for M.Sc. Biotechnology and M.Sc. Bioinformatics students.
Address of the centre
Name of Head & Coordinator: Dr. P.K. Pati Postal Address: Distributed Informatics Sub-Centre (DISC) Department of Biotechnology Guru Nanak Dev University Amritsar – 143 005 Phone Number: 0183-2258431 (O) Fax : 0183 - 2258272 Mobile : 09915091910 Email: [email protected] / [email protected]
85 Sub - Distributed Information Centres Himachal Pradesh University, Shimla Coordinator: Dr. T. C. Bhalla Summary of the progress made by the centre from its inception The Bioinformatics Centre of Himachal Pradesh University was established in 1999 with 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 created computational facili- ties which includes one server (DELL) and ten terminals with all necessary peripherals connected to server through LAN connectivity. Internet connection is available through BSNL (ISP). The softwares available at the Bioinformatics Centre includes; Offline Derwent Biotechnology Abstracts CD-ROM database, Exome software for protein & gene sequence analysis and pDRAW32. The Centre has successfully organized fourteen training/workshops covering various aspects of the Bioinformatics and has trained around 217 participants through these trainings/workshops. It has developed two databases i.e. Traditional fermented foods and beverages of Himachal Pradesh and Microbial and mushroom resources of Himachal Pradesh. Its major thrust area for research is sequence structure and functional relationship of some enzymes.
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 Microbial diversity, microbial enzymes, traditional fermented food and nutraceutical aspects of mushroom and stem cell.
Major activities of the centre during the year 2007-08 • Five-Day Workshop was organized from Sep 22-26.2008 entitled ‘Applications of bioinformatics tools and techniques in genomics, proteomics and drug design’. • Industrially important plant enzymes: Sequence structure and functional relationship. • Organized practical classes in ‘Computer Applications and Bioinformatics’ course for M. Sc. Biotechnology students. Infrastructure facilities in bioinformatics centre i) Computer Hardware Beside earlier infrastructure following facilities have been added Computer system Acer / HCL make : Ten HP Color Laserjet-2605DTN Network Printer : One HP Scanjet-4370/G3010 Photo Scanner : One HP Scanjet-4370/G3010 Photo Scanner : One
ii) Communication: Two Telephone lines: 0177-2832153, 2832154 Internet Facility, Email: hpuniv.btisnet.nic.in
Details about staff members working in the centre
Types of services provided The Centre provided the following services to the students, research fellows, and faculty members of the University: • Derwent Biotechnology Abstracts Offline Database, Nucleotide and Protein Sequence Analysis, Bibliographic and Patents Search, E-Mail and Internet Access, Training in Bioinformatics. • Books 107(covering diverse areas of bioinformatics),Journals 2
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Papers communicated and workshop attended • The Centre has communicated following research papers. i) Sharma Het al. (2008) In silico analysis of amino acid sequences in relation to substrate specificity and physiochemical properties of some microbial nitrilases. Journal of bioinformatics and proteomics. ii) Sharma et al. (2008) In silico analysis of amino acid sequences in relation to substrate specificity and physiochemical properties of some microbial amidases. Journal of bioinformatics and proteomics. • DBT sponsored workshop on “ Protein structure prediction and application in agricultures and veterinary” Sept 09,2008 MBGE, College of Basic Sciences, G.B.P.A.T University, Pantnagar, (UK) has been attended by the students working in the Centre.
Other achievements M. Sc. Project entitled ‘ Bioinformatic studies on nucleotide and amino acid sequences of cobalt transporting and related proteins’ by Kanika Narula has been done at this Centre.
Initiation of r&d activities in bioinformatics Structural, biophysical and biochemical aspects of various enzymatic Proteins and Nucleotide and protein sequence stud- ies of nitrile hydratase
Details of training/workshops organized and users trained This Centre has organized fourteen workshops/ training programs. About 217 professionals from various institutions/ organizations have been trained through these training/workshops.
Impact of the centre on growth of biotechnology • 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. • The training of college teachers in bioinformatics at the Centre has proved beneficial in sensitizing undergraduate students to the domain of bioinformatics. • 22 papers were published with the help our centre. Future activities • Sequence, structure and functional correlation of nitrilase metabolizing enzymes. • Microbial genome mining for noble enzymes. • Development of simple software’s for enzymes and microbial growth kinetics. • Development of a local database for some industrial enzymes. Additional details
Name of the coordinator: Professor T. C. Bhalla Postal address: Bioinformatics Centre (Sub-DIC), H.P. University, Summer Hill, Shimla-171005. Phone & fax number: 0177 2832153, 0177 2832154 Email: [email protected]; hpuniv.btisnet.nic.in
87 Sub - Distributed Information Centres Indian Intitute of Spices Research, Calicut Coordinator: Dr. Santhosh J. Eapen Summary of the progress made by the centre from its inception Since its inception in 2000, the Centre has emerged as a lead centre in Agricultural Bioinformatics. It provides computational support and training to students and scientists and offers traineeships and studentships to deserv- ing Bioinformatics students. The Centre has built up necessary infrastructure to support the Spice Bioinformatics/ Biotechnology programmes. During the short span of seven years several databases on various aspects of spices viz. genetic resources, their chemical constituents, pathogens of spices etc. haven been launched by the centre. As on today, the centre has developed 15 databases and 7 software tools most of which are made available online.
Area of Specialization of the centre: Bioinformatics applications in spice research. Major activities of the centre during the year 2008-09 • The Centre has developed three databases during the current year • SpicEST, a database of ESTs of two major spices, turmeric Curcuma longa L.) and ginger (Zingiber officinale Rosc.) was developed and hosted (www.spices.res.in/spicest). • Spice genes, the database of germplasm of spices was revised and updated for black pepper (Piper nigrum L.) and cardamom (Elettaria cardamomum Maton). • PASSCOM (www.spices.res.in/passcom) - This database includes nearly all the phytochemicals present in six spices namely black pepper, cardamom, nutmeg, clove, allspice and Garcinia, their chemistry, biological properties and druggability. • During the reporting period two bioinformatics training programmes were conducted and three bioinformatics papers were published in bioinformatics journals. • The centre has provided traineeship to two candidates and four bioinformatics students have availed the facilities for their MSc project work. Infrastructure facilities in the Bioinformatics Centre The Centre has 1 mbps leased line connectivity with three servers, 20 PCs, workstations and other necessary peripherals. Several scientific software packages such as 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 are made available. More than 100 books in Bioinformatics and several IT and Bioinformatics journals are being subscribed.
Details about staff members working in the centre
Types of services provided • Computational and information support to various R& D projects of the Institute. • Maintenance and updating of the institute website www.spices.res.in • Designing and developing customized databases and software. • Sustaining the intranet ‘SPICENET’ and the email facility ‘Spicemail’, E journals etc. • Providing 24 hours internet services and bioinformatics tools through the facility called E-lab to the institutes. • Designing, development and hosting of websites. • E-publishing – online journals, institute repositories etc. • Support to training programmes conducted in the Institute Initiative to validate the outcome of bioinformatics resources All databases developed by the institutes are utilized by other departments and nearby institutes and these databases would serve as reference database for the researchers. All in silico results are validated in wet lab.
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Collaborative works/ initiatives Active collaboration exists with nearby BTISNet centres, CPCRI, Kasaragod and Calicut University in organizing Bioinformat- ics trainings and sharing of resources. The Centre also collaborates with NIT, Calicut for conducting a Bioinformatics course for M.Tech students.
Databases/ Software packages developed • SPICEST - An annotated EST database on spices • Spice genes - A revised database of germplasm of spices • PASSCOM – A database on phytochemicals present in six spices namely black pepper, cardamom, nutmeg, clove, all spices and Garcinia. Papers published or presented in the conferences with reference 1. Balaji, S., Bhat, A.I. and Eapen, S.J. (2008). A phylogenetic reexamination ofCucumber mosaic virus isolates based on 1a, 2a, 3a and 3b proteins. Indian J. Virol. 19(1): 17-25. 2. Balaji, S. and Chempakam, B. (2008). Mutagenicity and carcinogenicity prediction of compounds from cardamom (Elettaria cardamomum Maton). Ethnobotanical leaflets 12: 682-689. 3. Eapen, S.J. and Riju, A. (2008). Agro-biodiversity informatics with special reference to spices. Biobytes 3: 14-18.
Initiation of R&D activities in Bioinformatics R&D activities have been initiated on EST analysis of various spices, druggability studies on chemical compounds in spices and Phytophthora genomics.
Details of Training/ Workshop organized and total no. of user trained • Summer School in Biochemistry, Biotechnology and Bioinformatics, 12 May to 12 June 2008, 20 trainees. • Training programme on Agri- bioinformatics: tools and application during 20-24 Oct 2008, 15 trainees. • Training programme on ‘In silico analysis and annotation of spice ESTs’ during 17-19 Dec. 2008. 11 trainees. Future activities The R&D activities in comparative genomics, chemoinformatics and EST analysis will be strengthened. Bioinformatics support will be extended for gene/QTL mapping, expression studies etc. All the existing databases and institutional repositories will be updated and maintained. A holistic database on spices will be made. The HRD activities will be continued.
Additional Details:
Name of the Coordinator: Dr. Santhosh J . Eapen Postal Address: Bioinformatics Centre Indian Institute of Spices Research, P. B. No: 1701, Marikunnu Post Calicut – 673012, Kerala Phone Number: 0495-2731410, 0495-2731566 FAX: 0495 2731187. Email: [email protected] Website: www.spicebioinfo.res.in Name of Contact Person(s): Dr. Santhosh Eapen Email: [email protected], [email protected]
89 Sub - Distributed Information Centres Indian Institute of Technology, Delhi Coordinator: Dr. Ashok Kumar Srivastava 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 Biotechnology. 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.
Major research activities in Biotechnology and its related field The department is very actively engaged in almost all emerging areas of biotechnological research e.g., Biopro- cess 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., M.S., Ph.D. and sponsored projects) of the department and also to the neighboring educational centres. Recently the centre has graduated from an Information Resource Centre to an “Instruction facility” for quality teaching and research particularly in Bioinformatics, Genomics and Proteomics, Mathematical Modeling of Bioprocesses, and Artificial Neural Network based bioprocess control.
Area of specialization of the centre The main teaching and research focus of the Department is in Biochemical Engineering & Biotechnology. It has a very popular Dual Degree program (B.Tech & M.Tech) in Biochemical Engineering & Biotechnology. The above program has elective courses on Bioinformatics, Genomics & Proteomics data analysis for DNA Microarray apart from the courses in other emerging areas of Biotechnology listed above. The main research areas of the department are summarized below Biochemical Engineering / Industrial Microbiology / Fermentation / Bioinformatics
Major activities of the centre during the year The Department organized the following practical courses: a) Short term course on Recent Biotechnology advances during June 11-27, 2008. b) Sixth Practical Summer Training in Biochemical Engineering & Biotechnology during May 13 – June 14, 2008. Infrastructure facilities in the Bioinformatics Centre A. Computer & Communication facilities 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): 10/5, 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: Academic licensed : Accelyrs Gene 2.5, Matlab (R2008a) with Bioinformatics Tool Box (Access through Institute LAN), Discovery Studio 2.1 modules (Application areas – Sequence Analysis, Protein Modeling and Simulation) Vendor licensed : Chem Office 2005 (version 13.1), LaserGene (version 5.0), Endnote (version 7.0), Reference Manager 10, Design Expert (Statistical Optimization Software), Office XP professional, Java 1.1, Lotus Smartsuite (version 9.6), Operating System media : Windows XP professional, Windows 2000 NT server, Windows 2000 academic, Windows 98, Windows Vista Business Other: 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). 90 XXth All India BTISnet Coordinators’ Meeting February 03-04, 2009
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
Details of Staff members working in the Centre
In addition to the above positions, we also have two positions of Studentship/Traineeship each who are trained regularly.
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: For the elective courses on Bioinformatics, Genomics & Proteomics for the dual degree (B.Tech & M.Tech), students heavily use the infrastructure facilities of the center. Beside the final year M.Tech students of the department and students from the other universities also do their dedicated 6-12 months major project work using the Centre’s facility.
Educational Activities with details of placement The courses on Bioinformatics (2-0-2, 3 credits), Genomics and Proteomics (3-0-0, 3 credits) and “Data Analysis for DNA Microarrays” (3-0-2, 4 credits) are offered for the B.Tech/M.Tech/M.S. students at IIT Delhi. Ongoing projects in Bioinformatics To study MATLAB tools for comparison of eukaryotic single cell organisms whose whole genome is sequenced and annotated (Aditi Gupta - Supervisors G.P.Agarwal, DBEB & Jayashree Santosh, Computer Service Centre), 2008-2009 Evolutionary rate study betweenS. cerevisiae and C. glabrata using A. gossypii/ K. lactiis as the out group species (Bhawna Arora - Supervisor G.P. Agarwal, DBEB), 2008-2009 Studies on protein aggregation property and mutational effects on á-synuclein (Anita Sarkar, Sonu Kumar - Supervisor D. Sundar, DBEB), 2008-2009
Initiative to validate the outcome of Bioinformatics Resources The Centre has been publishing papers in the area of Bioinformatics.
Collaborative works / initiatives The Center has active collaboration with various departments within institute e.g Mathematics, Chemistry and Computer Science & Engineering (CSE) of IIT Delhi. The department has also strong collaboration with Institute of Genomics and Inte- grated Biology (IGIB) New Delhi, All India Institute of Medical Sciences, (AIIMS), New Delhi and Jawaharlal Nehru University (JNU), New Delhi.
Databases/Softwares packages developed · Custom-made softwares for Bioprocess Modeling & Simulation · ZifBase : a database of zinc finger proteins and associated resources · MangrovesDB : a comprehensive web-based database of mangroves found in Pondicherry region of South India · FloraCheckList : a comprehensive checklist of medicinal plants found in Pondicherry region of South India · Catalogue of “Departmental Library” comprising about 2,000 records, searchable by author, title and keywords · Bibliographic database of Ph.D and M.Tech thesis of the department comprising about 572 records; about 150
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full-text versions of the Ph.D. and M. Tech. theses of the department using “Greenstone Digital Library Software” · Institutional repositories of theses, dissertation and other biological information · Other In-house developed specialized databases like Plant Cell Culture (PCC), Animal Cell Culture (ACC) etc. Papers published or presented in the conference with reference 1. Sarkar, A., Kumar, S. and Sundar, D. (2009). Studies on protein aggregation property and mutational effects on á- synuclein. Proceedings of the National Conference on Drug Discovery and Development (NDDC 2009), Delhi University, New Delhi, January 2009. 2. Sundar, D. (2009). Precision engineering of the genome. Proceedings of the Indian Science Congress (ISC 2009), North Eastern Hill University, Shillong, January 2009. 3. Sundar, D. (2008). Interrogating DNA-protein interactions for controlling gene expression at will.Proceedings of the 77th Annual Meeting of the Society of Biological Chemists of India (SBC 2009), IIT Madras, Chennai, December 2008, p.149. 04. Sundar, D. (2008). Molecular docking studes of DTNB and its related compounds to protein disulphide isomerase. Proceedings of the International Conference on Bioinformatics (InCoB 2008), Taipei, Taiwan, October 2008, p.56.
Initiation of R & D activities in Bioinformatics The department faculty are involved in research projects (Extramural and Intramural) Funding Agency : Department of Biotechnology (DBT), Govt. of India Innovative Young Biotechnologist Award (IYBA) Principal Investigator – Dr. D. Sundar Period of Support : 2006-09 (under review for extension for 3 more years) Amount of Support : Rs. 27 Lakhs “Molecular Tools for Targeted Genome Engineering”
Funding Agency : Department of Science & Technology (DST), Govt. of India Fast Tract Proposal for Young Scientist Principal Investigator – Dr. D. Sundar Period of Support : 2006-09 Amount of Support : Rs. 12 Lakhs “Molecular Recognition of DNA by Zinc Finger Proteins”
Funding Agency : Industrial Research & Development Unit, IIT Delhi Principal Investigator – Dr. D. Sundar Period of Support : 2008- “In silico analysis of rubber biosynthetic pathway genes”
Funding Agency : Department Information Technology (DIT), Govt. of India Principal Investigator –Dr. D. Sundar Amount of Support : Rs. 37 lakhs “Development of Tools for Designing Proteins to Engineer Plant and Mammalian Genomes” The department students also undertake one semester projects in the area of Bioinformatics.
Details of the training/workshop organized and total no. of user trained The Department organized the following practical courses: a) Short term course on Recent Biotechnology advances during June 11-27, 2008 (Number of participants – 20). b) Sixth Practical Summer Training in Biochemical Engineering & Biotechnology during May 13 – June 14, 2008 (Number of participants – 15)
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c) A short term course on Bioinformatics is proposed to be organized during March/April 2009 (Number of participants expected – 25)
Impact shown by the centre on the growth of bioechnology and allied areas i. 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. ii. Research Papers published in peer reviewed journals by using BTIS Sub – Centre’s Support. The Department has published more than 400 journal papers, 30 Books / Book Chapters, More than 150 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. Gowthaman, U., Jayakanthan, M. and Sundar, D (2008). Molecular docking studies of DTNB to Protein disulphide isomerase.. BMC Bioinformatics 9(Suppl 12):S14 doi:10.1186/1471-2105-9-S12-S14. 2. Jayakanthan, M., Wadhwa, G., Madhan Mohan, T., Arul, L., Balasubramanian, P. and Sundar, D. (2009). Computer aided drug design for cancer-causing H-Ras P21 Mutant Protein. Letters in Drug Design and Discovery 6(1): 14-20. 3. Sarkar, A., Kumar, S. and Sundar, D. (2009). Studies on protein aggregation property and mutational effects on á-synuclein (under review).
Future Activities 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 Due to increased emphasis on Computational Biology, Bioinformatics, Genomics etc. in the present scenario 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, Genomics, Proteom- ics, etc. which is the unique area of expertise of Biochemical Engineering and Biotechnology Department in the country. The centre has excellent expertise in strategic and emerging areas of biotechnology. Attempts will be made to develop Multimedia Course Materials for different key areas of Biochemical Engineering & Biotechnology and these can be eventu- ally put on the BTIS centre Web Server for access by other BTISnet Centres of the country.
Additional details:Nil
Name of the Coordinator : Prof. Sunil Nath Name of Faculty-in-charge : Dr. D. Sundar
Postal Address : Department of Biochemical Engineering and Biotechnology Phone Number : (011) 26596109, 26591066, 26596316 Email : [email protected] Website : http://web.iitd.ac.in/btis
Name of Contact Person(s): Prof. Sunil Nath, ([email protected]) Dr. D. Sundar ([email protected])
93 Sub - Distributed Information Centres Indian Institute of Technology, Kharagpur Coordinator: Dr. S. C. Kundu Summary of the progress The center provides facilities to the B.Tech, M. Tech and Ph. D students to carryout their project work and summer trainings in the field of Bioinformatics. 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 on the relevant areas of Biotechnology. A new laboratory credit course on Bioinformatics has been introduced this new year for the B.Tech and Dual degree students.
Major research activities in Biotechnology and its related fields • Scale up of recombinant proteins, therapeutic and diagnostic proteins, immunodiagnostics studies and bio-hydrogen production in different bioreactors. • Indian non-mulberry proteins and their medical applications as biomaterials. • Cloning, expression and purification of response regulator domains fromMycobacterium tuberculosis, Cloning and expression of chitinases and other genes of Entamoeba invadens. Area of specialization: Genomics, protein modeling and database development. Major activities during the year 2008 - 09 • A two-day (Sep 26th and 27th) intensive 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, Proteomics. • A three-day (Nov 22nd - 24th International Workshop on “Biomaterial for Tissue Engineering and Biotechnological Application” for the benefit of students and teachers. 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-XP, RHEL4, Linux, and Sun Solaris 9. Internet facility: 2*STM-1 link (300 mbps). b. Scientific software packages Sequence analysis: OMIGA 2.0, Sequencer 4.1.4, EMBOSS. Molecular modeling: GCG Wisconsin Package, MSI Insight II (Perpetual licensed), Modeler, Swiss PDB viewer, Discovery Studio. Staff members at present
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 through high-speed broadband Internet facility (Speed: 300 Mbps) and other computational facilities.
Educational activities with the placement details Institute offers two separate 3-credit (3 hours/week) courses with lab facilities to the students (UG/PG and research schol- ars). Through campus interview select B. Tech.
Initiative to validate the outcome of Bioinformatics resources Publications were made in peer-reviewed journals; every year an average of 75 students are being trained in the Centre; Creation of Tissue Engineering and Biomaterial database.
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Databases/ software packages developed This year a database called” Tissue Engineering and Biomaterial “is under development using CSS, Java Script, HTML, Adobe Photoshop and MySql.
Full papers published in 2008-2009 There are several publications in peer-reviewed Inter. J. related to Biotechnology (30) eg. Inter. J. of Virology, Biotechnology J, Transgenic Research, J. Bimolecular Techniques, Acta Cryst, Adv Material Research, J of Hazardous Materials, Bioresource Technology, Biophysical Chemistry, J. Struct. Biol., Toxicological & Environmental Chemistry, J. Gen. Appl. Microbiol, J. Mass Spectrum, J. of Economic Entomology, Macromol Biosci, Acta Biomaterialia, Biopolymer, Inter. J. of Biochemistry and Cell biology, J. Luminescence, Biotechnology and Bioengg and more....
Initiation of R&D activities in Bioinformatics Bioinformatics research activities are being carried out at the UG/PG / Ph.D student level by providing different Bioinformat- ics projects for their academic / project work. 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 ofEntamoeba histolytica and Mycobacterium tuberculosis, hydrogenase gene of Enterobacter cloacae and fibroin, sericin and seroin genes of economically important tasar silkworm, Antheraea mylitta. Future related activities Cloning of silk protein genes fibroin and sericin; Genome analysis of Entamoeba spp, production, analysis and creation of database for Indian non-mulberry silk worm ESTs. Molecular modeling of proteins and structure-function relationships of Tuberculosis organism; Plant metabolites, microbial bioremediation, Database on Tissue Engineering and Biomaterials. Silk proteins in cell based tissue engineering.
Additional details
Name of Coordinator: Professor S. C. Kundu Email: [email protected] Phone: 09434012848) Name of Co coordinator: Professor S. Dey Email: [email protected])
95 Sub - Distributed Information Centres Indian Veterinary Research Institute, Izatnagar Coordinator: Dr. Rajendra Singh Summary of the progress made by the centre from its inception 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. 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 these data were also used for developing and updating related databases. iii) A large number of new sequence information was submitted to EMBL GenBank Area of Specialization of the centre: Veterinary Bioinformatics. Major activities of the centre during the year 2008-09 I. Livestock disease Database : A livestock disease database is in the process of development by categorising the diseases on the basis of causing agents, species, etc containing brief description of disease, relevant photographs, illustrations, line drawings etc. The related materials have been collected and stored into digital form. The database will be very useful for veterinarians and farmers. II. Probe search for Blue Tongue: The centre is engaged in searching probes for Blue Tongue virus with 22 serotypes so that each one should be unique in identifying that serotype and can pick up all blue tongue serotypes. III. Micro-Array Analysis- Gene expression analysis studies for acute Myeliod Leukemia to find out putative drug targets using in silico approach was conducted at the centre and ten genes, who may be responsible for causing the disease, were identified. IV. Different databases and softwares were updated and improved respectively. V. We are offering two credit theory and one credit practical courses in the fields of Bioinformatics, Biostatistics and Information technology to Ph. D. and M. V. Sc. Students of the Institute. VI. Livestock database : The database has been developed containing almost all information about Livestock and allied sectors.
Infrastructure facilities in the Bioinformatics Centre A. Computer & Communication Facility :The following are the new development/augmentation of Bioinformatics: 512 kbps VSAT from EARNET. 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. PhD THESPACK 2. WILDLIFEPACK. C. Databases and other information Resources Livestock Disease Database, database tools for analysis of micro array data, Livestock Database etc. Details about staff members working in the Centre
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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. 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.
Collaborative works/initiative: Institute has more than ten National/International projects and Bioinformatics centre is providing all possible support in these research projects.
Databases/Software packages developed: 1. Livestock Databases 2. Bibliographic Databases 3. Softwares: i. THESPACK ii. PUBPACK iii. RUMPACK iv. LIGPACK v. FMDPACK. etc. Papers published or presented in the conferences with reference: One Manual and Nine research papers have been published in National and Inter-National Journals.
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. Livestock disease database is in the process of development.
Details of Training/ Workshop organized and total no. of user trained: During the year about 50 scientists and students have been trained in Bioinformatics and Information Technology. National Workshop : National Workshop cum Training Programme on “Bioinformatics” was organised from August 26 to 28, 2008 at Bioinformatics Centre, IVRI, Izatnagar. Students Trainees: i) Two student trainees were trained for six months in Bioinformatics on Cancer patients database and Sequence Alignment Analysis. ii) Two trainees who have already completed their degrees have been trained for six months in Bioinformatics on Microarrays and development of information databases. 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.
Future Activities The future plan can be delineated into following three major activities: (i) Scientific Support The: centre will cater the support to different National, International and Post Graduate Research Projects of the Institute (ii) Training and P.G. Education:The centre will organize short term and long term training programmes and workshops in Bioinformatics. The Bioinformatics introduced into course curricula of Ph.D. and Masters’ degree programmes of Deemed University, IVRI, Izatnagar will continue. (iii) Research and Development: i. National Database on Animal Diseases: The data from all state and central veterinary Institutions will be collected for development of this database to have a comprehensive information
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database on animal diseases. The database will be developed by using SQL as back end Java or .Net as front end. The database should be an unicode compatible so as to have the database in multilingual. ii. The study on Acute Myeloid Leukemia will continue during the period 2009-2010. With the help of our procedure using the microarray method, we may be able to generate genes that may be the possible cause of the disease and thus would establish the basis of drug designing as our next step of analysis in the coming year. iii. Design, Construction and Validation of DNA Chips for Virus Identification and Differentiation. The support for this national project will be continued by the centre in searching the probes for different viruses.
Additional Details
Name of the Coordinator: Dr. RAJENDRA SINGH 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]
98 XXth All India BTISnet Coordinators’ Meeting February 03-04, 2009 Institute of Life Sciences, Bhubaneshwar Coordinator: Dr. Subrata K. Das The Distributed Information Sub-Center (DISC) at Institute of Life Sciences established in 2002 under Biotechnology Information System (BTIS) programme with its pivotal objective being to support scientists at ILS or surroundings in- volved in biotechnology related work by using bioinformatics tools. Center is focusing on Molecular modeling of protein structures, molecular interaction and docking, functional genomics and database development.
Major activities of the Centre during 2008 In 2008 Mr. Sunil Kumar, Information Officer attended the EMBO world lecture course on “Recent Developments in Macromolecular Crystallography” organized by EMBL, Germany and NCL pune. The centre organized a National workshop on Functional Genomics and evolutionary Biology (November 26-28, 2008). Our centre is also working on the area of synonymous codon usages, and constraints selection studies in Prokaryotes and Eukaryotes using Multivariate Statistical techniques (MSA). In this regard, different data reduction and techniques like Correspondence Analysis (COA), Principal Component Analysis (PCA), Factor Analysis (FA) were used for finding hypothetical variables (components) that account for as much of the variance in multidimensional data (codon and amino acid usage) as possible. Two M.Sc Bioinformatics students were trained for 2 months. Based on the work carried out at the centre three papers have been published in reputed international journals. DISC personals delivered lectures at different institutes in the state for the awareness in the bioinformatics.
Papers Published in International journals in 2008-09 1. Sunil Kumar, Priya R Debata, Prakash C Supakar* (2008) Prediction of 3-dimensional structure of cathepsin L protein of Rattus norvegicus. J Proteomics Bioinform 1: 307-314. 2. Shachindra K. Pandey, Kunwar Digvijay Narayan, Saumya Bandyopadhyay, Kinshuk C. Nayak and Subrata K. Das*. 2009. Thiosulfate oxidation by Comamonas sp. S23 isolated from a sulfur spring. Current Microbiology. (In Press) 3. Sujogya K. Panda, V. Jyoti, Bhaskar Bhadra, Kinshuk C. Nayak, Sisinthy Shivaji, Fred A. Rainey and Subrata K. Das*. 2009. Thiomonas bhubaneswarensis sp. nov., a novel obligately mixotrophic, moderately thermophilic, thiosulfate oxidizing bacterium. International Journal of Systematic and Evolutionary Microbiology. (In Press) Staff Details
Future activities The research work on molecular modeling of protein structure, molecular interaction and docking studies and functional genomics will be continued.
Contact Details
Name of the coordinator: Dr. Subrata K. Das Postal Address: Institute of Life Sciences, Nalco Square, Bhubaneswar-751023 Phone No. : +91 674 2303342 Fax No. : +91 674 2300728 Email: [email protected] / [email protected]
99 Sub - Distributed Information Centres Institute of Bioresources & Sustainable Development, Imphal Coordinator: Dr. Sunil S. Thorat Major activities of the centre during the year 2007-2008 • The centre has engaged 2 (two) Traineeship and (4) Studentship for the year 2008-2009. • An official website for DISC with URL www.bicibsd.com is developed. • Three databases namely Zingiberaceae database, Fishes of Manipur and Ethnobotanical plants of Manipur are completed and will be uploaded on DISC website. • Database on Citrus, Musa and Cyanobacteria of Manipur are under development. • BTISNet Database is developed and is available on Centre’s website. • Centre is maintaining websites of the Institute as well as given charge of developing and maintaining other websites of the Institute. • The centre has been inducted for conducting the IBSD JRF-Ph.D programme of the Institute. • The centre is taking charge for conducting Practical training programmes of the Institute. • The centre has subscribed two databases namely Agris & Agricola to enhance the research and development supporting activities of the Institute. • Centre is maintaining DBT’s electronic Library Consortium (DeLCoN) to provide access and assistance to the Institute and other users. Infrastructure facilities in the Bioinformatics Centre Computer and communication facility: • Two Servers (Mail/Web and Power Database Solution), a Scanner, Color laser printer, 5 KVa UPS, Mac Book, Catalysts Manage Switch, KVM switch solutions, 7 Client IBM PCs, Portable Hard Disk, Plasma TV Screen for presentation a Digital camera and Handycam for Documentation. • A dedicated lease line internet connection of 2mbps was availed from PCIL for the Institute. Scientific Software packages: The Center has few scientific softwares like Genocluster and other software’s like Linux AS4, NOD 32 Antivirus, Microsoft Windows and Office Professional edition along with paper license, Microsoft Office 2007 Professional MOLP, Media, Windows Vista Business and a Microsoft Visual Studio 2005 Standard version.
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. • Training is provided on related areas to the Institute and other users.
Collaborative works/initiatives • Established collaboration with 3 pioneering organizations/individuals on database development with an un derstanding for data sharing and technical support. i) Tropical Botanic Garden and Research Institute, Palode, Kerala for the Zingiberaceae database ii) National facility for Marine Cyanobacteria (NFMC), Bharathidasn University, Tiruchirappalli for Cyanobacteria database and iii) Prof. W. Vishwanath, Department of Life Sciences for the Fish Database of Manipur. • The centre has active collaborative with Manipur University and Colleges affiliated to MU are in touch for necessary support and help from DISC, Imphal.
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Future activities • Providing access to scientific information in the area of specialization of the centre to the scientific community. • Collaboration with other North East Bioinformatics Centres for data Sharing. • Strengthening of the Bioinformatics centre with modern hardware and softwares • To organize joint workshops/training programmes in bioinformatics with BIF centres • Programme for the Development of Database and Software on Biodiversity Conservation and Documentation. • To conduct various awareness programme on biodiversity and bioresource conservation for school children of the entire north east. • Separate database on Flora, Fauna and Microbes of the region will be developed on important biodiversity covering most of the important characteristics available through the primary and secondary data from the region.
101 Sub - Distributed Information Centres Indian Institute of of Advance Research, Gandhinagar Coordinator: Dr. Desh Deepak Singh Summary of the progress made by the centre from its inception The centre was constituted as a sub-DISC in the year 2007 with the objectives of compilation of information on plants and their pathogens in a user friendly manner and compile data which will help in the understanding of the tropical patho- gens more comprehensively. Since inception three training programs have been held for faculty, scientist and industry representatives. Database on adhesins has been compiled and software tools for genome analysis which include ProtAnno for predicting adhesion like proteins, GluD for finding distance between sugar rings in carbohydrates, etc. have been devel- oped. Five students from other universities have finished their six months MSc projects in the centre and five are pursuing the same currently. Major efforts are underway for the genome analysis of pathogens especially the tritryps and other tropical pathogens.
Major research activities in Biotechnology and its related fields in the Institute Various research groups in the Institute are working in the areas of Plant biotechnology for gene prospecting and enhanced functionalities, understanding the factors responsible for virulence in pathogens like Vibrio spp. in the human health, understanding the role of various factors in apoptosis in cell biology, product scale up in industrial biotechnology and genome analysis in bioinformatics.
Area of specialization: Genome analysis, development of databases and software tools. Major activities during the year 2008-09 a) Genome analysis of tritryps for understanding the virulence factors responsible for causing virulence. Targets like surface molecules, MAP kinases, trans-sialidases, VSG, etc are being characterized to understand the variation and designing modulators. b) Development of databases on adhesins, plant pathogens are being developed. The database on adhesins is developed and available online. A database on the detailed information on diseases caused in plants by pathogens and their virulence factors is being developed. c) Tools development for genome analysis is being undertaken. Two tools ProtAnno for annotation of adhesins and GluD for finding distances between sugar rings in carbohydrates have been developed.
Infrastructre facilities The Department is well equipped in computational resources with state of the art equipments including Five node cluster system (Sun Microsystems), Desktops (Dell, HP) Workstations (IBM, Dell), Graphics work stations (SGI), servers (IBM), print- ers (HP).
Staff members Mrs. Shubhra Gupta (Information Officer) Mr. Bhavesh Kataria (Technical Assistant) Ms. Zarana Doshi (Trainee) Besides two faculty, two JRF, two project Assistants and trainees who work at the centre.
Services provided Online databases, tools and bio-resources freely available online from the website, training and human resource develop- ment.
Educational Activites Five MSc students from other universities have finished their MSc dissertation and five are currently pursuing. Two students in the centre are registered for PhD with Pune University.
Initiative to validate the outcome of Bioinformatic resources Research papers have been published and are being prepared for submission, poster presentations have been made in international conference
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Collaborative work For experimental work we collaborate with labs. in the Institute and other nearby research institutes.
Databases/softwares developed: Protanno, GluD, Adhesin-Profiling Papers published Two posters were presented at the European Molecular Biology (EMBO) Lecture series held at NCL Pune from November 9-14, 2008 entitled: i) Sushobhan, S. and Singh, D.D. “Comparative structural analysis of MAP kinases from L. major and Humans” (ii) Kataria, B. and Singh, D.D. “GluD: A program for finding distances between sugar rings in oligosaccharides” Initiation of R&D activates microRNA and glycan analysis and genome analysis.
Training workshops organized Two training workshops one from February 25-29, 2008 and second from December 22-24, 2008 for hand-on-training in bioinformatics were organized at IIAR.
Impact shown Human resource development through training, Poster presentations, invited lectures by coordinator in nearby colleges, and regular interface with researchers for bioinformatics analysis are undertaken on regular basis.
Future activites Training programs, development of resources.
Contact Dr. Desh Deepak Singh Co-ordinator, DISC, IIAR, Koba, Gandhinagar-382007,
Phone No.: 079-30514150, Email: [email protected], website: www.iiar.res.in
103 Sub - Distributed Information Centres Indian Institute of Integrative Medicine, Jammu Coordinator: Dr. G. N. Qazi Highlights of the Major activities of the centre during the year 2008-09 Besides the routine service providing activities, the Sub-DIC at IIIM Jammu carried out the following activities for strengthening the in silico research of the centre: Nor A structure prediction Computational aided 3D structure of NorA (which is significantly important protein for drug efflux) has been earlier proposed by us based on determination of the model by threading and the work presented at International Conference on Bioinformatics (INCOB 2007, Hongkong). Further refinement of the 3D structure determination has been done and the same has been presented at the International Human Genome Meeting (HUGO 2008, Hyderabad). QSAR of Efflux pump inhibitors QSAR studies of a library of 40 Efflux Pump Inhibitors (which inhibits the efflux pumps and are very important in increasing the potency of the known antibiotics) has been carried out and a highly statistical model with2 r = 0.962 and q2 have been developed. The manuscript is being prepared for publication. Refurbishing of the website The website of IIIM was completely refurbished in order to give it a new look, remove the junk information and make the website dynamic. First online Newsletter of IIIM launched The first ever online newsletter that highlights the important achievements of the institute was launched. It can be accessed via the institute’s website. This newsletter would be updated every month and after every three months, the printed version would be released. Proposed Mechanism of action of natural products (saponins) on TNF-á Docking studies of saponins on to a selected target, namely TNF-á has been carried out. The in silico results corroborates the involvement of dimer rather than trimer for its stabilization and consequent inhibnition of the receptor. The manuscript is being prepared for publication in JMC. Molecular Docking studies on selected Cancer targets Docking studies of a library of active molecules (anti-oxidants, anti-cancer, anti-inflammatory, anti-bacterial) from IIIM have been initiated on selected targets viz., Topoisomerase I & II, Tubulin, Histone deacetylase and Inose, in order to understand the mechanism of action and analyse the specificity of the molecules. After the preliminary screening, the molecules would be shortlisted for further refinement and flexible docking. Strengthening of in silico facilities A new high end molecular modeling software has been procured and configured, which would give a better analysis of in silico experiments and is also incorporated with flexible protein docking which takes care of the flexibility of the active side residues to a great extent. Database on Venom PhospholipaseA2 In continuation to our earlier work on PLA2 and its inhibitors (Patent application: NF0236/2006 dt. 12.10.2006, 0532DEL2008 dt. 05.03.2008), a comprehensive information about PLA2 in all the species of venom have been downloaded. A database on the above information is developed and is under testing on the intranet in order to get a copyright on the same. Medicinal Plants database A comprehensive web enabled medicinal plant database of IIIM has been developed, which is under testing on the intranet. This would provide a detailed information of the compounds extracted from a medicinal plants with details like ‘structure’, ‘common name’, ‘isolated by’, ‘isolation date’, ‘plant name and family’ besides some activity data and literature references in the initial phase.
Human Resource Development A total of about 40 students trained in the area of Bioinformatics and Information Technology.
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Future Activities • QSAR studies on the new series of potent compounds viz., N-series and MVRK series that has shown efflux pump inhibitory activity better than all the known EPIs reported in the literature on the overexpressedStaphylococcus aureus NorA strain. • Further improvement of the 3D structure of NorA efflux pump and molecular docking analysis of the library of compounds from IIIM to validate the studies to arrive at a robust structure of highly important membrane protein. • Regular updating of the institute’s website including the newsletter. • Further studies on the molecular docking of active compounds and docking studies on parthenin derivatives on to the selected targets viz., Topoisomerase I & II, Tubulin, Histone deacetylase and Inose. • Human resource development through trainings, workshops and demonstrations. • To file the copyright of the databases on medicinal plants and PLA2. Papers communicated • Nargotra A. et al (2008) Structural Characterisation and Refinement of NorA, a multidrug resistant efflux pump – an in silico approach. Poster presentation at Human Genome Meeting, HUGO 2008, Hyderabad, Sept 27-30, 2008. • Khursheed et al. Ovalbumin assisted diastereoselectivity during reductions of diketones and hydroxy ketones. Eu J of Org Chem. • Reddy M.V. et al., Design, Synthesis and Biological Evaluation of Stilbene based Anticancer agents. Presented at International Conference on New developments in Drug Discovery from Natural Products and Traditional Medicines. (2008) NIPER, Mohali. To be communicated • Nargotra et al., A highly statistical QSAR model of NorA efflux pump inhibitors. To be communicated in Bioorganic and Medicinal Chemistry letters. • Nargotra et al., Identification of an aromatic inhibitor of venom Phospholipase A2 using insilico approach. To be communicated after receiving the patent filed for the same. Contact Details
Dr. S.Koul, Bioorganic Chemistry Div, IIIM Jammu Sh. Abdul Rahim, Scientist, Sh. Amit Nargotra, Scientist Ph: +91 191 2569000-010 xtn: 269
105 Sub - Distributed Information Centres Karnataka Vetirinary, Animal & Fisheries Sciences, Mangalore Coordinator: Dr. I. Karunasagar Highlights of major research activities of the centre for the year 2008-2009 a. Complete genome sequence of Hepatopancreatic parvo virus (HPV) HPV is an emerging virus in shrimp aquaculture. We were able to generate the complete nucleotide sequence of this virus. Whole genome analysis using bioinformatics tools revealed the presence of one structural and two non-structural genes for this virus. The complete genome sequence has been deposited in GenBank (Acc.no. NC_011545). This is the first whole genome reported and submitted for any shrimp virus from India. b. Genotyping and characterization of variable regions of white spot syndrome virus (WSSV) WSSV from infected post-larvae and juveniles of cultured shrimp, wild shrimp and crabs collected from both east and west coast of India was genotyped based on variable repeat regions reported for this virus. The variable regions in ORF94, ORF125 and ORF75 were amplified, sequenced and analysed. These data suggest that combined analysis of all 3 variable loci could be used to differentiate and characterize specific WSSV strains. For general epidemiological studies, the best marker with maximum variation is ORF 94, followed by ORF 125 and ORF 75. The 3 repeat regions above were used to compare WSSV genotypes from disease outbreaks on 3 sets of farms from different locations in the state of Andhra Pradesh. The genotypes within each farm set were almost identical, but differed between farm sets, suggesting that WSSV transmission occurred directly through virus carriers or water exchange between adjacent farms at each location. These findings show that genotyping can be a useful epidemiological tool for tracing the movement of WSSV within infected populations. Two publications based on this work have already appeared in International journals. c. Analysis of 16S rDNA sequences of uncultured bacteria that are associated with marine sponges The biology of the bacterium-sponge relationship has elicited considerable interest among researchers investigating marine organisms as sources of an array of natural products and several bioactive secondary metabolites. As a first step, we investigated the microbial diversity associated with marine sponge Halichondria nigrocutis, Protylyssa sp. and Subertis carnosus prevalent along the coast of India. The phylogenetic affiliation of sponge-associated bacteria was assessed by 16S rRNA sequencing of cloned DNA fragments. Phylogenetic analysis of sequence data identified several microbial community associated with sponges. The 16 rDNA data pertaining to each microbial community has been deposited in GenBank and accession numbers obtained. d. Identify Type III secretion system in Vibrio vulnificus using genomics approach Bioinformatics analysis for the Type III secretion system inVibrio vulnificus has led us to th identification of 21 genes associated with this system. Structure prediction for nine genes using homology modeling has been completed. The structure-function relationship of the genes is in progress. e. Development of EST Bank for the tiger shrimp P. monodon WSSV infected Penaeus monodon cDNA library was constructed by extracting the mRNA from hepatopancreas, gills, muscle and hemolymph. The sequence generated have been submitted to EST database. Generations of more EST sequences are in progress. GenBank submissions The Centre has been able to deposit the following sequences to GenBank · Complete genome sequence of HPV (1) · Nucleotide sequences (157) - Uncultured bacterial spps. actinobacterium (45); firmicutes (23); cyanobacterium (9); alpha proteobacterium (7); gamma proteobacterium (8); delta proteobacterium (2); planctomycetes (7); chlamydiales (4) - Macrobrachium rosenbergii (15) - HPV (5); - all other taxa (57) · Expressed Sequence Tags (1038) Publications with the support of Bioinformatics · Bhowmick, P. P., Khushiramani, R., Raghunath, P., Karunasagar I. and Karunasagar I. 2008. Molecular typing of Vibrio parahaemolyticus isolated from seafood harvested long the south-west coast of India. Letters in Appl. 106 XXth All India BTISnet Coordinators’ Meeting February 03-04, 2009
Microbiol., 46: 198–204. · Divu, D., Karunasagar, I. and Karunasagar, I. 2008. Microsatellite DNA markers in the giant freshwater prawn, Macrobrachium rosenbergii: a tool for genetic analysis. Molecular Ecology Resources, 8:1040-1042. · Divu, D., Khushiramani, S., Shekar, M., Karunasagar, I. and Karunasagar, I. 2008. Isolation, characterization and evaluation of microsatellits DNA markers in giant freshwater prawnMacrobrachium rosenbergi from South India. Aquaculture. 284:281-284. · Joseph, B., Mertins, S., Stoll, R., Schar, J., Umesha, K. R., Luo, Q., Muller-Altrock, S. and Goebal W. 2008. Glycorol- Metabolism and prf A activity in Listeria monocytogenes. J. Bacteriol. 190:5412-5430. · Khushiramani, R., Girisha, S. K., Bhowmick, P. P., Karunasagar, I. and Karunasagar, I. 2008. Prevalence of different outer membrane proteins in isolates of Aeromonas species. World. J. Microbial. Biotechnol. 24: 2263-2268. · Kunyarat, D., Paiboon, S., Umesh ,K. R., Karunasagar , I., Thewarach, L., Christen, R. S., Hanne, S. and Maria, V. J. 2008. Improvement of PCR for Detection of Opisthorchis viverrini DNA in Human Stool Samples. J. Clinical Microbiol., 46: 366-368. · Parvathi, A., Umesha, K. R., Sanath Kumar, H., Sithithaworn, P., Karunasagar, I. and Karunasagar, I. 2008. Development and evaluation of a polymerase chain reaction (PCR) assay for the detection Opisthorchisof viverrini in fish. Acta Tropica. 107: 13-16. · Pradeep, B., Shekar, M., Karunasagar, I. and Karunasagar, I. 2008. Characterization of variable genomic regions of Indian white spot syndrome virus. Virology. 376: 24-30. · Pradeep, B., Shekar, M., Gudkovs, N., Karunasagar, I. and Karunasagar, I. 2008. Genotyping of white spot syndrome virus prevalent in shrimp farms of India. DAO., 78: 189-198 · Raghunath, P., Acharya, S., Bhanumathi, A., Karunasagar, I. and Karunasagar, I. 2008. Detection and molecular characterization ofVibrio parahaemolyticus isolated from seafood harvested along the southwest coast of India. Food Microbiol. 25:824- 830. · Shekar, M., Acharya, S., Karunasagar, I. and Karunasagar, I. 2008. Variable repeat regions in the genome of Vibrio vulnificus and polymorphism in one of the locus in strains isolated from oysters. Int. J. Food Microbiol. 123: 240-245.
Proposed activites during 2009-10 · Generation of ESTs for the tiger shrimpP.monodon · Analysing further the Type III secretion ofV.vulnificus and identifying the structure-function relationships using bioinformatics · Study on the outer membrane proteins for Aeromonas hydrophila and Edwardsiella sp. two most major pathogens infecting fish · Further analysis of the 3 major genes of HPV using protein-modelling · Conduct training programmes and human resource development
Contact details
Name of the Coordinator : Dr. I. Karunasagar Postal Address : Department of Fishery Microbiology 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
107 Sub - Distributed Information Centres Mahatma Gandhi Institute of Medical Sciences, Wardha Coordinator: Dr. B. C. Harinath 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 infectious disease diagnostic research and training. In addition to providing academic bibliography service and in-house Training programme for staff involved in Hospital Information service, the Centre organizes yearly National level Workshop / Seminar / Symposia etc. So far 11 such events have been organized which were well appreciated. Further, this Centre also publishes SEVAMED, a Quarterly Update on Infectious Disease Research and Traditional Medicine which is in its 10th 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 and JBTDResPub, a database on research publications on Immunodiagnostics in infectious diseases. Proceedings of National Symposium on Medical Informatics & CME on Hospital Information System as a reference book including the basics of computer and advances & its application in Medi- cal Informatics has also been published and available on www.jbtdrc.org. Centre has also 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.
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.
Infrastructure facilities in the Bioinformatics Centre • Computer & Communication facility: i. Computer Hardware: (i) Server - 3 (IBM Xeon, Compaq Proliant 3300 PIII-1, Zenith P-III) (ii) Dell Workstations (AW-T3400) - 3 (iii) PCs - 14; (iv) Laptop - 2; (v) Printers (Laser, HP Color Laser Jet, Canon Photo printer, Dot-matrics), (vi) Photocopier - ModiXerox Workcentre (model XD 155 DF), Canon iR1210 digital copier, Godrej G-1508 digital copier cum printer, Canon iR1600 Copier cum printer, (vii) Cisco Router, (viii) Patton Modem, (ix) Wireless router, (x) Switches, (xi) LCD Projector (2), (xii) Scanner Cannon 3000F, (xiii) Kodak Digital Camera, (xiv) Sony Handy cam. (xv) Spiral Binder etc. Bioinformatics Centre, Lab-1 (Immunology) & Lab-2 (molecular biology) and Central Library are networked through LAN. ii. Computer Software: Windows NT with service pack 6, Microsoft Windows NT 4.0 Service pack 4, Windows 98, 2000, XP, Office 2007, SQL Svr Standard Edtn 2005 Win 32, Visual Studio Pro 2008, Visio Std 2007, Developer Training Service Pack 3, Microsoft Visual Studio 6.0 Professional Edition with MSDN Library, Adobe Dreamweaver CS3 Win 9.0, Flash Pro CS3 Win 9.0, Adobe Photoshop Extended CS3 10.0, Win Adobe PageMaker 6.5, Wings 2000, Tally 7.2, Freely available online Bioinformatics software for sequence analysis, 3D visualization tools etc. are also being used. Communication Facility: Centre has got installed BSNL 1 mbps Leased Line. This has improved the connectivity & speed. This facility has been extended to Hospital Information System of this Institute and Central Library for PG students.
Details about staff members working in the centre Mr. Lingaraja Jena, Information Officer Mr. Pramod Deshmukh, Technical Assistant Mrs. Tripti Das, Data Entry Operator Mr. Ashish Kadam, Computer Operator Information Officer and Technical Assistant posts have been absorbed by the host Institute. Further absorption of 108 XXth All India BTISnet Coordinators’ Meeting February 03-04, 2009
other staff is under consideration. Major activities of the centre during the year 2008-09 • SEVAMED, a quarterly bibliography journal has entered 10th year of its publication. This has been well received by the scientists & medical teachers. • 11th National Workshop on Medical Informatics and CME on Biomedical Communication supported by DBT, MCI & ICMR was organized during November 20 - 22, 2008. Proceedings of the workshop for all India distribution are in press. • Online Certificate Course on Health Informatics - a curricular certification Course has been designed to deliver basic concepts in Health Informatics through on - line training in collaboration with Department of Bioinformatics, SVIMS University, Tirupati. This course is likely to start soon. • Two PG students from Orissa University of Agriculture & Technology, Bhubaneswar completed the six months Project Traineeship in Bioinformatics in this Centre. Two students are expected to join in February, 2009. • Centre has launched two more websites www.bicjbtdrc-mgims.in and www.arogyadham-seva.com this year. Collaborative works / initiatives • Collaborating with SVIMS University, Tirupati to develop syllabus for Online Certificate Course on Health Informatics. • Exploring collaboration with C-DAC, Pune in the Indo-UK Biotechnology and Biological Sciences Research Council (BBSRC) project on “A system Bioinformatics approach to the annotation of Mycobacterium and Salmonella Genomics”. The other institutes are Institute of Animal Health (Compton, UK), Sanger Institute (UK). Proposed activities during the year 2009-2010 • Designing of Mycobacterium tuberculosis protease database and annotation of different M. tb proteases (both protein & gene level) • Evaluation of the beneficial effects e-healthof info services related to Research and Health Informatics updates and Medical Tourism to medical teachers, research students and patients. • Continuation ofS evamed Quarterly an Update on Infectious Disease Research and Traditional Medicine to bring awareness and promote health research. • Development of Clinical Decision Support System (CDSS) by analysis of the field data of Filariasis, Tuberculosis etc. • Organization of National Level Workshops on Biomedical Informatics and Communication.
Additional Details
Name of Coordinator: Dr. B. C. Harinath, PhD (USA) Director, JBTDRC & Coordinator, BIC Email: [email protected]
Name of Contact Person: Dr. Satish Kumar, MD Professor, Biochemistry & Dy Coordinator, BIC e-mail: [email protected] Postal Address: Bioinformatics Centre, JBTDRC Mahatma Gandhi Institute of Medical Sciences Sevagram (Wardha) - 442 102 TeleFax: 07152 - 284038 Email: [email protected], [email protected] Web: www.jbtdrc.org, www.bicjbtdrc-mgims.in, www.arogyadham-seva.com, www.mindandbodyhealth.org.
109 Sub - Distributed Information Centres National Botanical Research Institute, Lucknow Coordinator: Dr. Sudershan Kumar Highlight of work done NBRI Bioinformatics (NBRI-subDIC) was set up for development of International Legume Database and Information Service (ILDIS) database of eight South Asia countries namely India, Nepal, Bhutan, Bangladesh, Sri Lanka, Maldives, Myanmar and Pakistan. Under this project NBRI Bioinformatics has developed a scientifically validated unique database of 2030 legumes of eight South Asian countries and establish the linkage with ILDIS, UK and database is available on internet at www.ildis. org. NBRI Bioinformatics has further advanced the work on several database like a) on updation and upgradation of legume database, b) development of database on all other groups of plants- plants of India database, c) herbarium specimen data- base for establishing a network and link with GBIF, d) collections of botanic gardens, e) Traditional Knowledge Digital Library (TKDL), and f) database on medicinal plants etc. Besides these database development efforts, NBRI-Bioinformatics has established a network using 2 mbps leased line from BSNL. This network serves the core requirement of various R&D work of above said projects and is being shared with other R&D groups of NBRI.
Major work done during the year 2008-09 includes as under (i) Updation and upgradation of legume database: It is absolutely essential to update and upgrade the international legume database and during the current year following work has been done: (i) Approx. 10069 records of legume taxa were edited to keep database update. (ii) 10569 citation were referenced against each accepted and synonym and 10569 reference to citations were also added (iii) 42000 descriptors records i.e. 6000 records each for root, stem, leaves, flowers, and fruits and flowering and fruiting time will be completed in this year. NBRI Bioinformatics has also attracted financial support following other projects and undertaken the R&D: (ii) Networking of Botanic Gardens of India: Under Department of Information Technology (DIT) sponsored project development of a software for automated identification of RET species and a database of species growing in botanic gardens is being developed. (iii) Establishment of a online nodal station for the Asia Pacific medicine Network (APTMNet) A database is being developed on medicinal plants of India and linkage will be established with APTM Network under the supervision of D/o AYUSH, Ministry of Health & Family Welfare, Govt. of India.. (iv) Traditional Knowledge Digital Library (TKDL) NBRI Bioinformatics is also developing a database of 2500 species for Traditional Knowledge Digital Library (TKDL) under CSIR network project.
Future Activities 1. To continue updation and upgradation of legumes of South Asia database with descriptors and distribution maps using GIS tools. 2. To update and upgrade plants of India database adding by establishing links to Molecular databases and also make database web enabled and launch online updation. 3. To update and upgrade website IBGN, through the support of DIT, Govt. of India. 4. To establish linkage of specimen records using GBIF protocol and also function as GBIF-India node and to strengthen network of botanic gardens, herbarium through GBIF module under the guidance of NBA. 5. To maintain APTMNet India nodal station under the supervision of D/o AYUSH, Ministry of Health and Family Welfare. 6. To work on new areas of biodiversity informatics: georeferencing and networking and on line query systems and other innovative aspects.
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7. To organize training courses/workshops as per need of various programmes. 8. To maintain network for undertaking all above 1-7.
Publications NBRI Bioinformatics group has been databases through online website and the following websites are developed and main- tain by NBRI Bioinformatics include: a) http://www.ibgn.org & b) http://www.ibgn-lko.org. Besides this NBRI Bioinformatics in partner in global website for South Asia Legume Database under the aegis of ILDIS (http://www.ildis.org).
Contact
Dr. Sudershan Kumar Scientist & Coordinator, NBRI-Bioinformatics National Botanical Research Institute Rana Pratap Marg, Lucknow 226 001 UP Ph.: 0522-0522-2204025, 2204026 Fax: 0522-2205673 Email: [email protected]
111 Sub - Distributed Information Centres National Dairy Research Institute, Karnal Coordinator: Dr. D. K. Jain Area of Specialization– Animal Biotechnology. Major research sub-areas The major areas of research include Embryo Biotechnology; Reproduction Augmentation; Livestock Genomics in gen- eral, and Buffalo Genomics in particular; Probiotic attributes lactobacilli in milk; Development of recombinant dairy enzymes, PCR based test kits for detection of food borne pathogens; Structural Biology/Bioinformatics of biological macro-molecules; Gene expression analysis and Proteomics of Mammary gland.
Major activities of the Sub-center during the year 2008-09 The Sub-centre continued to be actively involved in multifarious activities such as undertaking some research case studies including an evolutionary study on aspartic proteinase with implication in milk clotting using various bioinfor- matics software like Clustal X, Clustal W, PSI Blast, Mega software, NCBI Map viewer and many more for finding the evolution; providing e-mail and internet access to the scientists and students of the Institute; strengthening of labora- tory facilities through procuring new hardware and software, viz., Dell Workstations along with CLC Main Workbench for DNA, mRNA and protein sequence analyses; strengthening Genome Analysis work in Livestock in terms of produc- tion, reproduction and disease diagnosis; conducting various training programs and workshops for scientists/faculty and Post-Graduate (PG) students belonging to various academic and R&D institutions; invited expert lectures/ presentations by Institute Bioinformatics faculty at various seminars/ workshops/short-courses organized within/outside the Insti- tute; subscribing to forty five online international journals as well as providing the Institute scientists with online access (IP address based) to as many as 1153 important journals through Consortium for e-Resources in Agriculture (CeRA, http://cera.jccc.in/); initiative to establish Wi-Fi connectivity for the Institute Hostels; initiative to revamp the Institute Web site to Animal Sciences Web Portal; and software development through studentships/traineeships, for MIS and data analysis requirements of Institute researchers.
Staff members at the Sub-center
Academic programs This Institute offers Masters and Doctoral degree programs in the fields of Animal Biotechnology, Animal Biochemistry and Dairy Microbiology. A specialized course on Bioinformatics is given to these PG students. We also equipped our students with various Bioinformatics tools that are useful in their Molecular Biology & Genetic Engineering course. All the students are getting very good placement.
Bioinformatics publications(Alphabetically ordered on authors’ names) Jain, D. K., Sharma, A. K., 2008. A glimpse of information and communication technology activities at National Dairy Research Institute, Karnal. In: Proceedings (Souvenir) of the Golden Jubilee National Seminar on Dairy Education, Karnal (India), March 12-13. Jain, D. K., Sharma, A. K., Ruhil, A. P., 2008. Emerging computing and communication techniques for accelerated growth in dairying – an NDRI perspective. In: Proceedings of the Symposium on Accelerated Growth of Agriculture through Information Technology, 62nd Annual Conference of Indian Society of Agricultural Statistics, Tirupati (India), November 24-26. Kumar, S., Kolte, A . P., Yadav, B. R., Kumar, S., Arora, A. L., Singh, V. K., 2008. Genetic variability among sheep breeds by Random Amplified Polymorphic DNA–PCR. 2008. Indian Journal of Biotechnology, 7, October issue, 482-486.
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Kumar, R., Yadav, B. R., Dev, K., Singh, R. S., 2008. A simple protocol for DNA extraction from Staphylococcus Aureus. http://www. protocol-online.org/prot/Protocols/A-Simple-Protocol-for–DNA-E xtraction-from-Staphylococcus– Aureus-4999.html. Mohanty, A. K., Fisher, A. J., Yu, Z., Pradeep, M. A., Janjanam, J., Kaushik, J. K., 2008. Cloning expression characterizations and crystallization of Brp39, a signaling glycoprotein expressed during mammary gland apoptosis,Protein Expression and Purification (Online first). In press. Sharma, A. K., 2008. Connectionist Models to Predict Milk Yield – A Case Study. In:Proceedings of the 3rd International Conference on Advanced Computing and Communication Technologies (ICACCT–2008), Panipat (India), November 08-09. Sharma, A. K., 2008. Connectionistvis-à-vis conventional models for predicting milk yield in dairy cattle at an organized herd – an empirical study. In: Proceedings of the National Seminar on Emerging Opportunities for Commercialization in Dairying, Karnal (India), November 6-7. Sharma, A. K., Sharma, R. K., 2008. Predicting milk yield using connectionist models with cubic spline interpolation based initial weights. In: Proceedings of the 11th Punjab Science Congress, Patiala (India), February 07-09, 2008. Sharma, A. K., Sharma, R. K., Chakravarty, A. K., 2008. Connectionist vis-à-vis conventional models for predictions of lifetime milk production in Karan–Fries dairy cattle. Technia - International Journal of Computing Science and Communication Technologies, 1(1), 29–32. Kumar, S., Yadav, B. R., Bhardwaj, A., Jain, S., Yadav, H., 2007. Estimation of fat in milk samples. http://www.protocol-onli ne.org/prot/Protocols/Estmations-of-Fat-in-Milk-Samples-4788.ht ml. Sharma, S., Yadav, B. R., Bhardwaj, A., Jain, S., Yadav, H., 2007. Denaturing Urea-Polyacrylamide Gel Electrophoresis (PAGE) based microsatellite analysis. http://www.protocol-online.org/ prot/Protocols/Denaturing-Urea-Polyacrylamide- Gel-Electropho resis-PAGE-Based-Microsatellite-An alysis-4787.html. Yadav, B. R., Kale, D. S., 2008. Single Strand Conformation Polymorphism (SSCP) analysis using Nondenaturing Polyacrylamide Gel Elect. http://www.protocol-online.org/ prot/Protocols/Single-Strand-Conformation-Polymorphism- SSCP —analysis-using–Nondenaturing-Polyacrylamide-Gel-Elect-4991 .html. Yadav, B. R., Kumar, R., 2008. Syntenic approach for livestock genome mapping. In: Proceedings (Souvenir) of Annual Conference of ISAG&B and National Symposium on Livestock Genomics and Productivity Enhancement Food Security, New Delhi (India), July 3-4.
Training/Workshop organized i) National Training Program on “Application of Bioinformatic Tools in Animal Genome Analysis”, January 27 to February 16, 2009 [Ongoing]. ii) National Workshop on “Genome Analysis and Structural Biology”, October 21-23, 2008. iii) Staff Training on Use of MATLAB Software for High Performance Numerical Computation and Visualization.
Collaboration with external institutions The Bioinformatics Sub-centre has developed linkage with several Academic and R&D Institutions’ Bioinformatics/Computer Science Departments within the northern region of the country such as BISR, Jaipur; Banasthali Vidyapeeth, Banasthali; JNU and IIT, Delhi; ICFRE, Dehradun; GJ University, Hisar; APIIT, Panipat; Kurukshetra University, Kurukshetra; Thapar University, Patiala; and IMTECH, Chandigarh.
Additional Details
Name of Contact Person(s): Dr. D. K. Jain, Coordinator Dr. A. K. Sharma, Information Officer Postal Address: BTIS Sub-Centre, Computer Centre National Dairy Research Institute, Karnal–132001 (Haryana) INDIA Phones(O): +91 184 2259014 (DKJ); +91 184 2259015 (AKS)
113 Sub - Distributed Information Centres National Institute of Plant Genome Research, New Delhi Coordinator: Dr. Gitanjali Yadav Summary of the progress made by the centre from its inception The Sub-DIC at NIPGR has successfully installed, operationalized and established major computational, networking and scientific resources, including institute’s own web & academic emailing servers. Staff intake for all three project positions has been completed. Research activities have been initiated in sevral aspects of genomics and proteomics.
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 Pro- teomics in Plants. Differential Gene expression and analysis of plant stress responses
Area of Specialization of the centre Plant computational Biology, Molecular Evolution of protein families involved in stress response, Structural modeling for substrate specificity prediction.
Major activities of the centre during the year 2007-08 a. Structural Elucidation of differential stability/activity of two stress response protein homologs in Cicer arietenum. b. Automation of a method to detect the biosynthetic order of ORFs in an uncharacterized secondary metabolite cluster in microbial genomes. c. Discovery of a new line of mammalian defense against bacterial pathogens through characterization of a highly potent endogenous protein inhibitor of bacterial hyaluronidases. d. Construction of linkage maps for Catharanthus roseus from available EST data in public databases.
Infrastructure facilities in the Bioinformatics Centre A. Computer & Communication facility High end Linux and Mac Workstations & Servers, Laser Printer, Copier and Scanner, Tape Drives for data Back up. B. Scientific Software packages Accelrys Discovery Studio v 2.0 Cystoscape, Pymol, iWork, Endnote and R C. Databases & other information resources Reference Manager Database
Types of services provided Bioinformatics assistance, Installation of scientific software packages, LAN management, support, maintenance & data backup.
Details about staff members working in the centre
Initiative to validate the outcome of bioinformatics resources Several collaborations within NIPGR and externally with School of Env Sciences, JNU, New Delhi
Collaborative works/ initiatives Dr. M. Majee, NIPGR – C.arietenum MIPS analyses Dr. D. Chattopadhyay, NIPGR – Tomato Genome Sequencing Prof. S Kumar, NIPGR – EST Markers for plant genomes Prof. K. Datta, SES, JNU – Defense against bacterial infections
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Databases/ Software packages developed Intra-Inst Reference Manager Online server for predicting ORF order in bacterial genomes Online server for linker analysis of secondary metabolite genes Papers published or presented in the conferences with reference a. Yadav G, Prasad RLA, Jha BK, Rai V, Bhakuni VK and Datta K (2008).J. Biol. Chem, doi:10.1074/jbc.M804246200 b. Kaur H, Shukla RK, Yadav G et al (2008) Plant, Cell and Environment, 31:1701-1716. c. Chopra T, Banerjee S, Gupta S, Yadav G, Anand S, et al. (2008) PLoS Biology: Vol. 6, No. 7, e163 doi:10.1371/ journal.pbio.0060163.
Details of Training/ Workshop organized and total no. of users trained Nine Students have been trained to date. Six students are undergoing training currently.
Future activities To conduct annual workshops and discussion meetings. Expansion of center infrastructure. Continuation of current work & Expansion of research arenas
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/disc Name of Contact Person: Dr. Gitanjali Yadav Email: [email protected]
115 Sub - Distributed Information Centres National Institute of Oceanography, Goa Coordinator: Dr. C. T. Achuthankutty Bioinformatics Centre at NIO works towards improving the understanding of the marine biota in the Indian waters. Basic aim of the centre is to study and record the marine biodiversity of Indian waters, and to make it available in the form of digital data. The 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. The centre makes marine biodiversity data available in formats which is easy to understand and can be readily used by the policy makers, research community, educational institutions and stake holders. The centre sees itself as a dynamic component of the National Institute of Oceanography, and is actively following the mission of the institute which is “to continuously improve our understanding of the seas around us and to translate this knowledge to benefit all”.
Area of specialization of the centre: Marine Biodiversity Informatics Major activities of the centre during the year 2008 – 09 • Website launched for dissemination of marine biodiversity data and information www.niobioinformatics.in • Developed BIOSEARCH online database on marine organisms from Indian waters • Developed DigiMus-2.0, a software to digitize marine biodiversity specimen collections. • Initiated work on marine heat shock proteins, drug designing and databases on protein derived from marine organisms. • Training imparted to students from colleges in areas such as protein sequence analysis and various bioinformatics softwares. • Papers in different aspects of marine biodiversity informatics have submitted in scientific journals. Collaborative works /initiatives The Bioinformatics Centre of NIO is the Indian Ocean regional node of the Ocean Biogeographic Information System (OBIS). The main objectives of Indian Ocean Biogeographic Information System (IndOBIS) is to collect, collate and validate all the taxonomic data available from the Indian Ocean region and catalogue the data electronically and disseminate to the international community. OBIS is the data component of the Census of Marine Life (CoML), a global initiative to study the marine flora and fauna. The Indian Ocean CoML Secretariat has been established at NIO, Goa to coordinate the activities of the Indian Ocean rim countries.
Databases /Software packages developed • Web based information services through www.niobioinformatics.in • BIOSEARCH online database on Marine organisms from Indian waters • DIGIMUS Ver. 2.0 Biological specimen digitization software Papers published or presented in conferences with reference • Kakodkar, A.P., Kerkar S.S., Verghese, N.S., Kavlekar, D.P., Achuthankutty, C.T. Darwin Core based Data Streamlining with DigiMus 2.0 Biodiversity Informatics Journal (Accepted) • Achuthankutty, C.T; Kakodkar, A., and Nath, A.IV, (2008) IndOBIS and its relevance to the Gulf of Mannar Biosphere Reserve Proceedings of the symposium on “Biodiversity conservation in Gulf of Mannar biosphere reserve”, 20-21 September, 2008) • Molecular diversity of RelA enzyme in marine bacteria- A Bioinformatics analysis (Nath, AIV, Tresa, RAT, Alornekar, A; Varghese, NS, Proceedings of the International conference on biodiversity, environment and sustainability- challenges for future, 4-6 September, 2008) • Ingole, B.S. Remya T. 2009 Marine biodiversity along from Maharashtra coast (Ready for submission) Future activities The Bioinformatics Centre at NIO is committed itself towards improving the understanding of the marine biotic resources in the Indian waters. The main objective of the centre is to study and document the biotic resources in an organized manner and disseminate the information to all those who need it at any place and any time to aid in their effective management and conservation. • Database on Heat Shock Proteins from Marine organisms
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• Databases on bio-molecules derived from marine organisms.(Sponges, Holothurian) • 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: (0)832- 2450281 Fax number: (0)832-2450606 Email: [email protected] Website: www.niobioinformatics.in
Name of Contact Person: Shri Devanand Kavlekar Email: [email protected]
117 Sub - Distributed Information Centres National Institute Of Technology, Raipur Coordinator: Dr. M. K. Verma Major activities of the centre during the year 2008-09 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. Initiated & enriched the research en- vironment which resulted in: i. One National Workshop/Training on “Introduction to Drug/vaccine Designing” imparted a total 1575 man-hour. ii. One National Symposium (In Progress.). iii. Publications: National Journal: 1 International Conferences: 8 National Conferences: 1 iv. Projects Guided: UG -2, PG – 1, M. Phil - 1 v. International database enrichment: Two protein structures submitted to “La Sapienza” ‘Protein Model database ‘Rome. Major research activities in Biotechnology and its related fields at our institution a. Research work in Bioinformatics was carried by students of M.Phill./M.Sc./B.Tech Bioinformatics, Biomedical, Biotechnology, and Computer Technology. b. Research work initiated and carried in the Bioinformatics especially in Homology Modeling, Vaccine and Drug Designing and Evolutionary Analysis. c. Data base generation and Data mining were initiated by center. d. Research work carried in the field of Fuzzy Logic/ANN and Medical Bioinformatics. Infrastructure facilities in the Bioinformatics Centre a. Computer & Communication facility with Internet. b. Scientific Software packages: MATLAB TOOL BOX, Genechek and Genowitch, IRNA. c. Databases & Library facilities. . Collaborative works/ initiatives Development of Decision Support System for Asthma disease is in progress with Integral University Lucknow. Databases/ Software packages developed Database under process on Medicinal Plants for Arthritis, Epilepsy. Papers published or presented in the conferences with reference 1) “Computational approach for comparative analysis of in-silico 3D structures of Enolase [Bos Taurus]”, “National conference on Next generation computing & information system NGCIS 2009”, Kot Bhalwa, Jammu, India, Feb. 14-15, 2009. 2) “Bioinformatics tools based approach in identification and in-silico structure prediction of PRDX-2 protein involved in anti-oxidant activity in c.elegans”, ‘International conference Health Expo & Conference, 2008, Chandigarh, 3) “Application of artificial neural network approach for prediction of proteaosomal cleavage sites of Hepatitis D virus”, International conference Health Expo & Conference, 2008, Chandigarh, 4) “Parkinson disease pathway: Design a computational model for comparative study of c.elegans with homo-sapiens, mus musculus and cannis familiar International conference Health Expo & Conference, 2008, Chandigarh, 5) “In-silico 3D structure prediction of Enolase [Bos taurus]” has been accepted for poster presentation in theth 7 InCOB-Seventh International Conference on Bioinformatics 2008 at Taipei, Taiwan 6) “In silico designing of inhibitor against Tin2 for aging” HUGO’s 13th Human Genome Meeting Hyderabad.
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7) “An artificial neural network approach for prediction of proteaosomal cleavage sites for large delta antigen (HDAg-L) containing small delta antigen (HDAg-S) of Hepatitis D virus,” “International symposium on newer frontiers in biomedical research” Regional Medical Research Centre, N.E. region (ICMR), Dibrugarh 8) “Insilico vaccine prediction against Herpes Simplex Virus1 (HSV1)” “International symposium on newer frontiers in biomedical research” Regional Medical Research Centre, N.E. region (ICMR), Dibrugarh, 9) Paper Published in IX International symposium on vector & vector borne diseases -”Insilico 3D structure prediction of matrix protein1 of influenza A virus responsible for bird flu disease” Indian Council of Medical Research at Puri, Orissa -2008. Other details: Name of the Coordinator: Dr. M. K. Verma Postal Address: Sub-DIC Bioinformatics Centre, N. I. T. Raipur, G. E. Road, Raipur (C.G.) Phone Number: 0771-4062385 Mobile: 9425203472 Email: [email protected] Website: www.nitrr.ac.in Name of Contact Person(s): Dr. M. K. Verma Email: [email protected]
119 Sub - Distributed Information Centres North-Eastern Hill University, Shillong Coordinator: Prof. P. Tandon Summary of the progress made by the Centre from its inception The Bioinformatics Centre (BIC) at NEHU, setup and funded by DBT, GOI under the BTISnet program 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. BIC, NEHU: · Considered for upgradation to DIC with ‘Excellent’ remarks during the XIth Plan period as per the Sub-DICs’ 2nd review meeting during 29th October 2007. · inducted as one of the Examination Centers for conducting the National Level Bioinformatics Certification Exam (BINC), 2008 onwards. · hosting the XXth BTIS, DBT Co-ordinators’ meeting at NEHU during February 3-4, 2009 · has been sanctioned project“North East Parasite Information and Analysis Centre (NEPIAC): an in silico approach” from Department of Information Technology, Ministry of Communications and Information Technology, GOI.(Rs. 135 lakhs for 3 years w.e.f October’08)
Area of Specialization of the Centre: Biodiversity Informatics Major activities of the Centre during the year 2008-09 i) Lectures- cum- hands on training to participants of the UGC-sponsored Refresher Courses for College/University Teachers- Zoology: “Informtion Retrieval from Public Domain Biological Databases” 15th November, 2008; Botany: “Plant Bioinformatics: Recent methods and approaches” during 18th October 2008. ii) Training courses organised/announced - 1. “Molecular Biology Databanks and Integrated Data Analysis Tools: A Bioinformatics Approach” during March 25-29, 2008. 2. “In silico approach to Genome Analysis” scheduled to be held during Feb 5-11, 2009. iii) Developed and maintained the websites of: The 20th National Congress of Parasitology (http://www.zoology20thncp.qsh.in/) organized by Indian Society for Parasitology and Department of Zoology, NEHU, held during Nov 3-5, 2008 and The 96th Indian Science Congress (http://www.isc2009nehu.com/) held at NEHU during Jan 3-7, 2009 (for more than six months) iv) Participated in the “Meeting of the expert group to take forward Indian Bioresource Information Network (IBIN)” organized by National Bioresource Development Board, DBT, New Delhi (May 19, 2008) discussion meeting on “Indian Bioresource Information Network (IBIN): The Way Forward” organized by the University of Agricultural Sciences, GKVK Campus, Bangalore (August 19, 2008); and the Information Officer participated in 13the th Annual Genome Meeting of Human Genome Organisation held at Hyderabad, India (September 27-30, 2008).
Infrastructure facilities available in the Centre A. Computer & Communication facility Leased Line Internet Connectivity (2 Mbps), Implementation of LAN on a Structured CAT 5 UTP Cabling Network using Switches and Hubs, Servers (3 nos.), PCs (20 nos.), & Workstations (2 nos.), Printers (3 nos.), Scanner (1 no.), UPS (3 nos.), Projector (1 no.), etc. B. Scientific Software packages Accelrys Gene 2.5 (Sequence Analysis Work Bench), Matlab 7.0, Winspirs ver 4.1 for Biotechnological Abstracts, Reference Manager. C. Databases & other information resources Derwent Biotechnological Abstracts (July 1987 - March 2006), Reference Update Delux Edition (July 2002 - June 2004), Parasitology Database obtained through MOE&F. and other application Softwares from Microsoft , RHEL, SQL, Adobe and Apple etc.
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Details about staff members working in the Centre
Types of services provided Training, Database & Software Development; assistance in teaching of Bioinformatics course to M.Sc. students of Depart- ment of Biotechnology and Bioinformatics at NEHU, access to Internet and online Journals subscribed; technical support to NEHU, printing & scanning ~11,100 user hits as per the logbook (till December, 2008) maintained by the Centre.
Collaborative works/ initiatives i) The in house databases developed by the Centre, under process to be brought under the common portal of IBIN, NBDB, DBT. ii) The project entitled “North-East Parasite Information and Analysis Centre (NEPIAC):an in silico approach” in collaboration with IGIB, and TCGA, New Delhi. iii) A database on medicinal plants (nearly 400 species) currently under development under the “Network project Development of database of the Indian Himalayan region” sanctioned by NMPB, Department of AYUSH, MH & FW.
Databases/ Software packages developed i) The Helminth Parasite Spectrum in Northeast India (http://www.nehu.ac.in/BIC/Helminth_Parasite_NE/default. htm) 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) Helminth Parasite of Freshwater Fishes in India (under progress)
Recent Papers published in the peer reviewed journals/ Book chapters or presented in the conferences with reference A. Published/Accepted/Communicated i) Prasad, P. K., Tandon, V., Biswal, D.K., Goswami, L. and Chatterjee, A. (2008) Molecular identification of the Indian liver fluke,Fasciola (Trematoda: Fasciolidae) based on the ribosomal internal transcribed spacer regions. Parasitology Research, 103(6):1247-55 ii) Prasad P. K., Tandon V., Biswal D. K., Goswami L. M. and Chatterjee A. (2008) Use of sequence motifs as barcodes and secondary structures of internal transcribed spacer 2 (ITS2, rDNA) for identification of the Indian liver fluke, Fasciola (Trematoda: Fasciolidae). Bioinformation InCoB2008 Special Issue. iii) Goswami L.M., Prasad P.K., Tandon V. and Chatterjee A. (2009) Molecular Characterization ofGastrodiscoides hominis (Platyhelminthes: Trematoda: Digenea) inferred from ITS rDNA sequence analysis. Parasitology Research (accepted) B. Presented in Conferences i) Prasad, P. K., Tandon, V., Biswal, D.K., Goswami, L. and Chatterjee, A. Use of sequence motifs as barcodes and secondary structures of Internal Transcribed spacer 2 (ITS2, rDNA) for identification of the Indian liver fluke,
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Fasciola (Trematoda: Fasciolidae). INCoB 2008, Taipei, 21-23 Oct., 2008), Bioinformation
Details of Training/ Workshop organized and total no. of participants trained I) National Training Courses: Till date 15 nos. of national level training programmes; with a total number of 269 participants. II) Workshop & Seminars The DBT National Roving Seminar on Patenting in Biotechnology October 26, 2002; and National workshop on ‘Conservation and Sustainable Utilization of Medicinal Plants of North-East India’ May 27-28, 2004. Future activities A. Research Programmes: in areas of- I. Animal Science: The Department of Information Technology project entitled “NEPIAC: an in-silico approach” (October 08-October 11) will aim: To establish an integrated web-based approach database and research interface related to parasitology research: Functional and comparative genomics, proteomics, metabolomics, and evolutionary bioinformatics of pathogenic worm infections II. Major Bioinformatics Tools to be developed at the Centre 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 and developing e-learning bioinformatics modules. III. 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 and Barcoding of the North-East Biodiversity Resources. B. Teaching Programmes (proposed) Advanced P.G. Diploma in Bioinformatics (18 months), Certificate Courses (5 months), Credit Course in Bioinformatics that can be offered to the postgraduate and doctoral students of the University
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 1241/ 272 1242 Fax No.: (0364) 255 0150/ 255 0300 Email: [email protected]; [email protected]; [email protected], [email protected] Website: http://www.nehu.ac.in/BIC
122 XXth All India BTISnet Coordinators’ Meeting February 03-04, 2009 Punjab Agricultural University, Ludhiana Coordinator: Dr. (Mrs.) Parveen Chhuneja Area of Specialization of the centre : Bioinformatics & Agriculture Details about staff members working in the centre Name of staff Designation Working since Absorbtion status 1. Parminder Singh Information Officer Resigned on 4th November, 2008 Joined regular position 2. Vacant Bioinformatic Assistant Appointed but joined - 3. Gurbax Singh Data Entry Operator 24th Dec.2001 till date Not absorbed
Major activities of the centre during the year 2008-09 • Developing database for wild wheat and rice germplasm. We have a collection of >800 accessions of wild wheats and >350 accessions of wild rice germplasm. The data for various phenotypic traits is being compiled for developing a database for wild wheat and rice germplasm for utilization by the pre breeders for germplasm enhancement. • Conducting training on the “Bioinformatics: Basics and its use in gene cloning” for Molecular Biologists and Biotechnologists of the university. Dr Rajinder S Ranu, Professor, Colorado State University, USA and Dr Saurabh Raghuvenshi, Delhi University, South Campus imparted training to 30 scientists working on molecular biology, tissue culture, transgenic technology, horticulture and plant breeding. • Installation & Training on International Crop Information System (ICIS) for field data management and field selections. Dr Weng and Dr Arllet from International Rice Research Institute (IRRI) installed the ICIS software and gave hands on training to scientists working on wheat breeding and molecular biology. • Maintenance of Local Area Network of (approx. 200 nodes) in the Department of Plant Breeding, Genetics and School of Agricultural Biotechnology. • A parallel centre has been established in the newly founded School of Agricultural Biotechnology. Seven computer systems of the sub distributed center were installed in the School of Agricultural Biotechnology for providing computing facilities to the students and research scholars of Biotechnology. Communication facility in the Bioinformatics Centre Lease Line Internet connectivity enhanced from 1Mbps to 10Mbps (from Radio Link to OFC)
Types of services provided • Internet connectivity and computing services provided to faculty, students and research workers of various departments of the university • Maintenance of Local Area Network of (approx. 200 nodes) in Department of Plant Breeding & Genetics and School of Agricultural Biotechnology. Major research activities in Biotechnology and its related fields at your institution A School of Agricultural Biotechnology was established in April, 2008 with an aim to strengthen the field of Biotechnol- ogy in the Punjab Agricultural University. PAU is a premier agricultural institute in this region with very strong breeding programmes in major field crops including wheat, rice, maize, oilseeds, cotton and pulses. The major emphasis of School of Agricultural Biotechnology is the application of biotechnology for increasing productivity. The main focus of the all the biotechnological research projects is the germplasm enhancement in field crops using wide hybridization, molecular mark- ers and transgenic technology. DBT is in the process of approving a major research project on ‘International Wheat Genome Sequencing Consortium-India: Physical mapping and sample sequencing of wheat chromosome 2AL’ at a total cost of >13 crores to be undertaken in the School of Agricultural Biotechnology, PAU, Ludhiana. Under International Wheat Genome Sequencing Consortium, several countries have undertaken physical mapping and sequencing of the whole wheat genome. With DBT’s support PAU represented India in this consortium for physical mapping and sample sequencing of wheat chromosome 2AL. This project involves extensive Bioinformatics support for data management.
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Educational activities with details of placement B.Sc & M.Sc courses in Biotechnology have been started from the academic session 2008-09. A total of 50 students have been admitted in the B. Sc Biotechnology (Hons.) programme and 11 students have been admitted to the M. Sc. Biotechnology programme. Course curricula for both the programmes were developed and implemented.
Initiative to validate the outcome of bioinformatics resources Research workers are utilizing various Bioinformatics tools in their research endeavors extensively such as sequence search, BLAST, comparative mapping, primer designing, gene/QTL mapping etc.
Databases/ Software packages developed Development of the database for wild wheat and rice germplasm is in progress. We have a collection of >800 accessions of wild wheats and >350 accessions of wild rice germplasm which will be included in the database.
Initiation of R&D activities in Bioinformatics • Designing primers for mapping of genes for biotic and abiotic stresses • Designing primers for TILLING in diploid wheat • Mapping of new genes for biotic and abiotic stresses in wheat & rice Details of Training/ Workshop organized Title of the Training Date No. of participants Bioinformatics: Basis & its uses in gene cloning December 11-14, 2007 30 Impact shown by your centre on the growth of biotechnology and allied areas The Bioinformatics center has made possible the availability of 24 hour internet connectivity to the faculty and research fellows of the Department of Plant Breeding and Genetics and School of Agricultural Biotechnology, PAU, Ludhiana which has made possible use of Bioinformatics tools for searching and downloading DNA sequences from NCBI and TIGR sites.
Future activities for 2009-2010 • Intervention through Bioinformatics tools for utilizing the information generated in rice and wheat genomics. • Utilizing Bioinformatic tools for data management, storage and analysis for the project on ‘Physical mapping and sample sequencing of wheat chromosome 2AL’. Advanced biocomputing facilities will be set up under this project. • Elucidating the structure of putative novel alien genes using rice genome sequence information • Conducting trainings on the use of Bioinformatics in the field of genomics • Providing computing and networking facilities to the agricultural scientists • Developing a database for wild wheat & rice germplasm
124 XXth All India BTISnet Coordinators’ Meeting February 03-04, 2009 Rajiv Gandhi Centre for Biotechnology, Trivandrum Coordinator: Dr. Sathish Mundayoor Major activities of the centre during the year 2008-09 A. Softwares and databases development to support research activities in RGCB B. Molecular modeling and simulation studies to support various research activities of groups in RGCB. C. Hands-on training in Computer Aided Drug Designing for RGCB research students D. Project guidance and hands-on training for B.Tech and M.Sc students from various institutions and universities. Databases/ Software packages developed 1. TRIPS-Mtb: Amino acid repeats in protein sequences-their diversity and functional implications in Mycobacterium tuberculosis. It is a unique database of its kind that incorporates different kinds of amino acid repeats in proteins of M.tb. Protein sequences were retrieved in fasta format from Refseq and were analysed for amino acid rich regions and tandem repeats using an in-house developed pattern searching programme. The information generated as output was pooled into a database for detailed analysis of their role in genetic diversity and functions specificity in Mycobacterium tuberculosis. The database can be of good assistance to researchers in the field of mycobacterium involved in the study of amino acid repeats, serodiagnostic and vaccine development and can be useful for further analysis of internal repeats, their conservation and their implication in protein structure and function. 2. Mycogets:- A database of potential drug targets in Mycoplasma genitalia: insilico analysis of essentials genes and its metabolomics- Computational genomic technologies have created a paradigm shift in the target-based drug discovery process. This approach is appealing because it holds the promise of identifying more-efficacious compounds with fewer undesirable side effects. The bacterial genes that are non-homologous to human genes and essential for the survival of the pathogen represent a promising set of novel drug targets. Such a study on essential gene in Mycoplasma genitalium G37 has thus led to the selection of the most relevant proteins that can be targeted for effective drug design and vaccine development. The results of this study were organized in to a database. These gene products can be subjected to further analysis and modeling studies leading to the design of specific drugs against them. 3. ADMycob: Mycobacterium Adhesins Database. It is a unique database of its kind for mycobacterium adhesin molecules. Adhesins are potential targets for vaccine development against Drug Resistant pathogens. Many hypothetical proteins were identified as adhesins using Seapath software (developed by IGIB, New Delhi). ADMycob contains all the sequences of the 6 mycobacterial strains currently available in the public domain. They are classified as adhesins, nonadhesins and twilight. The database can be of good assistance to researchers in the field of mycobacterium, especially those interested in drug target and drug discovery. It helps to identify hypothetical proteins which are probable adhesins, and thereby aid in further studies on structural and functional analysis of those proteins. 4. Pro-reap Scan: A Perl program developed to scan protein sequences for occurrence of patterns and profiles stored in Swiss-Prot database. This tool facilitates the retrieval and analysis of amino acid repeats in the huge dataset very easily. All the identified repeats and corresponding details can be store in a MySQL database. TRIPS-Mtb database was developed utilizing this programme. Papers/Posters in Conferences • Krishnankutty Sivakumar, Biju Thomas, Devarajan Karunagaran., “Three diamensional structure of the closed conformation(active) of human merlin reveals a central alpha helical domain and masking of actin binding site in the FERM domain” (accepted for publication in International Journal of Bioinformatics Research and Application(IJBRA),2009) • P. J. Vivek, K. C. Sivakumar and E. V. Soniya, “Homology Modeling and Interaction Studies of Calcium Dependant Protein Kinase from Zingiber officinale Rosc.” presented at INTERNATIONAL SYMPOSIUM ON INDUSTRIAL BIOTECHNOLOGY (BIOVISION 2008) on November 15 - 17, 2008(Received Best Poster Award).
Details of Training/ Workshop organized and total no. of user trained • Conducted two days “Workshop on Computer Aided Drug Design” on 1st and 2nd of August 2008. 40 participants attended from across the country • Three trainees were selected under Studentship/Traineeship programme and were trained in perl programming, bioperl, database development, and bioinformatics tools for docking and molecular simulations studies etc. • 38 external students from various universities/colleges had undergone hands-on training in bioinformatics tools available with this facility. 125 Sub - Distributed Information Centres
Future activities • Development of databases and softwares relevant to RGCB research • Research and development in Bioinformatics. • Human Resource Development in Bioinformatics 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: Sivakumar.K.C Email: [email protected], [email protected]
126 XXth All India BTISnet Coordinators’ Meeting February 03-04, 2009 Sikkim State Council of Science and Technology, Sikkim Coordinator: Shri. B.C. Basistha Sikkim Bioinformatics Centre is a Distributed Information Sub-Centre established under State Council of Science and Technol- ogy, Department of Science and Technology, Government of Sikkim in the year 2001 with the technical and financial support of Department of Biotechnology, Government of India. The Centre actively involves in collection of information on various biological resources, retrieval of biological information and creation and management of databases.
Computer and communication facility The Centre is equipped with a dual processor server, P-4 PCs, Laptops, Scanners, DeskJet and laser printers and a Xerox machine. Softwares available- Phylo draw 0.8,Hex. 4.5, Rasmol version 2.7.4.2, Swiss PDB viewer, Arguslab 4.0.1, Cn3D 4.1, Windows XP, Avast antivirus, McAfee antivirus, trend Micro Neatsuite and PC-illin. The centre has 24 hours internet connec- tivity provided by the State National Informatics Centre through RF Antenna along with 512 Kbps leased line internet con- nectivity provided by Bharat Sanchar Nigam Ltd. Free internet and library facilities are provided to the research scholars.
Database & other information resources The center has prepared database on scientists working on different related fields , Bio-resources and Biodiversity of the state working on various fields of science, database on 450 species of orchids, 36 species of Rhododendron, and 200 species of medicinal plants has been prepared. Database on butterflies and birds of Sikkim is also being prepared. A upgraded web site for Bio-Informatics Center is being launched.
Major activities of the centre • The First Interactive BTISnet Meet for Bioinformatics centers of North Eastern states was successfully held at Sikkim on 12th and 13th Nov. 2008 with the support of DBT, GOI. • The independent website of the center and animation CD on cell and its organelle, cell division, protein synthesis and DNA replication prepared by the center was also released on the BTIsnet Meet for North East Bioinformatics Centers. • The center has produced two volumes of compilation on the published papers, book chapters and popular articles on bioresources of Sikkim. • The center also publishes periodical informative scientific news letter – “Bio-gyan” to keep the scientific fraternity and students abreast with latest biotechnological advancements and to inculcate a scientific temperament amongst them. • Phylogenetic analysis ofDendrobium species available in Sikkim has been done using phylip and phylodraw. Phylogenetic analysis of Rhododendron species is also being done at the center. • The XVIIIth Annual BTISnet Coordinators Meet was organized successfully by the Sikkim Bioinformatics Centre at Chintan Bhawan on 3rd and 4th February 2007, • Three days training program on “Introduction and Scope of Computational Biology” was organized by Bioinformatics Centre, Sikkim State Council of Science and Technology from 3/12/2007 to 5/12/2007. • Three day training on environment genomics and biodiversity was conducted from13th March 2008 to 15th march 2008 for science gradates and post-graduate students. • Papers published or presented in the conferences with reference: • Basistha, B.C., Sharma, N. P., Arrawatia. M.L , and Sen, A. Ecology ofHippophae salicifolia D. Don of Temperate and Sub Alpine Forests of North Sikkim Himalayas – A case study- Paper for oral presentation accepted at 15th International Frankia and Actinorhizal Plants Meeting 2008 to be held on 19th -23rd October 2008 at Bariloche, Argentina. • Basistha , B.C., Sharma. Prakash. “Animation” its role in easy understanding of biological life process. Biogyan, volume -3, 2008.p.p. 2 (in press) • Lepcha, S.R., Chhetri, Geetamani, and Das, A. P. The Genus Juncus (Tourn). L. in East Sikkim (India) with special reference to Pangolakha Wildlife Sanctuary. Pleione 1(2), 2007. pp. 6-14. • Basistha, B,C. Sea buckthorn a wonder plant of cold desert. The Orchid December 2006. pp. 46-47.
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• Lepcha, S.R. The role of protected areas in conservation of plant –biodiversity in Sikkim Himalayas. The Orchid, December 2006. pp. 30-34. Future activities • Collaborative works in the field of Biotechnology and Bioinformatics with other BTIsnet centers, and other research institutes within and outside the state. • Preparation of database on traditional knowledge of folk/faith healers of Sikkim and database on diseases of horticultural crops. • Strengthening of Bioinformatics center with more hardware and soft wares, further up gradation of already prepared databases and creation of more databases on various bio resources of Sikkim. • Publication of reports on Biodiversity of Sikkim and news letters. Up gradation of library with more reference books, journals and e-journals on Biotechnology, Bioinformatics and Biodiversity of Sikkim,. • To conduct more number of workshops and trainings on Bioinformatics and Biotechnology. • Summer trainings and projects to the graduate and post graduate students in the field of biotechnology and bioinformatics and Biodiversity of Sikkim. • Development of the present sub center on Bioinformatics into full fledged center. Additional details
Coordinator: Sh. B.C. Basistha Sikkim Bioinformatics Centre (DISC) Sikkim State Council of Science & Technology, Sikkim Email: [email protected] ; [email protected] Website: www.bioinformaticssikkim.gov.in
128 XXth All India BTISnet Coordinators’ Meeting February 03-04, 2009 T.M. Bhagalpur University, Bhagalpur Coordinator: Dr. R. P. Upadhayay 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 incep- tion the Centre has developed good infrastructure. 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 250 users comprising of teachers, staffs and students of T.M. Bhagalpur University have availed the services of the Centre. 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.
Major research activities in Biotechnology and its related fields at your institution: A. Genomics B. Dynamics of Genomics & proteomics General protein finger printing and isozyme polymorphism Area of Specialization of the centre: Dynamics of genes and proteins Major activities of the centre during the year 2008-09 The major activities of the centre are as follows: • Regular theory and practical classes to the M.Sc. Biotechnology students on Computer Applications & Bioinformatics. • 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. Infrastructure facilities in the Bioinformatics Centre: A. Computer & Communication facility · 3 Servers (Web, Mail and Database), 12 clients workstation, One Laptop Intel P-M Processor 1.66 GHz. · One Multimedia Projector (Sony) Networking Equipments: · Modem: One External, · Internet Connection: 512 kbps BSNL Broadband Connectivity B. Scientific Software Packages · Exome, Exome Blast, Exome – ED, 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. Details about staff members working in the Centre Name Designation Area of Specialization Period of working Dr. R.P.Upadhaya Coordinator Molecular Biology since 01-11-2005 Er. Rakesh Ranjan Technical Assistant* Statistics & Comp. Appl. since 22-06-2006 Mr. Saket Vinayak Data Entry Operator* Comp. Appl. & Hardware since 28-06-2006 * The university has approached State Government for permanent absorption of manpower within the University. 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.
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• Provided practical training in Computer based applications, software analysis, computational methods etc to Doctoral and Post graduate students. Education activity with details of placement P.G. Diploma in Bioinformatics will begin from this academic session.
Collaborative works / initiatives Collaborative works are primarily in the area of Biotechnology thus a Bioinformatics club has been established where teach- ers, researchers and students extent maximum utilization of the resources available at Bioinformatics Centre.
Databases / Software 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.
Papers published or presented in the conferences with reference • Upadhyay R.P. & Singh Vandana “Bioinformatics: 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. 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. Details of Training /workshop organized and the total number of user trained Proposed National Workshop from 22nd – 24th, Jan.’ 2009 on Database, Data-Mining & Retrieval of Informations. 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. 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. • Starting P.G. Diploma course in Bioinformatics from next academic session. • 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 Coordinator: 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
130 XXth All India BTISnet Coordinators’ Meeting February 03-04, 2009 Tamil Nadu Agricultural University, Coimbatore Coordinator: Dr. P. Balasubramanian The Distributed Information Sub Centre (DISC) has been functioning at 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. • A bioinformatics lab has been established with facilities for sequence analysis, molecular modeling and database development with internet connectivity @ 512 kbps for the benefit of scientists and students • Organized 27 bioinformatics training programs since inception • Curriculum development for MSc (Bioinformatics), B. Tech (Bioinformatics) and for the Open and distance learning PG Diploma program in Bioinformatics at TNAU.
Major research activities in biotechnology The Department of Plant Molecular Biology and Biotechnology of TNAU conducts research in the following areas for the genetic enhancement of crop species. • Development of genetically modified egg plant with cry 1Ac against shoot and fruit borer • Genetic engineering of rice cv. IR64 for drought and salinity tolerance using the gene for trehalose biosynthesis • Nutritional improvement in rice: Golden rice program and Iron enrichment in rice through transgenic approach • Regeneration and genetic transformation of cotton, banana, tomato, papaya, groundnut and soybean • Genetic engineering and marker assisted selection for low phytate maize • QTL mapping and marker aided selection for drought tolerance in rice and cotton • Characterization of root proteome of rice for water stress • Cloning and characterization of abiotic stress inducible promoters from rice • Development of agriculturally important databases Major bioinformatics activities (2008-09) Three agriculturally important databases have been developed. They include: • Sprome: A database on abiotic stress inducible promoters in rice (web hosted) • T-Fabs: An abiotic stress responsive transcription factor database in rice • TNAU Rice: A germplasm database on TNAU released rice varieties Three offline tools have been developed for sequence analysis • PrebZip: Predicts bZIP transcription factors in eukaryotic sequences, developed using Java. • ExSeR: Extracts sequence from sec. structural regions given a PDB file, developed using Perl. • SeForCE: Sequence format converter and extractor, works with nucleotide and protein sequences, developed using Perl. Bioinformatics educational activities The Department of Plant Molecular Biology and Biotechnology had started MSc program in Bioinformatics in the year 2004. Students with bachelor degree in agriculture and allied sciences are eligible to join this program. From the academic year (2006-07) a four year undergraduate program B. Tech (Bioinformatics) had been started. Besides, a one year PG Diploma program in Bioinformatics had been started as distance learning course.
Proposed activities (2009-10) Development of tools to identify pathogen defense response genes in plants, and to identify microRNA’s in rice. To take up research on structure-function relationships in orthologous proteins in plants. To develop a website exclusive for bioinfor- matics centre of TNAU. To offer trainings in selected areas of bioinformatics.
Publications in bioinformatics Arul L, Benita G and Balasubramanian P. 2008. Functional insight for â-glucuronidase in Escherichia coli and Staphylococcus sp. RLH1. Bioinformation, 2 (8): 339-343 Sundheep R, Arul L, Nagarajan P and Balasubramanian P. 2008. Sprome: A database on promoters of abiotic stress 131 Sub - Distributed Information Centres
inducible genes in rice. International Journal of Integrative Biology, 2 (3): 153-156 Arul L, Benita G, Sudhakar D, Thayumanavan B, Balasubramanian P. 2008. â-glucuronidase of family-2 glycosyl hydrolase: A missing member in plants. Bioinformation, 3 (5): 194-197 Jayakanthan M, Wadhwa G, Madhan Mohan T, Arul L, Balasubramanian P and Sundar D. 2009. Docking and virtual screening studies for new leads of H-Ras P21 mutant protein. Letters in Drug Design and Discovery, 6: 14-20
Papers presented Vignesh D, Arul L and Balasubramanian P. 2008. Tfabs - Database on abiotic stress responsive transcription factors in rice. In: National Symposium on Emerging Trends in Bioinformatics (Sep 24, 2008 at Coimbatore) organized by the Dept. Bioinformatics, Bharathiar University, Coimbatore, India. (Won the best paper award) Kalpana R, Arul L, Srividhya V, Vignesh D and Balasubramanian P. 2008. Computational approach to identify zipper proteins in prokaryotes and eukaryotes. In: National Symposium on Emerging Trends in Bioinformatics(Sep 24, 2008 at Coimbatore) organized by the Dept. Bioinformatics, Bharathiar University, Coimbatore, India. Ramalingam J, Arul L, Vignesh D and Balasubramanian P. 2008. TNAU Rice: A data base for rice varieties released at Tamil Nadu Agricultural University. In: National Symposium on Emerging Trends in Bioinformatics (Sep 24, 2008 at Coimbatore) organized by the Dept. Bioinformatics, Bharathiar University, Coimbatore, India.
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], [email protected]
132 XXth All India BTISnet Coordinators’ Meeting February 03-04, 2009 Tamilnadu Veterinary and Animal Science University, Chennai Coordinator: Dr. P. Dhanpalan Summary of the progress made by the center since its inception • Information Dissemination Service (Since 1992) : Provided for 15646 research scholars from 68 universities, 195 colleges and • Education:Offering PG diploma in Bioinformatics course from 2004-2005 • M.Sc (Bioinformatics) course proposed. • Software packages developed : (i) An application tool - Information Retrieval Package (ii) Student Relational Database Management System (SRDBMS) based on VCI Syllabus. • Databases created : (i) Abstracts of Research findings on poultry by TANUVAS scientists (up to 2000) (ii) Abstracts of PG theses (1996-2003) (iii) Abstracts of completed research schemes of TANUVAS(1998-2003). • Training Programmes conducted : 27 batches on “Information Retrieval • System” and 16 batches on “Bioinformatics and Information Technology” • Studentship/Traineeship projects completed : 17 Major research activities in Biotechnology and its related fields in our institution Completed research schemes in Biotechnology -27 On going research schemes in Biotechnology- 10 Area of Specialization of the center: Veterinary and Animal Sciences including Fisheries Sciences Major activities of the center during the year 2008-2009 4.1 Education activities Offering PG Diploma in Bioinformatics and Bioinformatics papers to M.Phil and M.V.Sc scholars 4.2 Training programmes organized: 2 batches on Information Retrieval System and 2 batches on Bioinformatics and Information Technology. 4.3 Offline Information Retrieval: During 2008-2009 (up to Dec 2008), 460 research scholars and scientists have benefited (Total users: 15646) 4.4 Online Information Retrieval: During 2008-2009 (up to Dec 2008): 1546 teaching faculties and research scholars of TANUVAS have availed the online facilities. (Total users: 36807). 4.5 Establishment of Wet lab : A wet lab was established @ Rs.2.3 lakhs with 6.5 worth equipment to carryout mo- lecular biology works 4.6 512 KBPS (1:4) leased Line internet connectivity was renewed at a cost of Rs.1.20 lakhs for the year 2008-2009 4.7 No. of staff attended Training / Seminar etc., : 4 4.8 No. of staff delivered Guest lectures : 5 4.9 Awards won : 2
Infrastructure facilities in the Bioinformatics Centre A. Computer and Communication facility: IBM server, LINUX server IBM, HCL, Lenovo desktops etc.,Black and colour Printers & Scanners LCD Data Projector and OHP Projector etc. to facilitate online and offline information retrieval and training. B. Communication Facilities:512 Kbps leased line and 128 Kbps broadband internet connectivity and Seminar Hall with state of art computer aided teaching facility C. Scientific Software Packages and application tools : Exome version 1.1, Lasegene Tool, Gene tool, MS SQL server 2000 Visual studio.net. etc., D. Databases & other information resources : 1.Databases on CD ROM: VETCD BEASTCD, MEDLINE, ASFA , FSTA BIOSIS, DERWENT biotechnology abstract, current contents CDROM,NUCSSI, E. Other Information sources: Text Books : 33 Nos. Journals: Advanced Bio Tech, cheiron, Indian Journal of Biotechnology, Biospectrum, Biospectrum Asia, Genetic Engineering and Biotechnology news
133 Sub - Distributed Information Centres
F. Online Access to e-journals : http.//www.Blackwell-synergy.com http://www.doaj.org,http://www.openJ-Gate.com, www.highwirestandford.edu., http://www.bioinformatics.oupjournals.org http://nopr.niscair.res.in Details about staff members working in the center
* retired on superannuation on 30-09-2008 ** transferred to University Research Farm, Madhavaram as computer operator
Types of services provided • PG Diploma in Bioinformatics – One year duration • Training programmes • Online and offline Information Retrieval Services • Studentship/traineeship projects and Research projects by external college students • Database creation Educational activities with details of placement Courses offered for M.Phil and M.V.Sc (Animal Biotech) and PG Diploma in Bioinformatics.PGDBI Students are well placed.
Inititiative to validate the outcome of the Bioinformatics resources Bioinformatics students (M.Sc., /B.Tech/M.Tech) from different colleges in Tamilnadu undertake their dissertation with faculty at BTIS, MVC. Fairly good numbers of students/ academic staff members from Chennai and nearby institutes also regularly access the facility/ take suggestions relevant to their work from BTIS staff
Collaborative works/initiatives Experts are invited from various academic institutions for delivering lectures on various topics on bioinformatics to trainees. The Bioinformatics Centre offers consultancy in the field of Bioinformatics in choosing research project of Bioinformatics students and for setting up Bioinformatics Laboratory and development of syllabus for PG programmes for colleges and Universities.
Papers published or presented in the conferences with reference: 18 Initiation of R&D activities in Bioinformatic R& D activities of the centre is focused in the areas of Comparative and functional Genomics, Protein structure prediction, Protein interaction studies etc.,
Details of training/workshop organized and total no. of user trained • 16 training on “Bioinformatics and Information Technology” and 265 faculties and research scholars have been benefited.
134 XXth All India BTISnet Coordinators’ Meeting February 03-04, 2009
• 27 training on “Information Retrieval System” and 454 PG scholars and 189 teaching faculties of TANUVAS have been benefited • One training on “ Computer appreciation Programme” and 27 technical staff of TANUVAS benefited. Impact shown by center on the growth of biotechnology and allied areas No of papers published : 18. The primary impact of this centre is in manpower training in bioinformatics at levels at various levels includes professors, lecturers, scientists, postgraduates etc., from various institutes in different parts of India. 265 participants were trained in 16 workshops conducted since 1999. There is a growing demand from many city colleges / institutes to hold the 4 or 5 bioinformatics training in a year. All scientists and researchers of the institute working in- dif ferent areas of biological sciences used the internet facility provided by BTIS The Sub-DIC is assisting research scholars and scientists from neighbouring departments / institutes in updating their knowledge in bioinformatics through bioinformatics resources available in the centre.
Future activities i. Education: PG Diploma and M.Sc Bioinformatics ii. Conduct of training programmes iii. Studentship and Research projects to external college students iv. Literature retrieval service through offline and online v. Winter school on Bioinformatics vi. Creation and updation of database. Additional Details
Name of the Coordinator: Dr.P.Dhanapalan,Ph.D., Postal Address: Professor and Head & Project Co-odinator Bioinformatics Centre & ARIS Cell Madras Veterinary College, Vepery, Chennai-600 007. Phone Number: Direct: 044-25360106/25365418, 044 – 25381506-Ext.264 Mobile Number: 9444137465 Fax: 044-25360114 E-mail: [email protected], [email protected], [email protected], [email protected] Website: www.tanuvas.ac.in Name of the contact person: Dr. P. Dhanapalan, Ph.D
135 Sub - Distributed Information Centres Tropical Botanical Garden and Research Institute, Thiruvananthapuram Coordinator: Dr. P. N. Krishnan Summary of the progress made by the centre from its inception The Bioinformatics Centre of TBGRI was established in 1998 with focus on biodiversity informatics. In view of establishing a national nodal centre for biodiversity informatics, TBGRI has started a Bioinformatics sub-centre in a separate campus at Puthenthope, near to Techno Park, Thiruvananthapuram in 2001. Since then, the Centre has developed several bioinfor- matics tools and gathered enormous quantity of quality information and made available on the web. Recently, Kerala State Council for Science Technology and Environment (KSCSTE), Govt. of Kerala has recognized the potential of the Puthenthope Centre and granted approval to establish a state-wise biotechnology hub and a bioresource centre in this campus. As an initiative a DNA Barcoding Centre was started in July 2008.
Major research activities in Biotechnology and its related fields at your institution (1) Conservation Biotechnology, (2) Bioproduction of plant specific compounds, (3) Bioprospecting and DNA-based technolo- gies, (4) Biodiversity Informatics, (5) Plant tissue culture based commercial propagation, (6) Barcoding of life forms, and (7) Training, extension and conventional Biotechnology
Area of Specialization of the centre: Bioinformatics and Biodiversity Data Management Major activities of the centre during the year 2008 - 09 • Developed beta version of a software package for digitizing the herbarium of TBGRI. • Data collected from 45 sacred groves and made available on the URL www.tbgri.in/sacredgroveonline • Updated information on the database of TBGRI plants. • Updated information on the database Plant Info www.tbgri.in/plantinfo • Database on endemic plants of India made available on the web. www.tbgri.in/endemicplants • Reshaped and updated information on the websites www.bioinfotbgri.org and www.tbgri.in • Barcoding of Plant species is in progress. • Maintaining BTISNet publication and library resource web portal. • Provided facility and guidance to 6 M.Sc. Bioinformatics students for their dissertation works. • Reviewed the newly created web site of BTISNet. • Established WAN facility between the main campus of TBGRI, Palode and STE-TBGRI, Puthenthope • Organised one three days national workshop, one two days national seminar, provided two days training on database creation at CPCRI, Kasaragod and delivered 5 invited lectures in various seminars/workshops/training programmes. • Database development on Zingiberacae - a collaborative programme of TBGRI and the Institute of Bioresources and Sustainable Development (An Institute under DBT, Govt. of India), Imphal is in progress. Databases/ Software packages developed Plant Info version – I, Seed Pack version – I, LitFriend version – I, Fungal Database – Meliolales, Garden Info version – I, BioLit, Sacred Groves of Kerala, Wild Ornamental plants of the Western Ghats, BTISNet Publication & Library, Endemic plants of Kerala.
Papers published or presented in the conferences with reference Sreekumar S, Biju CK and Krishnan PN (2008) DNA Barcoding, Published by TBGRI, Thiruvananthapuram. (10 page booklet in Malayalam – 1000 copies). Sreekumar S, Biju CK and Krishnan PN (2008) Biodiversity Informatics: species identification and documentation. Proc. Nat. Semi. On Recent Trends in Biodiversity Conservation and Documentation, organised by M.G. Govt. Arts College, Mahe, 6 and 7 November, 2008. pp. 21-23. Sreekumar S, Biju CK and Krishnan PN (2008) DNA barcoding of life forms: An emerging tool for rapid identification and documentation of species diversity. Training programme organized by CPCRI on ‘Principles and applications of Bioinformatics’. 3-7 November, 2008. pp. 41-47. Sreedevi S, P N Krishnan and P Pushpangadan (2008) Cadmium induced oxidative damage and antioxidant responses 136 XXth All India BTISnet Coordinators’ Meeting February 03-04, 2009
in roots of Black gram [ Vigna mungo (L.) Hepper] Indian J Plant Physiology, !3(1):1-7. Sreekumar S, Biju C K and P N Krishnan (2008): Biodiversity information resources available at Tropical Botanic Garden and Reseach Institute. Biobytes Vol. 3 :21-27 Sustainable Utilisation of Bioresources through Biotechnology and Bioinformatics’ (2008) Sreekumar S, Biju CK, William Decruze and P.N. Krishnan (eds.), National Seminar Extended Abstracts, Published by TBGRI, Thiruvananthapuram. pp. 1 - 100.
Future activities • To establish a centre for barcoding of plant species and a National web enabled barcoding data repository for the identification of plant species. • To develop a National web portal for biodiversity Informatics and interlink the available information resources, thereby the users can access the biodiversity related information from a single window. Additional Details
Name of the Coordinator: Dr. P. N. Krishnan Postal Address: Head, Biotechnology and Bioinformatics Division, TBGRI, Palode, Thiruvananthapuram Phone Number:04722869622 Fax No.0472 2869646, 0471 2753050( STEC) Email: [email protected],[email protected] , [email protected] Website: www.tbgri.in , www.bioinfotbgri.org , www.tbgri.in/stec.htm
Name of Contact Person: Dr. S. Sreekumar, Scientist B & Information Officer, Saraswathi Thangavelu Extension Centre (STEC), TBGRI, Puthenthope, Thiruvananthapuram 695 586. Email: [email protected]
137 Sub - Distributed Information Centres University of Kashmir, Kashmir Coordinator: Dr. Khurshid I. Andrabi
Summary of the progress made by the center from its inception • 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 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. Area of Specialization of the Centre: Polymorphism studies in pure ethnic population [Kashmir]. Major activities of the center during the year 2007-08 • Information Officer, Bioinformatics Centre was deputed for training on CCNA. • Organizing a National level workshop on “Drug Designing” in March 2009. • The center has procured a Bio-Cluster Grid. • Procured 512 Kbps Internet lease line connectivity. Infrastructure facilities in the Bioinformatics Center A. Computer & Communication facility • SUN Bio-Cluster Grid • IBM Xeon Server Core Duo • VSAT (SCPC) with I Mbps bandwidth from Ernet. • 512 kbps Internet connectivity from Bharti Ltd. B. Databases & other information resources • The center procured Bio-Cluster Grid (Integrated Bioinformatics software & hardware solution) • CLC Combined Workbench. Details about staff members working in the center Name Designation Specialization Period of working/Absorption Prof. K.I. Andrabi Coordinator Molecular Biology 19 years Mr. Mujtaba Shafi Information Officer J2EE plat form Linux, Networking 5 + years (Yet to be absorbed) Advertised Tech.Asst Ms. Arifat Ara Data Entry Operator 8 +years.(Yet to be absorbed) Papers published or presented in the conferences with reference i. Research Papers published in peer reviewed journals by using Bioinformatics Support • Hameed, M., Ahmad, B., Khan, R.H., Andrabi, K.I., and Fazili, K.M. (2009). Tertiary butanol induced amyloidogenesis of Hen Egg White Lysozyme (HEWL) is facilitated by aggregation prone alkali induced molten globule like conformational state. Protein and peptide letters 6 ( In Press) • P Kaiser, Jan N, Hussain M, Raina C, Prashad R, Johri S, Verma V, Qazi GN, Andrabi KI (2008) Functional cloning and predictive structural modeling of two lipolytic enzymes from Bacillus strain.World J Microbiol Biotech ( Under Rivision) • Jan N, Hussain M, Andrabi KI (2008): Programmed Cell Death or Apoptosis: Do Animals And Plants share anything in common Biotechnology and Molecular Biology Reviews 3 (5), 111-126 ii. Bioinformatics Research Papers Published, in peer Reviewed journal by your centre. Masood & Mujtaba Shafi, Bioinformation 1(2): 56-57 (2005).
138 XXth All India BTISnet Coordinators’ Meeting February 03-04, 2009
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 • Drug Designing (To be organized) Future activities • The centre is in the process of initiating a process with LeadInvent, an incubation unit resident in the Technology Business Incubator in Indian Institute of Technology, Delhi for providing full-fledged training on Bioinformatics. This is with the purpose to generate the quality human resource development. • 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]
139 Bioinformatics Infrastructure Facility (BIF) for Biology Teaching Through Bioinformatics (BTBI)
Alagappa University, Karaikudi Coordinator: Dr. S. Karutha Pandian 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. This national facility is also being used by the students of the Post M.Sc., Advanced Diploma in Molecular Diagnostics sponsored by DBT, Govt. of India. Two PhDs were produced using this facility and 19 more research students are using this facility. Broadband internet connectivity of 2 MBPS 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. Thirteen Research Papers have already been published in International Journals with decent impact factors using the computational facility of the Centre. Database has been 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.
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: 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). Area of Specialization of the Centre Marine Microbial Biotechnology, Microbial Genomics and Proteomics and Environmental Biotechnology
Major activities of the Centre during the year 2008-09 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. We have proved that the quaternary ammonium compound cetyltrimethylammonium bromide (CTAB) acts as an environmentally friendly bactericidal agent against bacteria associated with stripped goat skin
138 XXth All India Coordinators’ BTISnet Meeting February 03-04, 2009 and the CTAB treated skin can be preserved in ambient temperature for more than a month. (Babu TG et al 2009; World J Microbiol Biotechnol. This has opened new avenues for replacing the age old sodium chloride based preservation of goat skin. Marine alkaline protease from Bacillus pumilus has been successfully applied for dehairing of goat skin. This has been validated at the Central Leather Research Institute. We have purified this enzyme and the purified enzyme with a molecular weight of 28kDA has also shown promising dehairing activity. 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, Post M.Sc., and PhD students in bioinformatics. A National Workshop on Genome Informatics was conducted during January 5-7, 2009 and twenty candidates have got hands on training through this Workshop.
Infrastructure facilities in the Bioinformatics Centre A. 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). B. 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. Action is being initiated for getting application software such as GCG Wisconsin Package, Biosuite (from TCS) and Sigma Plot, Discovery Studio (from Accelrys), DTMM, Reference Manager and Coral Draw C. 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, PDB, etc., The BIF has been subscribing Nature, Nature Biotechnology, Nature Reviews of Microbiology, Science and NISCAIR Jour- nals. Dr. R.A.L. Sathiyanathan RA Biochem 19.11.06-31.10.08 Ms. R. Beema Shafreen RA Bioinformatics 27.11.08- to date Mr. D. Bakkiyaraj RA Biotech 27.11.08- to date 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 55 students of M.Sc. Biotechnology, 19 students of Post M.Sc., Advanced Diploma in Molecular Diagnostics, 19 research scholars and 7 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
139 Bioinformatics Infrastructure Facility (BIF) for Biology Teaching Through Bioinformatics (BTBI)
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 passed this Programme have got placement in Research Institutes, Biotech Industries and Academic Institutions in India and abroad. 2. Post M.Sc., Advanced Diploma in Molecular Diagnostics- offered since 2008. DBT, Govt. of India has sanctioned 1.04 crores for this programme and each student is paid a stipenship of Rs. 5000 p.m. 3. Doctoral Programme in Biotechnology- offered since 2002. 4. 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. 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. 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 virus (BSNV) “ is being carried out in collaboration with the Fisheries College & Research Institute (Tamil Nadu Veterinary and Animal sciences University), Tuticorin. Databases/ Software packages developed Ribosomal database 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. The database includes the information about bacterial isolotes from stripped goat skin and the 16S rRNA sequences of Group A streptococcous. The data can be accessed from www.alagappabiotech.org/biobank.htm
Papers published or presented in the conferences with reference 1). Ganesh Babu T, Nithyanand P, Chandrababu NK and Karutha Pandian S (2009) Evaluation of Cetyltrimethylammonium Bromide as a potential short term preservative agent for stripped goat skin. World Journal of Microbiology and Biotechnology (in press) 2). N. Suganthy, P. Kesika, S. Karutha Pandian, K. Pandima Devi (2008). Mangrove Plants Extract: Radical Scavenging Activities and Its Battle against Food Borne Pathogens. Research in Complementary Medicine (in press). 3). N Suganthy, S Karutha Pandian, K Pandima Devi (2008). Cholinesterase inhibitory effects of Rhizophora lamarckii, Avicennia officinalis, Sesuvium portulacastrum and Suevada monica: Mangroves inhabiting Indian coastal area (Vellar Estuary). Journal of Enzyme Inhibition and Medicinal Chemistry. (in press). 4). N. Suganthy, S. Karutha Pandian, K. Pandima Devi (2008). Cholinesterase inhibitors from Sargassum and Gracilaria grassa: Seaweeds inhabiting South Indian coastal area (Hare Island, Gulf of Mannar). Natural Product Research. (in press). 5). K Pandima Devi, N Suganthy , P Kesika , S Karutha Pandian (2008). Bioprotective properties of seaweeds: In vitro evaluation of antioxidant activity and antimicrobial activity against food borne bacteria in relation to polyphenolic content.. BMC Complementary and Alternative Medicine, 8: 38 6). K. Pandima Devi, P.V. Kiruthiga, S. Karutha Pandian, G. Archunan and S. Arun (2008). Olive oil protects rat liver microsomes against benzo(a)pyrene induced oxidative damages- an in vitro study. Molecular Nutrition and Food Research, 52, S95-102 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.
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Details of Training/ Workshop organized and total no. of user trained Workshop Title Duration No. of Participants (i) National Workshop on Genomics, Proteomics and Bioinformatics Mar 14-16, 2007 75 (ii)National Workshop on Genome and Proteome Analysis Jan 07-09, 2008 25 (iii) National Workshop on Genome Informatics Jan 05-07 2009 20 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 76 No. of Ph.D. Scholars Passed out 02 No. of Ph.D. Scholars currently availing the facility 19 No. of Papers Published 13 Workshop Manual Released 02 No. of candidates trained through Workshops 120 Future activities Organization of four days training workshop for the teachers/research scholars from Universities/Colleges will be organized during January 2010. Undertaking research in the area of Marine Microbial Genomics for biotechnological prospects and for protecting the environment. Sustained 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: Prof. S. Karutha Pandian Email: [email protected]
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Assam Agricultural University, Guwahati Coordinator: Dr. Probodh Borah 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 five training programmes have been conducted on different aspects of bioinformatics tools and their application in biological research and a total of 93 biology teachers/researchers of various institutes within and outside state participated in these programmes. Additionally, so far 115 faculty members/subordinate staffs of the host institute have been trained in nine batches under a computer literacy programme conducted by the centre. A website (www.vetbifguwahati.ernet.in) has been developed and launched. An e-portal for the students of the college (e-Vet-Edu) has been developed, which is available in the internet through the website of the centre.
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 various animal pathogens, molecular characterization of verocytotoxigenic Escherichia coli, plasmid profiling and molecular characterization of Clostridium perfringens, production of cell culture adapted duck plague vaccine, molecular characterization of local isolates of classical swine fever virus and porcine rotavirus, development of potassium thiocyanate extract vaccine of Pasteurella, cryo-preservation of ova and application of embryo transfer technology in goat, cow and yak etc.
Area of Specialization of the centre: Animal Biotechnology Major activities of the centre during the year 2008-09 so far (i) Infrastructure of the centre has been further strengthened by procuring new hardware and software. (ii) Two short-term training programmes were conducted from September 23-26, 2008 and December 02-05, 2008, where 20 teachers/ researchers each were trained on molecular techniques and bioinformatics tools and their application in biological research. (iii)A total of 20 more faculty members of the host institute have been offered training on computer applications, increasing the total number of faculty members trained to 115. Infrastructure facilities in the Bioinformatics Centre A. Computer & Communication facility: 17 computers, 4 servers, one colour Laserjet, one Lasejet 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 (20 KV UPS). B. Scientific Software packages: Visual Studio, My SQL, CLC Combined Workbench, Geneious Pro, Exome, Bioedit, Phylip, ClustalW etc. C. Databases & other information resources: VETCD (1989-1999) D. Online subscription to www. sciencedirect.com website activated and available through the faculty LAN E. Work order for development of a lecture cum training hall has been issued. Necessary furniture, 22 new computers, one LCD projector, one electronic board and a Photostat machine have been already procured for the same. Details about staff members working in the centre
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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.
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.
Initiative to validate the outcome of bioinformatics resources Through publication of research articles in reputed journals.
Collaborative works/ initiatives Teachers/researchers of neighbouring institutions like Guwahati Medical College, Regional Dental College, Guwahati, Gauhati University, Cotton College, B. Barooah College, Institute of Advanced Studies in Science & Technology, Guwahati etc. have been trained and offered facilities for use in their research works.
Papers published or presented in the conferences with reference Barman N.N., Reema Deb, Ramamurthy T., Sharma R.K., Borah P., Wani S.A. and Kalita D. (2007). Molecular characterization of shiga like toxin-producing Escherichia coli (STEC) isolates from pigs oedema. Indian J. Med. Res. 127: 602-606. Sharma, P., Sharma, R.K., Borah, P. (2007) Immunological properties of outer membrane protein of pathogenic porcine strains of Pasteurella multocida. Indian J. Comp. Micrbiol. Infec. Dis. (Submitted). Sharma, P., Sharma, R. K., Borah, P. (2007). Protein profile and physico-chemical characterization of outer membrane protein of pathogenic porcine strains of Pasteurella multocida. Indian J. Anim. Sci. (Submitted). Sharma, R.K.; Rahman, M.S.; Borah, P.; Nath, N.C. and Rahman, H. (2007). Characterization of Clostridium perfringens isolated from captive animals and birds. Compendium of International Congress on Advances in Zoo and Wild Animal Health and Management and Symposium on Impact of Diseases on Conservation of Wild Animals. pp.88-89. Talukdar, A.; Hazarika, R.A.; Borah, P. and Barua, A.G. (2008). Survival of shigatoxin producing Escherichia coli (STEC) O157: H7 in simulating media for beef gravy. Paper presented in the 53rd Annual Technical Session, Assam Science Society held at Guwahati on March 15, 2008. Initiation of R&D activities in Bioinformatics: Work has been initiated Details of Training/ Workshop organized and total no. of users trained (i) “Bioinformatics Tools and Their Application in Teaching Biological Sciences” from March 20-22, 2007. No. of participants = 12 (ii)“Bioinformatics Tools and Their Application in Biological Research” from December 03-06, 2007. No. of participants = 20 (iii)“Molecular Techniques and Bioinformatics Tools and Their Application in Biological Research” from February 18-21, 2008. No. of participants = 21 (iv)“Bioinformatics: Current Approaches and Applications” from September 23-26, 2008. No. of participants = 20. (v) “Molecular Techniques and Bioinformatics Tools in Biological Research” from December 02-05, 2008. No. of participants = 20.
Impact shown by your centre on the growth of biotechnology and allied areas The centre is encouraging faculty members and students for using the facilities available at the centre for promoting their teaching and research activities. An e-learning module “e-Vet-Edu” has been developed which is available through the website of the centre. The Internet facility is being used extensively by the faculty members and PG students. Five papers have been published/presented in seminars with the help of the centre so far.
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Future activities The future activities envisaged include development of a database of indigenous livestock and wildlife of the north-east India, continuation of training programmes to develop human resources in bioinformatics and molecular biology, introduction of a bioinformatics course in the post-graduate programme of the university, starting of postgraduate programme in animal biotechnology, 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 Phone No.: 0361-2307329 (R), 0361-2334990, 2337700 (O), Mobile: 094351-16191 Email: [email protected] Website: www.vetbifguwahati.ernet.in
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Assam University, Silchar Coordinator: Prof. G.D.Sharma Introduction Department of Life Science, Assam University, Silchar desired to establish Bioinformatics Infrastructure Facility under financial assistance of DBT, Govt. of India with mission and vision as follows-
Our Mission 1. Strengthening Biology Teaching through Bioinformatics Tool 2. Organizing workshops on different aspects of Bioinformatics. Our Vision: Carrying out researches utilizing the Bioinformatics Infrastructure Facility. Some important dates 1. Department of Life Sciences, Assam University, Silchar applied to DBT, Govt. of India for setting up Bioinformatics Infrastructure Facility ( BIF) on 01.10.2007. 2. The proposal was approved on 14.02.2008 3. First installment of the grants amounting to Rs. 15,000,00/= was released in June 2008. 4. Official process for purchase of servers, pc etc. initiated on 16.6.08 5. Sealed tenders from different authorized dealers opened on 23.6.08 6. Technical expert’s opinion on different quotations was taken on 25.6.08 7. Technical committee meeting for finalizing the purchase order held on 1.9.08 8. Authority’s approval for purchase accorded on 22.9.08 9. Purchase order to CMS Computers, Kolkata was issued on 24.9.08 10.Bioinformatics Laboratory set up began from 27th December 2008. 11.Bioinformatics Laboratory Inaugurated by Hon’ble Vice Chancellor, Assam University, Silchar on 19th January 2009. 12.Organized two days workshop on Basic Bioinformatics on 19th and 20th January 2009. Initiatives by the centre A. As per guidelines of DBT, Govt. of India executive committee has been constituted as follows— 1. Chairman: Prof. Tapodhir Bhattacharjee, Vice Chancellor, Assam University, Silchar 2. Coordinator/Member Secy.: Prof. G.D.Sharma Pro Vice Chancellor & Dean, School of Life Sciences,Assam University, Silchar 3. Host Institute nominee/ Deputy Coordinator: Dr. M.Dutta Choudhury Reader, Department of Life Science, Assam University.
4. Nominee of BTIS, DBT: Yet to be included 5. Outside expert from nearby BTIS: Yet to be approved by DBT 6. JS Or PA DBT or their Representatives: Yet to get information from DBT B. Procurement of equipments: Order for procurement of equipments as specified by DBT in it’s sanction letter has been issued on 24.9.08 to CMS Computers, Kolkata. All equipments have been received and installed and BIF laboratory has been inaugurated by Hon’ble Vice Chancellor, Assam University on 19th January 2009. C. Attending Training Programme: 1. In order to run the centre with trained manpower two of our research scholars Viz; Pankaj Chetia M.Sc; PGDBI and Suvasish Choudhury M.Sc, M.Phil got training from NIPER, Chandigarh in Bioinformaics. 2. Dr. M.Dutta Choudhury attended workshop on Bioinformatics organized by Bioinformatics Centre, NEHU, Shillong from 25-28 March 2008.
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3. Mr. Pankaj Chetia has been sent to Pondicherry University to get training in Pharmacoinformatics held from 14-16 Oct., 2008. 4. As Deputy co-ordinator Dr. M.Dutta Choudhury attended Interactive meet of Bioinformatics centre of North East held in Gangtok from 12-13 Nov. 2008. 5. Dr. M.Dutta Choudhury visited National Centre for Pharmacoinformatics at NIPER Chandigarh from 16-20 Nov 2008 for a proposed training . *For above training funds provided by Assam University other than DBT Fund. D. Organized Workshop on Basic Bioinformatics from 19-20 January 2009 where 40 participants covering all science departments of the university participated. The Seminar was Inaugurated by Hon’be Vice Chancellor, Assam Unversity. E. Paper presented in Seminar/ Symposium 1. Mr. Shuvasish Choudhury presented oral paper entitled “Ethnobotany to Drug Discovery: An Experimental Approach” under Young Botanist Award at 31st Indian Botanical Conference at University of Alllahabad in November 17-19 2008 on behalf of Bioinformatics Centre, Assam University, Silchar. 2. Abstract entitled “Pharmacoinformatics: A promising tool for Drug Designing” published in Advanced Abstract of National Seminar on Recent Progress in Physical Sciences organized by Karimganj College under UGC and DST, GoI. F. Our Future Activies: 1. For strengthening Biology Teaching through Bioinformatics tool, the centre has proposed following training schedule ( tentative) a. Title of the training course: Bioinformatics and its Application in Drug Designing Date: 25-29 Oct. 2009 b. Title of the Training course: Bioinformatics and its application in understanding molecular evolution Date: 10-14 January 2010
Name of the Coordinator: Prof. G.D.Sharma Pro Vice Chancellor & Dean School of Life Sciences Assam University, Silchar
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Berhampur University, Berhampur Coordinator: Prof. H. N. Behera Berhampur University belongs to South Orissa, estd. In the year 1967 with different courses in science, arts and commerce. It was established keeping in the view of upliftment of the people of Southern Orissa through proper education. It has revolutionized the students of Southern Orissa by encouraging them in the field of science and research. This University has started M.Sc in Biotechnology course in the year 2005. The BIF Centre was established in the School of Life Sciences in the year 2006. The BIF Centre of our university provides learning and training in Bioinformatics to the science students of our university and affiliated colleges. The main aim of our center is to create professionals, teachers and scholars in the field of Bioinformatics. Berhampur University has received an initial grant of Rs. 20,000,00/- (Rupees Twenty Lakhs) towards the establishment of BIF Centre for Promotion of BTBI (Biology Teaching through Bioinformatics) under BTISnet programme of DBT, New Delhi during the financial year 2006-07 in two instalments(1st and 2nd ). With this sanctioned amount we have purchased non-recurring equipments like Servers (2 Pieces), Desktops along with licensed operating systems (10 pieces), printers (2 pieces), Photocopier, a scanner and contingency that were as per the specifications mentioned by DBT. The Centre is operated in a well-furnished room. The total cost towards the above said equipments with maintenance of the room was 14.5 lakhs. The remaining 5.5 lakhs is available with the University finance section towards the travel grant, Bioinformatics Workshop, seminars that is going to be conducted shortly. The first UC & SE for the above said expenditure amount has been sent to The Director, DBT, New Delhi, Govt. of India by the Registrar, Berhampur University. As per the requirement and for the smooth functioning of the BIF Centre, DBT has sanctioned an amount of Rs. 3.01 lakhs on 1st November 2007out of which Rs 1.51 lakhs was towards the salary of a man power designated as Research associate and Rs 1.50 was towards the purchase of equipments and softwares. As per the norms, a research personnel namely Mr. Santosh Kumar Behera designated as Research Associate has been appointed on 4th January 2008 after a successful conduct of Walk-in-interview on 26th December 2007. A copy of his appointment letter and joining report has been sent to The Director, DBT, New Delhi, Govt. of India. The grand total sanctioned amount received by our BIF Centre is 23.01 lakhs out of which Rs 14.5 lakhs was already spent towards the non-recurring equipments and Rs 1.51 was been spent towards the salary head of Research Associate. The second UC & SE for the said expenditure amount has already been sent to The Director, DBT, New Delhi, Govt. of India by the Registrar, Berhampur University. As it is the only Centre in our area we provide training in implementation of Bioinformatics in basic biological sciences to the science students with different faculties of our University and different colleges running U.G and P.G courses. We also provide guidance to the M.Phil and Ph.D scholars in their research work. The Biotech students and faculty members of our University and affiliated colleges were trained in Bioinformatics in our Centre. As there is a huge rush in our Centre, due to lack of space we are now planning to shift to a new room, which is located in the upstairs of our present room for providing adequate space to our Centre. The plan to shift to the new room has already been informed to The Director, DBT, New Delhi, Govt. of India. During this period we have paid the total amount to the Research Associate that was sanctioned for his salary. At present we haven’t received any sanctioned amount for this session towards his salary. Therefore another sanction is required for the smooth functioning of the center.
Proposed activities of the centre during the year 2009-2010 • Conducting of workshops and seminars on Bioinformatics. • Provide hands on training programme in Bioinformatics to the science students and scholars. • Proposal to have a web site for our BIF Centre. • Research publications from our center.
Prof. H.N.Behera Coordinator, BIF Centre, Berhampur University, Bhanja Bihar, Orissa
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Bharathiar University, Coimbatore Coordinator: Dr. P. Shanmughavel 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. The department is engaged in various innovative projects in various disciplines supported by National and International agencies like DBT, UGC & ITTO, Japan. The department also conducts M.Phil and Ph.D courses. The Postgraduate students passed out from the department were easily absorbed in various research Institutions not only in India but also in Foreign Countries. Many of our students are pursuing their Doctoral programs in countries like France, UK, Germany and Singapore. The Department of Biotechnology (DBT), India has approved a Center For Bioinformatics for the establishment of Bioinformatics Infrastructure Facility (BIF) for the promotion of Biology Teaching through Bio-Informatics (BTBI) at our Department under the Biotechnology Information System Network (BTISnet). To its credit the Department also has collaboration with the Global Forest Information Service (GFIS), Vienna, Austria to exchange research information’s.
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. Major activities of the centre during the year 2008-09 Research Schemes Awarded
* Infrastructure facilities in the Bioinformatics Centre A. Computer & Communication facility 5KVA online UPS with 10 Nos of batteries A – One University Fund 2001 ISDN Router CISCO University Fund 2001 ISDN Connectivity VSNL University Fund ——— Sun Netraj Server Sun Solaris University Fund 2001 Unix based student workstation Sun Solaris University Fund 2001 Unix based sun enterprise server Sun Solaris University Fund 2001 Sun Network Appliances Sun Solaris University Fund 2001 LCD Projector Panasonic University Fund 2001 HP model DX 2180 Intel Pentium (22 nos) HP University Fund 2006 HP model DX 2180
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Intel Pentium (11 nos) HP DBT Fund 2007 B. Scientific Software packages -Important computational biology softwares. C. Databases & other information resources “A Digitized Inventory of Tropical Timber Resources of India” Details about staff members working in the centre Name Designation Specialization Period of working N. Jayakumar Reader Data Mining 2008 onwords P.T.V.Lakshmi Lecturer Phytomatics 2005 onwards Sundra Balaji Lecturer Structural Biology 2008 onwords Jayam Lecturer Biochematics 2008 onwords Types of services provided Teaching and Research Development of Database and Software Educational activities with details of placement Students have participated in various seminars, conferences and academic competitions in the emerging fields of Bioinformatics conducted at National and International institutes and won prizes and added laurels to the department. All the post graduate and diploma students were easily absorbed by the Bioinformatics company and research institutions.
Initiative to validate the outcome of bioinformatics resources Awarded three M.Phils in the field of Bioinformatics. Collaborative works/ initiatives.
Databases/ Software packages developed 1. Database Model for Industrial Plantations. 2. Digitization and Automation of Tropical Forest Biomass 3. Nucleotide and Protein Manipulation tool Papers published or presented in the conferences with reference Papers Published in Bioinformatics: 2009 • Marimuthu Parthiban, Mohan Babu Rajasekaran, Suryanarayanarao Ramakumar, Piramanayagam Shanmughavel (2009) Molecular Modeling of Human Pentameric ±7 Neuronal Nicotinic Acetylcholine Receptor and Its Interaction with its Agonist and Competitive Antagonist. Journal of Biomolecular Structure & Dynamics, 26, 0739-1102 • Radhika Ramachandran and Primanayagam Shanmughavel (2009) Role of Microbicides in the Prevention of HIV and Sexually Transmitted Diseases – A Review. Bioinformation (In press) • P.Lakshmi priya and P.Shanmughavel (2009) Docking Studies on Flavin and Phenosafranine to Inhibit the Human Ribonucleotide Reductase. Bioinformation (In press) • Indumathi, P.Shanmughavel (2009) MolBuild - Tool for protein and nucleotide structure visualization. Bioinformation (In press) 2008 • Gayathri Devi Chandramoorthi, Shanmughavel Piramanayagam , Parthiban Marimuthu (2008) An Insilico approach to High Altitude Pulmonary Edema - Molecular modeling of human ²2 adrenergic receptor and its interaction with Salmeterol Nifedipine.J.Mol.Modelling 14, 849-856 • Seenivasagan Renganathan, Kasimani Renganathan, Marimuthu Parthiban, Kalidoss Ramamoorthy, Shanmughavel Piramanayagam (2008) Comparative Modeling of Viral Protein R from Human Immunodeficiency Virus 1 (HIV 1) J. Proteomics and Bioinformatics. 1, 073-076 • Vijayakumar Saravanan and Piramanaygam Shanmughavel (2008) SiRNA Scanner — a Fuzzy Logic based tool for small interference RNA design, J.Proteomics and Bioinformatics. 1, 154-160 • S.Anandakumar, Saravanan and Piramanaygam Shanmughavel (2008), Indian Medicinal Plants Protein Dataset, J.Proteomics and Bioinformatics. 1, 230-232
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• Radhika Ramachandran and Piramanayagam Shanmughavel (2008), Preparation and Characterization of Biopolymeric Nanoparticles Used In Drug Delivery, Journal of Bioequivalence & Bioavailability, accepted • S.Anandakumar, Saravanan and Piramanaygam Shanmughavel (2008), Computational Annotation for Hypothetical Proteins of Mycobacterium Tuberculosis, Journal of Computer Science & Systems Biology. 1: 050-062 International Conference in Bioinformatics 1. P.Shanmughavel, Gayathri Devi ,Chandramoorthi and R. Vijayan (2008). An In silico approach to High Altitude Pulmonary Edema : Molecular modeling of ²2 adrenergic receptor and its interaction with Salmeterol & Nifedipine. 1st international conference on drug design and discovery - 3rd - 6th February, 2008. Dubai, UAE.
Books Published 1.Practicals in Bioinformatics Dr.Shanmughavel .P and Dr.Gulshan wadhwa (2008). Initiation of R&D activities in Bioinformatics Nanotechnology and Drug Delivery Site-specific drug delivery systems using biopolymeric nano particles. Molecular Modeling and Drug Design Model the structure of human ²2 adrenergic receptor which will be useful in the treatment HAPE. Phylogenetic Analysis Construction of phylogenetic tree to study evolutionary relationships. Comparative Genome Analysis Comparison of complete genomes to study the hidden information in the genome design, function and evolution. Functional Annotation of Hypothetical To develop new tools to predict function of hypothetical proteins. proteins Integrated Bioinformatics System To develop integrative analysis methods for biological data Details of Training/ Workshop organized and total no. of user trained • Inauguration of DBT Bioinformatics Centre and one day National seminar on Industrial Bioinformatics, 25th Feb.2008. • One day National Seminar on Bioinformatics. “ MOTIF 2008” -September 25th 2008 Future activities • A Database on Pulping and Paper Making Properties of Fast Growing Plantation Wood Species. • Development of Teaching & e-learning modules in Bioinformatics. • Electronic Catalogue of Endangered and Endemic Flora of Tamil Nadu. • Tamil Nadu Medicinal Flora Information System. • Digitization of biodiversity information. • Biodiversity mapping project. • Identification of high priority databases and software’s that need to be developed. • Development of web directory. • Establish linkages with International resources in biodiversity and forest informatics. • To establish a state of art ‘Digital Library’ in the areas of Environmental studies, fully searchable by fieldcodes such as the compound, structure, toxicity, pathology, gene, gene group, SNP metabolic pathway and network. Postal Address
Dr. P. Shanmughavel, PhD, D.Sc. 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, Ph.D, D.Sc. Email: [email protected]
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CCS Haryana Agricultural University, Hisar Coordinator: Dr. Sudhir Kumar Summary of the progress made by the centre The Bioinformatics Section, CCS Haryana Agricultural University, Hisar became operational in May, 2007 in a newly renovated wing of College of Basic Sciences & Humanities. The Section has latest hardware, commercial as well as GPL software and an internet leased line (2 MBPS) connectivity. A M. Sc. Programme in Bioinformatics in running successfully since 2004.
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 Area of Specialization of the centre Teaching Bioinformatics Bioinformatics in Agricultural Sciences (rice crop of interest) Sequence analysis Multimedia Databases Virtual Screening Major activities of the centre during the year 2007-08 Teaching Consultancy to researchers Infrastructure facilities in the Bioinformatics Centre ` Computer & Communication facility ` PCs – 50 ;Servers – 2 ; 8-Node Linux Cluster – 1 ` Internet connectivity – 2 MBPS ` Telephone and Fax – 01662-289114, 234003; 284310 (Fax) Scientific Software packages - GPL software, MOE, ChemOffice, PAUP Databases & other information resources ` PDB (local mirror) Details about staff members working in the centre Name: Ms. Vasu Arora, RA Specialization: Bioinformatics – Programming languages, sequence analysis Period of Working: May, 2008 to date Types of services provided: Teaching, Internet access, bioinformatics consultancy Educational activities with details of placement M.Sc. Bioinformatics – started in 2004 Placement – 2004-06 batch - 16/17 2005-07 batch - 9/13 2006-08 batch - 9/15 Initiative to validate the outcome of bioinformatics resources NONE as the BIF is two year old only
Collaborative works/ initiatives Creation of Multimedia database of crop plant diseases (with the Department of Plant Pathology, CCS HAU, Hisar) Departmetn of Maths & Statistics, Biotechnology & Molecular Biology, Animal Biotechnology, Genetics, Zoology & Aquaculture and Botany & Plant Physiology – for teaching and research
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Databases/ Software packages developed Database –one underway Software – One (Statistical analysis for agricultural Scientists) Papers published or presented in the conferences with reference B. Yadav, P. Kharab and Sudhir Kumar (2008). Three dimensional structure prediction of Tannase. EMBO World Lecture Course on Recent Developments in Macromolecular Crystallography at NCL, Pune. November 9-14, 2008. Initiation of R&D activities in Bioinformatics · Parallelization of bioinformatics algorithms · Tools for sequence analysis and gene finding · Virtual screening for HIV-1 RT and Tuberculosis inhibitors Details of Training/ Workshop organized and total no. of user trained · A ten days’ workshop Biological Databases, Sequence and Phylogenetic Analysis in Plant Sciences during March 3rd - 12th, 2008. 30 participants · ICAR sponsored Winter School Bioinformatics for Agricultural Sciences February 19 – March 11, 2009. Proposed Activities (2009-10) · To revise the course curriculum and implement the same in 2009-10 session · To hold a Summer School (30days) for PG students · To start Ph.D. in Bioinformatics · 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: 9466242051; Email: [email protected]; [email protected] Website: http://hau.ernet.in/bioinfo
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Cotton College, Guwahati Coordinator: Dr. Rita Mahanta The Center The Bioinformatics Infrastructure Facility(BIF) in Cotton College is established with release of the first installment of Rs. 15.00 lakhs out of the total grant of Rs. 20.00 lakhs sanctioned by the Department of Biotechnology, New Delhi towards the promotion of Biology Teaching Through Bioinformatics (BTBI) in Cotton College, Guwahati. The Center (BIFCCG) is headed by Dr. Indra Kumar Bhattacharyya, Principal, Cotton College, Guwahati, as the Chairman and Dr. Rita Mahanta, Department of Zoology Cotton College, Guwahati as the Coordinator.
Present Status and Progress so far The infrastructural space is fully organized as a separate unit in the institute complex and the Executive Committee is formed as per the Guideline. The suggested hardware is procured and installed in the centre and is brought to the functional state. At present the facilities in the centre is being fully utilized by the faculty and students of the institute involved with the already existing Certificate and Diploma Courses run by the institute in addition to the existing facilities before establishing the present centre. Already three short term training programme on Application of Bioinformatics tools is arranged for the in-house students and the neighboring colleges during December 2008 and January 2009. Undergraduate and post-graduate students and research scholars of the parent institute are regularly utilizing the internet browsing and download facility from the centre.
Future Activities • The Centre plans to hold and organize periodic short term sensitization and orientation programmes targeted for faculty members, in house students, neighboring students and interested persons in the allied field in separate batches matching with their line of interest and prospects of utilization of the available Bioinformatics sites and tools. • A short term training course for Research Scholars and Teachers involved in undergraduate teaching in life science and Biology is organized on 11th and 12th February, 2009. • The centre is planning to introduce and organize few programmes of 7 to 14 days duration in the form of target oriented workshops for generating some in-house database or solving some specific bioinformatics problems as a team work. • It is planed to organize an in-house response cell in the center for interactive problem solving sessions with the interested students of the institute. • It is proposed to introduce a Diploma Course in Bioinformatics under the facilities of the Centre and in collaboration with other BIF centers associated with the DST for generating a steady pool of Bioinformatics personnel in the locality. • To generate a website for the BIFCCG.
Coordinator: Dr. Rita Mahanta E-mail: [email protected] [email protected] Phone No.: 03612131697 Mobile No.: 09864274691
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College of Veterinary Sciences & Animal Huabandry, CAU, Aizawl Coordinator: Dr. Santanu Banik A Brief Profile The Central Agricultural University was established on 26th January 1993 with its headquarters at Imphal, the capital city of Manipur under the Central Agricultural University Act 1992 of the Parliament (Act No. 40 of 1992). The University has its jurisdiction over the states of Arunachal Pradesh, Manipur, Meghalaya, Mizoram, Sikkim and Tripura.
The objects and mandates of the University as stipulated in the Act are: • to impart education in different branches of agricultural and allied sciences as it may deem fit; • to further the advancement of learning and prosecution of research in agriculture and allied sciences; • to undertake programmes of extension services in the states under the jurisdiction; • and to undertake such other activities as it may determine, from time to time. To meet its mandates, the University has established 7 (seven) constituent Colleges in different states of the North Eastern Hill region. 1. College of Agriculture, Imphal, Manipur 2. College of Veterinary Sciences & Animal Husbandry, Aizawl, Mizoram 3. College of Fisheries, Agartala, Tripura 4. College of Horticulture & Forestry, Pasighat, Arunachal Pradesh 5. College of Home Science, Tura, Meghalaya 6. College of Agricultural Engineering Post-harvest Technology, Gangtok, Sikkim 7. College of Postgraduate Studies, Umiam (Barapani), Meghalaya Education Degree Programmes The Central Agricultural University has undergraduate and postgraduate programmes in agriculture and allied sciences. Different Colleges of the University are offering Bachelor degrees in Agriculture, Veterinary Science & Animal Husbandry, Fisheries, Horticulture, Forestry, Home Science and Agricultural Engineering & Post-harvest Technology and M.Sc., M.V.Sc. and M.F.Sc. degrees in most of the disciplines of Agriculture, Veterinary & Animal Husbandry and Fisheries, respectively. System of Education The University is following semester system of education with 10-point scale of grading. The University has adopted model academic regulations and syllabi as proposed by the ICAR/VCI, with some minor changes to suit the regional needs.
Infrastructure and facilities All the constituent colleges of the University are equipped with state-of-the-art instruments/facilities to meet teaching and research requirements. All the laboratories have internet connectivity. The information is disseminated by strong video conferencing among the colleges. Research: The university is engaged with molecular characterization, genetic and sequence analysis of different plant, animal and fish species of domestic, wild and aquatic origins relevant to the north-eastern states. Further, the university is conducting quality research in different aspects of agriculture, veterinary, fishery and allied sciences. The College of Agriculture is dedicated to conduct research to give priority to farmers’ production constraints, participative approach and applied research that offer practical solutions in food grain production in north eastern hilly states. The mandate of the College of Fishery is to conduct research to meet the needs of the fisheries sector in the north- eastern states. The College of Veterinary Sciences and Animal Husbandry has the mandate to carry out research programme on different aspects of qualitative and quantitative production of animal and animal products, disease diagnosis, surveil- lance and monitoring in the north-eastern states.
Establishment of Bio-informatics Laboratory The Department of Biotechnology, Ministry of Science & Technology, Government of India, New Delhi has sanctioned a
154 XXth All India Coordinators’ BTISnet Meeting February 03-04, 2009 project to the College of Veterinary Sciences & Animal Husbandry, Central Agricultural University, Selesih, Aizawl (Mizoram) for the establishment of a Bioinformatics Infrastructural Facility (BIF) towards the promotion of biology teaching through bioinformatics (BTBI) vide letter No. BT/BI/04/055/2001; dated 14th February, 2008. For the establishment of the BIF at CAU, Aizawl (Mizoram), the Department of Biotechnology has released an amount of Rs. 15.00 Lakh (Rupees Fifteen Lakh) only vide DD No. 548604; dated 03.04.2008 issued in favour of Regional Central Agricul- tural University, Aizawl instead of the Registrar, Central Agricultural University, Imphal. This was immediately pointed out to the concerned authority for necessary correction and the DD was returned to the Department of Biotechnology in original. In response, the Department of Biotechnology has issued a “corrigendum” dated 8th September, 2008 and released a new DD for the said amount issued in favour of the Deputy Comptroller, Central Agricultural University, Imphal (Manipur). This has delayed the operationalization of the Centre.
Progress in Bioinformatics Infrastructural Facility (BIF), CAU, Aizawl The College took keen interest for establishment of Bioinformatics Infrastructural Facility (BIF) at the earliest and has taken the following actions according to the requirements of the project: a) An executive committee consisting of six members including one outside expert from nearby BITS center has been established. b) The Centre had created the uniform e-mail id to communicate with other Bioinformatics centre under the programme. c) An independent space, which will house the Bioinformatics Laboratory, has been furnished with all the required facilities. d) Orders have been placed for purchase of specified hardwares and softwares. e) Employed a Computer Technician to look after the networking and other computer related problems. Future activities to be carried out a) To fully operationalize the Bioinformatics Laboratory. b) Organize training programme in the field of bioinformatics.
Contact details
Dr. Santanu Banik, Coordinators, BIF College of Veterinary Sciences & AH, CAU Selesih, Aizawl-796014 (Mizoram) e-mail: [email protected]/[email protected]
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Dhanamanjari College of Science, Imphal Coordinator: Dr. Oinam Shashikumar Singh Dhanamanjari College (D. M. College), Imphal, Manipur, was established on Tuesday, the 6th August 1946. It is one of the oldest institutes of higher studies in the entire northeastern region. D.M. College was established at the behest of Maharani Dhanamanjari Devi, who generously donated a substantial amount of Rupees ten thousand for establishment of the College. Her Majesty also persuaded Maharaja Churachand Singh, KCSI, CBE, to patronize the establishment of such an institution, the first of its kinds in the state. The newly established college was named as Dhanamanjari College in recognition of the valuable service rendered by Her Majesty, the Maharani Dhanamanjari Devi. In 1948 the college came under the management of the state. D. M. College of Science, Imphal came into being in the year 1975 with the bifurcation of the parent Dhanamanjari College (estd.1946) into two daughter colleges – one an Arts college and another in a Science college. The D.M. College was earlier affiliated to the Calcutta University in 1946. In August 1949, the College became affiliated to Guwahati University. During the period between 1949 and 1981, the College emerged as one of the most popular Colleges of the North East India by way of capturing top positions by the students of this college in most of the disciplines, in addition to their superb performances in sports and other co-curricular activities. In 1972 the then post -graduate classes at the college got merged with the Jawaharlal Nehru University Centre, Imphal, which was later on shifted to Canchipur, the present site of the Manipur University. In 1981, Manipur University was established and all the colleges in Manipur became affiliated to it.
D. M. College of Science D. M. CollegeT have 14 departments, namely, Anthropology, Botany, Chemistry, Computer Science, Defense Studies, Electronics, English, Environmental Science, Geology, Mathematics, Physical Education, Physics, Statistics, and Zoology. The Bioinformatics Infrastructure Facility Centre is located at Room no. 14 of Zoology Department of the the DM College of science. The DBT sponsored Centre was established with an initial fund of Rs. 15,00,000/- (Rupees fifteen lakhs) sanctioned by the Department of Biotechnology, Ministry of Science & Technology, Government of India vide their letter No. No. BT/BI/12/042/2007 dated 26th March, 2008.
The Executive Committee of the Centre has the following members:
The Centre also has a Purchase Sub-Committee having 4 (four) members. The Coordinator, as per relevant resolutions of the EC and PC, takes up the necessary actions regarding the establishment of the centre, including procurement of computer equipments, etc. Major computer equipments of the facility are now installed and operational. These include 2 (two) IBM servers, 10 IBM Desktop computers, one 6 KVA Emerson UPS, one Color Laser Printer and one HP all in one Printer. The Centre now has a BSNL Broadband internet connection with unlimited download volume. Subscription to six volumes of McGraw-Hill Con- cise Encyclopedia Collection online is presently operational for 2008-2009 (Informatics India Ltd. Bangalore). Works are going on regarding construction of a website for the centre and necessary arrangements have already been made with Vediksoft Solutions, Hyderabad. Process for subscription to Geneious Pro 4.0.2 from Bioware Division ORSBY Engineering LTD. Bangalore is under consideration. The Centre is considering organization of a short-term training programme on Basics of Bioinformatics for Biology students, Research scholars and teachers with a view to bring an awareness regarding the subject.
Dr. Oinam Shashikumar Singh Coordinator, BIF Room No. 14, Dept. of Zoology, D. M. College of Science, Imphal -795001 Manipur, INDIA. Phone: 0385 2440616; 9436020795; e-mail: [email protected]/[email protected]
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Dibrugarh University, Dibrugarh Coordinator: Prof. R.N.S. Yadav About the Centre The Dibrugarh University Bioinformatics Infrastructure Facility (BIF) was established in June 2008 with the help of the grant received from the Department of Biotechnology, Ministry of Science & Technology, Government of India. The First installment of the sanctioned grant (Rs. 15/- lakh) has been received vide the letter No. Grant/DBT/GIA/2917/2007- 08 cash dated 25.04.08 from DBT, New Delhi and the following action has already been taken towards the establishment of Bioinformatics
Infrastructure Facilities • An independent room (22’ x 22’) has been provided by the University in the Department of Life Sciences building for setting up of BIF. • The work of required electrification, Air conditioning, furniture and fixtures and networking of the BIF room has already been completed. • Purchase orders for the supply of equipments like Server (High and Medium end) Desktops, Photocopier, scanners and printers etc. have already been made to the respective firms following the rules and regulations of the University for Purchase. These equipments have been received and installed. • Software’s like Window Svr. Std. 2008 with media, Visual studio pro 2008, SQL Svr Std. 2005 office 2007 Norton Antivirus2007 Red Hat Linux vs • 4.5ES 86 and EM 64 T and ISA sever std 2006 with media has been purchased and installed • At present the Centre is provided internet connectivity from the University VSAT having 2 Mbps and leased line (10 mbps) internet connectivity • An Executive committee has also been constituted the meeting of which is scheduled on 7th January 2009. • The Coordinator participated in the two – day interactive meeting of North East State’s Bioinformatics Centre Coordinators held on 12th -13th November at DISC, Sikkim State Council of Science & Technology, Department of Science & Technology, Gangtok - 737101 (Sikkim). • An Executive committee has also been constituted and the first meeting of the committee meeting was held on 7th January 2009. Summary of the Progress made so far Since its inception in June 2008, we have marched forward steadily. The Centre has got adequate facility of information and communication including necessary hard ware and software.
Present Use of the Facility Currently the facility is extensively used by the Teachers, Research scholars and students of Department of Life Sciences, Centre for studies in Biotechnology and Bioinformatics and the Departments of Statistics and Computer Science of the University.
Future activities Planned • A short term hand on training course for scientists/teachers/ Research scholars has been proposed from 5th to 7th March 2009 with an objective to create awareness among participants for the use of Bioinformatics tools such as Biological Databases, Sequences and Search tools, Phylogenetic Analysis Comparative Genomics etc.by the way of lectures, demonstrations and hand on session. • In house awareness program for college students of colleges under Dibrugarh University. • The Centre is preparing itself for running a Certificate course in Bioinformatics (3 months) for the Post graduate students to train them for the use of Bioinformatics in the field of Life Sciences/ Biotechnology research
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Dr. B. R. Ambedkar Center for Biomedical Research, Delhi Coordinator: Dr. Madhu Chopra 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 2007-08 has been provided to show scientific progress during this period.
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
Area of Specialization of the centre • Medicinal Chemistry and Natural Products • Molecular Genetics and Medical Biotechnology • Clinical Biochemistry and Immunology • New drug discovery and commercialization Major activities of the centre during the year 2006-07 1. 6th Annual Symposium on Frontiers in Biomedical Research November 30-December 2 2006 2. Summer undergraduate Research Training Programme (Annual) Infrastructure facilities in the Bioinformatics Centre A. Computer & Communication facility Computer Labs with A Cs 2 Capacity of Computer Labs 12 X 2= 24 Lease Line connection provided by the University.
B. Scientific Software packages
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Details about staff members working in the centre Professor= 3; Reader= 1; Lecturer = 5 Types of services provided: Teaching and Research Educational activities with details of placement Ph.D. Students: Completed : 65, Ongoing : 60 Students Qualified CSIR-UGC-NET Examination (1999-2008): 140 Career options by students: Research 97 % ; Other Jobs 3 % 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
Papers published or presented in the conferences with reference Papers: • Autoacetylation of Purified Calreticulin Transacetylase Utilizing Acetoxycoumarin as the Acetyl Group Donor Seema Bansal , Prija Ponnan , Hanumantharao G. Raj ,Susan T. Weintraub, Madhu Chopra, Ranju Kumari, Daman Saluja et. al. Applied Biochemistry and Biotechnology, DOI 10.1007/s 12010-008-8357-2, Published Online [Springer] • Molecular Modeling Study on Chemically Diverse Series of Cycloogenase-2 Selective Inhibitors: Generation of Predictive Pharmacophore Model using Catalyst, Madhu Chopra*, Ruby Gupta, Swati Gupta and Daman Saluja Journal of Molecular Modeling (2008) 14:1087–1099 [Springer] • Loss of kinase activity in Mycobacterium tuberculosis multidomain protein Rv1364c, Preeti Sachdeva, Azeet Narayan, Richa Misra, Vani Brahmachari and Yogendra Singh, FEBS Journal (2008), doi:10.1111/j.1742- 4658.2008.06753.x Invited Lectures • Invited Talk, Madhu Chopra, Pharmacophore modeling and virtual screening in drug design, 2nd National Conference on Mathematical Techniques: Emerging Paradigms for Electronics and IT Industries (MATEIT-2008) , 26-28 September 2008, Deen Dayal Upadhayay College, University of Delhi • Invited Presentation, Madhu Chopra, “Molecular Modeling Study on Chemically Diverse Series of Cyclooxygenase-2 Selective Inhibitors: Generation of Predictive Pharmacophore Model using Catalyst” at 91st Canadian Chemistry Conference and Exhibition, Edmonton, Canada, May 24-28, 2008. • Oral Presentation, Madhu Chopra at 12th ISCB Conference (ISCBC-2008) International Conference on the Interface of Chemistry-Biology in Biomedical Research, Feb 22-24, 2008, BITS Pilani. • Invited Lecture, Madhu Chopra at 7th Annual Symposium (FBR 2008), Workshop on Bioinformatics and Molecular Modeling in Drug Design, ACBR, January 28-30, 2008. M.Sc. Projects • An Analysis Of Host Molecular Mimicry And The Effect Of Insertion Sequence Elements On The Mycobacterium tuberculosis H37Rv GENOME, Latika Bhonsle, under supervision of Prof. Vani Brahmachari. • Phase II Data Analysis of IGVdb Consortium focussed on Chromatin Remodelling Proteins” Kushal Kr. Banerjee, under supervision of prof. Vani Brahmachari • In silico docking of aryl hydroxamic acid derivative into HDAC8 binding site, Ashta Gupta, Under supervision of Dr. Madhu Chopra. R &D activities in Bioinformatics • Design, Synthesis and Evaluation of Non Peptidic CCK-B/Gastrin Receptor Specific Antagonists for Targeting CCK-B receptor Expressing Tumors. • Computer-Aided Design of Novel NSAIDs as Selective Cyclooxygenase-2 (COX-2) inhibitors to target tumors: Mechanistic study of anticarcinogenic role of NSAIDs • In Silico Prediction : mechanism of transacetylation activity of Calreticulin. • Mining the Human Genome for Global regulatory Genes: Characterization and Functional analysis
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• Role of Epigenetics in Genome Function and Transactions. • Cloning and functional characterisation of ETO-binding protein in normal and acute myeloid Leukemia. Details of Training/ Workshop organized and total no. of user trained • 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 Participants 15 • One day workshop for undergraduate students: “Computer Aided Drug Design” 20th December, 2008 (12 participants) Impact shown by your centre on the growth of biotechnology and allied areas • Year of Course Commencement : 1998 (M.Sc.-Ph.D. Combined Programme in Biomedical Sciences) • Visiting/Guest Faculty: 20 • Research Publications (Last 7 years) : 85 • Patents & Technologies Transferred : 5 • Number of Projects: (i) Industrial : 3 (ii) Government Agencies : 52 Additional Details
Name of the Coordinator: Dr. Madhu Chopra Postal Address: Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi 110007 Phone Number: 011-27666272 Mobile: 09810488199 Website: www.acbrdu.edu Name of Contact Person(s): Dr. Madhu Chopra Email: [email protected], [email protected], [email protected]
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Fakir Mohan University, Balasore Coordinator: Dr. Amarendra Narayan Summary of the progress made by the centre from its inception The necessary infrastructure could be procured by Sept 2008. The BIF facility is awaiting shifting to a new campus where the Biotechnology building is built. It is going to be effective from 2009 with the proposed M. Sc. program in Bioinformatics and other teaching programs in Life Sciences.
Major research activities in Biotechnology and its related fields at your Institution: Stress signaling and adaptive strategies of living systems, Marine Biotechnology, Biosensors, Nano-biology, Blood related problems.
Area of specialization of the centre: Teaching in Biotechnology and Biosciences. Major activities of the centre during the year 2008-09 Consolidating the School of Biotechnology and the BIF centre
Infrastructure facilities in the Bioinformatics Centre Hardwares and softwares for the BIF centre was procured as per DBT specifications.
Details of the staff members working in the centre One - Data entry operator a.ssisting in the BIF activities
Types of services provided: Internet access to open access science journal and database sites.
Educational activities with details of placement M.Sc. Biotechnology P.G. Programs in other fields of Biology including M.Phil. and Ph.D.
Initiative to validate the outcome of Bioinformatics resources Bioinformatics is taught as a compulsory credit course in M.Sc. Biotechnology as well in other Post-Graduate courses including M.Phil. courses, and Ph.D. students are individually trained about the practical aspects through their supervisors in the BIF centre.
Collaborative works/initiatives Besides initiative in the domestic academic and research sectors, collaborative research initiatives were established through (i) DBT-Overseas Associateship (Two), (ii) DST-BOYSCAST (One) Fellowship program, (iii) DST-BAS Indo-Bulgarian Collaborative Research Program (One) and (iv) other collaborations with groups in USA, Japan and Europe, to work on topics of genomics and proteomics which extensively uses Bioinformatics tools. Papers are under preparation and will be published in due course. Papers published or presented in the conferences with references a. A.N. Misra (2008) An introduction to Phenomics. – Training cum Workshop on “Phenomics and Systems Biology”, 5-6 Dec 2008. b. A.N. Misra (2008) Systems Biology: past, present and future. – Training cum Workshop on “Phenomics and Systems Biology”, 5-6 Dec 2008. c. A.N. Misra (2008) Concepts in the development of Bioinformatics towards Systems Biology. - Training cum Workshop on Bioinformatics. Assam Agric Univ., Guwahati 2-4 Dec 2008. d. A.N. Misra (2008) Bioinformatics in the era of Systems Biology. - National workshop on Bioinformatics. LNM Mithila University, Darbhanga 16-17 Nov. 2008. e. A.N. Misra (2008) Fluxomics - National workshop on Bioinformatics. LNM Mithila University, Darbhanga 16-17 Nov. 2008.
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Initiation of R&D activities in Bioinformatics Students are enrolled in Ph.D. program related to Bioinformatics and few more are waiting for registration to Ph.D. program in 2009.
Details of Training/ Workshop organized and total no. of user trained (i) 25-26 March 2008 Workshop Training Program on “Basics of Bioinformatics”, FMU, Balsore: 30. (ii) 5-6 Dec 2008 Training cum Workshop on “Phenomics and Systems Biology”, Resource person: Prof. R.J. Strasser, Univ. of Geneva, Switzerland: 25. Impact shown by your centre on the growth of Biotechnology and allied areas Research initiatives are made in collaboration with ICT and Applied Physics faculties.
Future activities Teaching and research programs in Bioinformatics and other fields of Life Sciences..
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
*(shifting to Jnana Vijnana Vihar, Nuapadhi soon)
Phone: 06782-261580 Mobile: 94372-95915 Email: [email protected], [email protected]
Name of Contact Person(s): (i) Prof. Dr. Sukanti Priya Patnaik (ii) Dr. A.C.Kar Vice-Chancellor Registrar Fakir Mohan University Fakir Mohan University Vyasa Vihar, Vyasa Vihar, Balasore-756019 Balasore-756019 Orissa Orissa
(iii) Mr. S. Marandi Controller of Finance Fakir Mohan University Vyasa Vihar, Balasore-756019 Orissa
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Forest Research Institute, Dehradun Coordinator: Er. Neelesh Yadav Summary of the progress made by the centre from its inception Forest Research Institute –Dehradun is received the grant for BIF on November, 2007.The centre has been established in the historical and magnificent main building of FRI. A core group has been created in the institute to take special research initiative for Bioinformatics. FRI is the premier and oldest 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. The various training programs conducted in biodiversity informatics & related subject. The bioinformatics centre is working in close relation with the GIS cell to achieve Spatial biodiversity informatics.
Major research activities in Biotechnology and its related fields at your institution The FRI has a well established infrastructure of bioinformatics & GIS laboratory, library, herbarium, arboreta and experimental field areas for providing scientific and training services. The Bioinformatics & GIS, genetics & tree propagation , Forest pathology (Molecular biology lab) , tissue culture discipline , Nanotechnology research in forestry, Statistical modeling of trees & biodiversity are the main research domain those are working biotechnology aspect of forestry.
Area of Specialization of the centre Forestry Biodiversity Informatics ,Bioinformatics Education & Human Resource Development, Database of DNA finger- printing 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
Major activities of the centre during the year 2007-08 • Conducted three training programs on biodiversity informatics for the research scholars and scientists of the institute. • Developed the dedicated website of BIF centre ,FRI • Developed the database of forest pathology herbarium and DNA marker database of cedrus deodara species • Further development of Herbarium software of botany division. • Conducted in-house training programs on computer basics and internet technology to research staff of institute. • Organize the workshop cum meeting on “Role of GBIF in India” at W.I.I.- Dehradun with the delegation of GBIF Denmark. Infrastructure facilities in the Bioinformatics Centre A. Computer & Communication facility : The BIF centre have the 12 Desktop computers (Core 2 duo based processor), 10 Desktop computers (Intel V Pro), Web server, database server, Internet leased line connection( 256 kbps) is available, Color Laser printer, photocopy machine, scanner. B. 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) etc. C. Databases & other information resources : i. Web based interactive database for Dehradun Herbarium (Approx 3,30,000 specimens) has been develop by the centre and the data entry work is going on. ii. The database of Forest insects is developed. iii. Forest pathology herbarium (mycology collection of 12000 specimens) database is under progress. Details about staff members working in the centre
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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 , NFLIC and FRI University .
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 Masters Diploma in Management of Natural Resource Management · 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. 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.
Collaborative works/ initiatives IARI, IIT Roorkee, Forest Survey of India, IGNAF-Dehradun, ENVIS center of FRI, IIRS Dehradun , WII Dehradun.
Databases/ Software packages developed 1. Digital Botany Herbarium System. 2. National Insects Database System. 3. Forest Pathology Herbarium database 4. Deodar Information System 5. Website of FRI Papers published or presented in the conferences with reference A. Forestry Bioinformatics, Neelesh Yadav, a paper presented in Scientific Data and Knowledge within the Information Society, 20th CODATA International conference, Beijing, China. B. Role of Bioinformatics in Forestry Research, invited lecture delivered at State Biotechnology conference-2008: Current Trends & Future Perspectives at Forest Research Institute University, by Neelesh Yadav and published in proceedings. C. Dehradun herbarium Digitization published in the proceeding in “International Seminar on Plant Taxonomy in Biodiversity Management and Human Welfare” held at FRI Dehradun on 1-3 December. 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.
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Impact shown by your centre on the growth of biotechnology and allied areas: NA (Because BIF FRI-dehradun recently established)
Future activities • To establish a national database repository for forestry biodiversity informatics and provides biodiversity data analytic tools and techniques. • 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. 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 2224233, Mobile: 9411385495 Email: [email protected] & [email protected] Website: www.icfre.gov.in OR http://friuniversity.icfre.gov.in/
Name of Contact Person: Er. Neelesh Yadav, Scientist Incharge, IT Cell,FRI Email: [email protected]
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Gauhati University, Guwahati Coordinator Dr. D.K. Sharma The Bioinformatics Centre, Gauhati University (DBT-BIF) has procured the necessary components prescribed by the DBT. The separate accommodation of the Bioinformatics Centre with necessary infrastructure facilities has been completed. As per the advice of DBT advisor Dr. T. Madan Mohan in the North East State’s Bioinformatics Centre’s meet held in Sikkim State Council of Science & Technology, Gangtok (on 12-13th November 2008), the centre has nominated two Co-coordinators.
Important activities Human Resources Development The Centre has organized its first training course on “Applications of Computer in Biological Sciences” in the month of January 09, with the participation of 15 Research Scholars and College teachers. The objective of the training was to train young Research Scholars and College/ University Teachers working in any area of Life sciences, to enable teaching and R&D activities in the field of in silico Biology. Faculty for the Training Course were eminent guest speakers from Gauhati University and neighbouring institutions (DOEACC Society Guwahati, Institute of Advance Studies in Science and Technology, Assam Agricultural University) working in the field of Bioinformatics, Biotechnology, Biostatistics, Molecular Biology and Structural Biology. • The Course Contents of the Training Course were - • Introduction to Bioinformatics and its applications • Introduction to Biological databases and information retrieval • Basics of IT tools and applications • Introduction to Biostatistics & Statistical packages • Introduction to Bioinformatics software tools • Dry Lab practical on above topics Information retrieval facility The Bioinformatics Centre, Gauhati University has fully utilized the DBT sponsored BIF facility for providing online Bioinformatics lectures, tutorials, study materials and also by organizing awareness camps, invited lectures, popular talk etc. for P.G. students of Life Sciences. The Departmental Research Scholars are very happy with the easily available online bibliographic database resources like PubMed, MedLine etc. through the Centre’s Internet facility.
Achievements in Bioinformatics • The Bioinformatics Centre, Gauhati University has designed software for exploring the Turtles and Tortoises of Northeast India which has been communicated in IUCN Turtle and Tortoise Newsletter. The software is presently available in the form of CD, which will be upgraded as an online database resource very soon. • Mr. Chittaranjan Baruah, a Research scholar associated with the Centre has presented Bioinformatics Research papers in the 19th All India Congress of Zoology held in Department of Zoology, Gauhati University (29th to 31st December,08) and in the 96th Indian Science Congress, NEHU, Shillong (3-7 January,09). Proposed activities during the year 2009-2010 • The Centre is planning to design its own website for extension and promotion of online Bioinformatics information, education and applications. • The Centre is planning to introduce an Advance P.G. Diploma course in Bioinformatics as a value added course to the existing courses in Zoology/Botany/Biotechnology. • Publication of a Bioinformatics newsletter on current bioinformatics education and research activities. • Awareness camps on “Bioinformatics and Modern Biology” for undergraduate and Post graduate students. • The Centre is planning to establish Career guidance/information facility for Bioscience students. • Collaboration for Biodiversity information and conservation, health related data collection and Data bank utilization.
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Guru Jambheshwar University of Science & Technology, Hisar Coordinator: Prof. J. S. Rana The Bioinformatics Center of GJUS&T was established by Department of Biotechnology Govt. of India, New Delhi in the year 2006. The centre is located in the Department of Bio & Nanotechnology, of GJUS&T, it is equipped with the basic hardware and software facilities for catering to the needs of the students and researchers in the area of biotechnology and molecular biology. This centre has the following facilities: Hard ware: This center has Xeon server X 2.8GHz server/ 533/ 512 Mb 36X2 Gb , Hot plug SCSI Tower server , 42 number Pentium IV Processor dual core , 512 Mb RAM machines running on Window XP operating system .All computers connected with server through LAN. Internet connection is available through BSNL Broad Band ( database) server and it can be accessed through all nodes. Software : It has Win NT 2000 server , Win 98, Win XP . The centre has online access to public database, for information retrieval in the field of biotechnology and Bioinformatics and providing following services • Bibliographic and patent search • E mail and internet access • Training in Bioinformatics Major Achievements • A five days hands on training program cum workshop on Bioinformatics from 3-7th Oct. 2008 was conducted • The furniture for the laboratory has been procured. • Three bays air-conditioned laboratory has been established from BIF. • Independent Telephone line along with broad band internet by BSNL installed from BIF. • Two servers have been purchased through this grant. • All the software have been procured • Photocopier and network printer have been procured • Introductory Bioinformatics course introduced in M. Sc. Biotechnology and M.Tech. Nano Sc. & Tech. Future Plan & Activities • To propose to conduct a long term training programme • To further strengthen the research facilities for Bioinformatics • To start M.Sc. Bioinformatics course specialized in the areas of Food and industrial Biotechnology • To further stringthen the facility for Gene expression data analysis (using dimensionality reduction and supervised/ unsupervised classification methods, gene–marker recognition and mining, and analysis of gene-expressional time series) • To update our facilities for studying Protein structure alignment methods, including computational discovery of embedded sequence-structure-functional relationships. Additional details
Name of Coordinator: Prof. J.S. Rana Contact: Chairperson Department of Bio and Nano Technolgy, Guru Jambheshwar Unveirsity of Sc. & Tech. Hisar-125001, Email: [email protected]
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HNB Garhwal University, Garhwal Coordinator: Prof. Asha Chandola Saklani 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 January 2007 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 & Bioinformatics tools – College teachers, 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 and community health care, simultaneously generating data base amenable to application of Bioinformatics tools. • Preparation of course material –CD ROMs, Web based etc. • Researches which require use of bioinformatics tools are being carried out. 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);KDD, genetic/molecular basis diseases, phytochemistry, natural dyes, microbial.
Area of Specialization of the centre Environmental Endocrinology, IDD and thyroid hormone profiles, Immunoassay technology, Conservation Biology, Molecular Physiology, Mol Phylogeny, Acoustics
Major activities of the centre during the year 2007-08 • 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. • Replaced m-education (mobile technology) by broadband services for e-learning and information retrieval at SRT (rural) Campus of HNBGU (UG/PG/Research) • Total no of students using internet facility : 664 (BSc, BA, BCom, MSc, LLM streams) • No of teachers using internet facility regularly: 09 • Set up a network for Biology & allied teaching- support & counseling for 10+ students via media schools in rural Himalaya. Trained about 30 school teachers and UG students in computer applications from neighboring schools • Organised 01 Workshop (12 days) and 03 Learn-while Serve Biology outreach camps in interior villages : Uppu, Satyo/Pujaargaun and Sohankoti of district tehri Garhwal. Research: Commenced work on thyroid hormone receptors, generated DNA profiles of Himalayan birds and fish (with CCMB); generated data base on Iodine deficiency disorders, thyroid hormone profiles, health & nutritional status in rural Himalaya, genetic diversity of Himalayan populations, commenced work on genetic basis of neuro-developmental disorders and Molecular phylogeny of Him finches
Infrastructure facilities in the Bioinformatics Centre A. Computer & Communication facility: SRT Campus node 01 server,10 computers on wi-fi LAN, 02 Telephone connections. Broad band. 04 Mobile modems; printer, scanner, photocopier Chauras campus node: 09 computers 01server on wi-fi LAN broadband, printer, scanner, photocopier Scientific Software packages: Avisoft, Geneious Pro, GraphPad Prism, Costat, Instat, SPSS, MEGA, PHYLIP
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Details about staff members working in the centre HNBGU Chauras Campus
SRT Campus BIF- node
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.
Educational activities with details of placement Bioinformatics offered as 01 compulsory credit and 09 credit Elective course in MSc Biotech/Zoo. 14 students selected by BCIL for industrial attachment. 02 qualified GATE 01 NET, 01 TIFR, joined ACBR, 02 NII DU south campus etc
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. BIF services were brought through Biology outreach camps in interior rural villages
Collaborative works/ initiatives Following projects/PhD programs initiated with: CCMB Hyderabad: Mol phylogeny of Himalayan finches, Dept Genetics, DU Mol basis of neurodev disorders ACBR Delhi Mol detection cervical cancer NDRI Karnal: Probiotic culture, IVRI Bareilly PCR based detection of Zoonotic Salmonella IARI Delhi Mol
Databases/ Software packages developed DB him finches, Iodine deficiency disorders being developed& about 3,000 thyroid hormone profiles generated from him villages
Papers published or presented in the conferences with reference a) Hormones, behavior & ecosystems: exciting spillover for bioinformatics research Metabolic Networks & Drug Designing, BHU, Varanasi Nov 28-30, 2008.
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b) Phylogeography & population diversification in finches using molecular & acoustic tools Avian Biology GK University, Haridwar, Uttarakhand Nov 2008 Initiation of R&D activities in Bioinformatics Bioinformatics tools are used in on going researches mentioned above
Details of Training/ Workshop organized and total no. of user trained Student Interactive workshop for govt school/ inter college teachers, teacher trainees Student-oriented skills for quality teaching & research 30 science through computers and environment 03 biology Outreach camps in interior villages: Uppu, Satyo/ Pujar gaun and Sohankoti Tehri Garhwal ( 90 users) Impact shown by your centre on the growth of biotechnology and allied areas See column 04 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 • 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 • 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 Research thrusts • Data base compilation on avifauna / ichthyofauna • Data base generation avifauna, avian song repertoire, incidence of diseases, diagnostic facilities, mountain bioresources • Phylogeography & Genetic diversity of finches • 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 State and eventually to the country and the world Additional details
Coordinator: Prof. Asha Cahndola-Saklani FASc Post Box. 45, HNBGU, Srinagar Garhwal Uttarakhand-246174 Ph: 09412018010 Email: [email protected] Dy. Coordinator: Dr Dinesh K Sharma, Dept Zoology, SRT Campus, HNBGU, Tehri Garhwal, UK Phone number: 9410300277 Email: [email protected]
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Indian Institute of Technology, Madras Coordinator: Dr. N. Manoj Summary of the progress made by the centre from its inception The Bioinformatics Infrastructure Facility (BIF), housed at the Department of Biotechnology, IIT Madras was setup with grants from the DBT (New Delhi) and IIT Madras. 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.
Major research activities in Biotechnology and its related fields Various research areas of biotechnology include: Vascular Biology; Systems Biology; Structure function relationship of ion channels, hydrolases; Biocatalysis; Mechanisms of signal transduction pathways; Design and synthesis of siRNAs; QSAR/ QSPR and Drug design; Bioreactor design; Computational Neuroscience; Biomechanics and Rehabilitation engineering; Molecular dynamics of proteins for drug discovery; Cancer biology; Virology; Human genetics
Major activities of the centre during the year 2007-08 The BIF has provided support for the teaching programs, particularly in courses in Bioinformatics, Biomechanics, Struc- tural 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, literature survey, data analysis, bioinformatics analysis, use of specialized molecu- lar modeling and drug design software.
Infrastructure facilities in the Bioinformatics Centre A. Computer & Communication facility: 12 Dual core iMacs running Mac OSX; 1 High end multi processor Mac PRO; 4 HP Pentium IV Graphics workstations; 4 HP Xeon 3D-Graphics workstations; 6 HCL Dual core Pentium PCs; 7 SUN Linux workstations; 12 Pentium IV PCs; 2 SGI Octane workstations; 2 HP printer/scanner/copier; Accessories like external DVD writer, Hard disks, etc. All the computers are connected to the internet on a 33 mbps LAN. B. Scientific Software packages: InsightII, Cerius2, Autodock, Molecular visualization software, commonly used Bioinformatics programs
C. Databases & other information resources: The BIF is extensively used for online literature access through the IIT Madras library e-Gateway. Details about non-faculty staff members working in the centre 1. Ms.Bhuvaneshwari Technical Assistant (Temporary position) Information Technology Jan’ 07 2. Mr.R.Ravisankar Research Assistant (Temporary position) PG Dip in Bioinformatics Jun ‘08 Types of services provided The internet facility of BIF is extensively used to download and browse and print online literature. All major web resources like web servers and sequence and structure databases are used. The graphics workstations are extensively used for molecular modeling studies. Other linux workstations are used for computationally intensive tasks. Additionally the BIF is used by students who come for short term projects at IIT Madras from institutions around the country.
Educational activities The BIF supports the educational activities of the biotechnology department that include the B.Tech and M.Tech degree students. Additionally, the facility also provides support to research activities by supporting the project associates, MS and PhD students for their research projects and course work.
Some recent high impact papers published 1) Molecular dynamics simulations of ligand-induced flap closing in HIV-1 protease approach X-ray resolution: establishing the role of bound water in the flap closing mechanism. (2008). Singh G, Senapati S. Biochemistry. 47(40):10657-64. 2) Self-assembled reverse micelles in supercritical CO2 entrap protein in native state. (2008). Chaitanya VS, Senapati S. J Am Chem Soc. 130(6):1866-70.
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3) QSAR for commercially available inhibitors of COX-2. (2008). Sivakumar PM, Doble M. Med Chem. 4(2):110-5. 4) The repertoire of GPCRs in the sea squirt Ciona intestinalis. (2008). Kamesh N, Aradhyam GK, Manoj N. BMC Evol Biol. 1(8):129. Initiation of R&D activities in Bioinformatics R&D activities here are limited to use of bioinformatics analysis in several BTech, MTech and Summer projects and in PhD projects of the Biotech. dept at IIT Madras.
Details of workshop & total no. of user trained “Workshop on Techniques in Bioinformatics” is planned for the period 5-7th Mar 2009.
Impact shown by your centre on the growth of biotechnology The primary impact of this centre is in manpower training at levels that includes undergraduates, postgraduates and research scholars numbering about 300, of the Biotechnology Dept, IIT Madras. In 2008, 10 papers that utilized the BIF were published in journals and conferences
Future activities The BIF grant will be used for purchase of additional software/hardware to support computational facilities.
Additional Details
Name of the Coordinator: Dr. N. Manoj Postal Address: Department of Biotechnology IIT Madras, Chennai - 600036 Phone Number: 044-22574113 Mobile: 9940149208 Email: [email protected] Website: http://biotech.iitm.ac.in/bif/bif.html Name of Contact Person: Dr. N. Manoj Email: [email protected]
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Indira Gandhi Krishi Vishwavidyalaya, Raipur Coordinator: Dr. D. K. Sharma Summary of the progress made by the center from its inception The Department of Biotechnology, IGKV, Raipur offers admissions to Ph. D. and Ph. D. through DBT sponsored and self-finance scheme and has different well equipped laboratories and a small library to caters to the immediate needs of the students and researchers. The project on “Creation of Bioinformatics Infrastructure facility (BIF) for the promotion of Biology Teaching through Bioinformatics (BTBI) at IGKV, Raipur under the Biotechnology Information System Network (BTISnet) program” was implemented on 30th April 2007 with financial support from the Department of Biotechnology, Government of India New Delhi. The BIF facility is extensively being used by the students, researchers and teachers of Department for thesis related research and teaching activities. Several thesis related research is based on the use of bioinformatics tools.
Major research activities in Biotechnology and its related fields at your institution The Department of Biotechnology, College of Agriculture, IGKV Raipur has contributed in Biotechnology and its related field :- Six Gall Midge (insect) resistance genes in rice tagged and mapped with DNA markers. Standardized of high efficiency regeneration protocol mosses Stevia rebaudiana, white serus, rubber plant Chrysanthemum, Tomato, Lathyrus and Coix. Evaluation and Characterization of rice accessions for nutritional quality traits. in silico Saturation mapping of QTL region and R genes associated with biotic and abiotic stress. Screening of genomic sequences of M. grisea and Trichoderma sp. for identification of microsatellite motif repeats for primer designing. Mushroom breeding (Pleurotus spp.) Collection, purification and characterization of Trichoderma and pseudomonas fluorescence isolates from different geographical locations of Chhattisgarh.
Area of Specialization of the center 1) Biotechnology (Mappigng and Tagging of genes, Collection, isolation and characterization of beneficial micro- organisms, High efficiency in-vitro regeneration protocols, Transformation) 2) Bioinformatics (Development of In silico high resolution genetic and physical map, Nutritional Biofortification). Major activities of the center during the year 2007-08 Admissions of the students to M. Sc. Agri. Biotech PG program. Proposed research activities every year during kharif and rabi on nutritional biofortification projects. Standardization of high efficiency regeneration protocol for various crops, ornamental, medicinal crop. High resolution mapping ( in silico and wet lab) of biotic and abiotic stress tolerant genes and QTLs. Biochemical and Molecular Characterization of fluorescent Pseudomonas, Trichoderma spp. Hands on workshop on DNA marker, genomics and transgenics. Biosafety meeting for Transgenic research
Infrastructure facilities in the Bioinformatics Center A. Computer & Communication facility: Bio-informatics laboratory with ten numbers of PCs, high and medium end server, internet facility and combined Scanner printer photocopier. B. Scientific Software packages: Operating system like Windows 2008 enterprise server edition / Redhat Linux, M.S. Office 2007, staden package, primer designing program, SSRIT tool, NTSYSpc, fast PCR, fasta to multi fasta converter, DNA base counter, and other available through the net. C. Databases & other information resources: 1) Downloaded genome sequence data bases on Rice, Trichoderma, Xanthomonas spp. Pseudomonas spp. Maganporthe grisea. 2) Collected several papers in (pdf format) from annual rev. National and International Journals freely accessible on the net and different other libraries where the online journals are available. Details about staff members working in the centre
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Types of services provided The center extends facilities of computer lab and internet facility to all the P.G. and Ph. D. students and teachers / scientist of the department of Plant Breeding and Genetics, Pathology, Entomology etc for thesis related research activities, besides rendering the computational knowledge to them.
Eduational activities with details of placement Generates HRD by organizing regular training programs in the recent development in the field of Biotechnology. The Department has developed collaborations with national and International institutions for student’s thesis related and other scientific research activities. More than 35 M. Sc. and 6 Ph. D. have been awarded in the Department. The students of Department of Biotechnology have got placements in the institutions of National and International repute for job or for pursuing Ph. D..
Initiative to validate the outcome of bio-informatics resources The Department has its specialization in mapping and tagging of genes and therefore we make use of Bio-informatics for generating position specific molecular markers for wet lab studies. Make use of biological literature and database for thesis related research and teaching activities.
Initiation of R&D activities in Bio-informatics Generation of In silico high-resolution map: 1) encompassing resistance gene homologues associated with important biotic stress tolerance 2) quantitative trait loci associated with grain length of rice in rice. 3) Nutritional Genomic approaches for understanding of metal related genes in rice 4) Pathogenesis related genes in Magnaporthe grisea 5) dbESTs for Molecular Taxonomy of Trichoderma. Details of Training/ Workshop organized and total no. of user trained No. Specific training program on Bio-informatics have been organized but we have trained and acquainted several students (PG and Ph. D.) of Department of Biotechnology with the use of bio-informatics for thesis related research / seminar and thesis related reference collection / downloading of genome sequence database for routine teaching/ and other teaching related materials / images / important links for different types of softwares and data bases etc. The Department plans to organize a three day national workshop-cum training this year (2008-09) on Bio-informatics. Department regularly organizes 15 days Training on DNA marker technology/ Transgenics/ genomics every year in the month of September with intake capacity of 45 students. Till date six training programme have been organized.
Impact shown by your center on the growth of biotechnology and allied areas Recently a Project on Agri Bioinformatics Promotion Programme has kindly been sanctioned by Bioinformatics Initiative Division, DIT, Ministry of Communications & IT, Electronics Niketan, 6 CGO Complex, Lodi Road, New Delhi-110 003
Future activities 1) To organize hands on training and seminar for familiarizing the applications of Bioinformatics in biology teaching. 2) Development of high-resolution in-silico database on various organisms for wet lab studies. 3) To establish collaborations with other institutions and BTISnet centers for information resources and expertise. Additional Details Name of the Coordinator: Dr. Anil S. Kotasthane Associate Professor / Dr. D. K. Sharma Professor and Head Postal Address: Department of Biotechnology, College of Agriculture, Indira Gandhi Krishi Vishwavidyalaya, Raipur 492006., C.G., INDIA Phone Number: 91-771-2442069 /2442131; Mobile: 09424203212 / 09826139382; Email: [email protected] / [email protected] Name of Contact Person(s): Dr. Anil S. Kotasthane Associate Professor, Department of Biotechnology , College of Agriculture, Indira Gandhi Krishi Vishwavidyalaya, Raipur 492006., C.G., INDIA Email: [email protected]
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National JALMA Institute for Leprosy & other Mycobacterial Diseases, Agra Coordinator: Dr. Vishwa Mohan Katoch Title Creation of Bioinformatics Infrastructure Facility (BIF) for the promotion of Biology Teaching through Bioinformatics (BTBI) scheme of BTISnet (DBT funded Project) Scientists: Vishwa Mohan Katoch (Coordinator) and Devendra Singh Chauhan (Co-coordinator) Research Scholar:Farukh Azam
Objective 1. To establish BIF to support the teaching activities of biology and its allied areas of the host institute in particular and the neighboring institutions in general. 2. To build up information resources, prepare databases of interest to its users and to develop relevant information handling tools and techniques. 3. To assess information requirements, organize creation of necessary infrastructure and to provide information and computer support services to the users. 4. To establish linkage with BTISnet at DBT for sharing information resources and expertise. 5. To organize Training/ Workshops for familiarizing the applications of Bioinformatics in biology teaching and learning activities. Background The Bioinformatics Infrastructure Facility (BIF) at NJIL&OMD, Agra was established as a part of the BTIS-Network of Department of Biotechnology, Govt. of India in the year 2007. The facility supports the research staff of the Institute for searching of literature to analysis of the data generated through the medium of internet. The Facility also procured some of the important software essential for Bioinformatics analysis, comprising of Genious-Pro and Discover Studio package.
Work Done Since the establishment of this facility the Institute has organized three workshops. The selection of participants including students as well as teaching faculty for these workshops was based on a write-up justifying their need so that they can motivate their future research and teaching covering Bioinformatics aspects. We invited faculties from different places who are mainly involve in the field of sequence analysis, genomic data mining, protein modeling, docking and drug designing. We have also organized a workshop especially for students from Agra region to provide them exposure about various bioinformatics tools. A series of demonstration and lectures were also given by faculty of Institute. As reported last year work on homology modeling is in continuation for proteins identified in the Institute. These proteins have role in efflux mediated drug resistance in Mycobacterium tuberculosis as well as for metabolic proteins of M.leprae. we have also done Phylogenetic analysis of M.tuberculosis efflux pump proteins. Several online Bioinformatic tools is also being used for different ongoing studies in the Institute. Apart from these workshops, a large no of research scholars from different Universities as well as from local colleges are also engaged in primer designing, BLAST analysis, prediction of efflux proteins, multiple sequence alignments etc. This facility is also providing its support to another project entitled, “Establishment of National Database on Tuberculosis “This project is sanctioned by the Department of Biotechnology. Our Institute is working as a nodal centre, which includes six other national research laboratories. The aim of this project is to build a national database on Tuberculosis, which covers all the necessary epidemiological, therapeutic and scientific data. The development of the database has been initiated in June, 2008 using Oracle as the back-end and Visual Basic as the front-end tools.
VM Katoch Secretary, Govt of India ( Department of Health Research) & Director General, Indian Council of Medical Research and Coordinator Bioinformatics Infrastructure Facility (BIF) at JALMA, Agra
175 Bioinformatics Infrastructure Facility (BIF) for Biology Teaching Through Bioinformatics (BTBI)
Jamia Hamdard University, Hamdard Nagar Coordinator: Prof. Shakir Ali
176 XXth All India Coordinators’ BTISnet Meeting February 03-04, 2009
Jamia Millia Islamia University, New Delhi Coordinator: Mr. Jahiruddin Summary of the progress made by the centre from its inception in the year 2008 · The Department of Computer Science has produced One Ph.D Thesis in the area of Bioinformatics Topics are: Modeling and Simulation of Genetic Regulatory Network. The JAMIA BIF would like to strengthen in these 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. 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.
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.
Major activities of the centre during the year 2008-09 The Department organized a 3 days national level training Programe under BIF from 9-11 January 2008 on ‘Semantic Web and Ontologies in Bioinformatics’ and will organize another 2 days training Programe on 19-20th February, 2009 on “General Bioinformatics”.
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. 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
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. Educational activities with details of placement The placement record is 70% 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.
Papers published or presented in the conferences with references Total of 2 research papers in the areas related to Bioinformatics in the Department of Computer Science are published in this year.
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Details of Training/Workshop organized and total no. of user trained The Department organized a 3 days national level training Programe under BIF from 9-11 January 2008 on ‘Semantic Web and Ontologies in Bioinformatics’ and will organize another 2 days training Programe on 19-20th February, 2009 on “General Bioinformatics”.
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.
Future activities · To purchage software tools related to Bioinformatics. · To Organize two training programmes in coming year. Additional Details
Name of the Coordinator: Jahiruddin Postal address: Department of computer science, Jamia Millia Islamia (a central university), Jamia Nagar, New Delhi-110025 Phone Number: 011-26980014 Mobile: 9871507112 Email: [email protected]
178 XXth All India Coordinators’ BTISnet Meeting February 03-04, 2009
Jiwaji University, Gwalior Coordinator: Dr. Ishan Patro Summary of the progress made by the centre from its inception Desired computational and information technology facilities are being extended to the faculty and researchers in the University. The one-time grant for establishing the Centre was sanctioned in September 2006. The Facility has been established. Database development is being explored in the areas of 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. We have established a MoU to work together in areas of Neuroinformatics with HighHopes Biotech, Agra.
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. Major activities of the centre during the year 2008 The Centre supported the teaching of Bioinformatics to the students of M.Sc. Neuroscience and M.Sc. Molecular Human Genetics (DBT sponsored programmes). Many researchers have been using the facility for their research activity leading to publications. A Seminar-cum-workshop is being palnned on Imaging and Informatics during March 2009.
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.
Papers published or presented in the conferences with reference The researchers at this University have contributed towards publications in the following manner: Saxena Kapil, Patro Nisha and Patro Ishan (2007) FK506 protects neurons following peripheral nerve injury via immunosuppression. J. Cellular & Molecular Neurobiology, 27(8): 1049-1457. Patro, I.K., Saxena, Kapil, Tiwari Shashank and Patro, Nisha (2008) FK506 helps motor coordination recovery following sciatic nerve transection in the young but not in the senile rats. International J. Neuroprotection & Neuroregeneration, 4(2): 145-150. Nisha Patro, Meghna Shrivastava1, Surya Tripathi1 & Ishan K Patro, (2008) S100â upregulation: A possible mechanism of deltamethrin toxicity and motor coordination deficits. Neurotoxicology and Teratology, DOI: 10.1016/ j.ntt.2008.12.001; Reference: NTT 6032. Patro, I.K. and Patro, Nisha (2008) Recent Indian studies on aging of the brain. In Neuroscience in India 2008, Published by Indian Academy of Neurosciences.
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Rohilla Manoj Singh and Tiwari Pramod Kumar. 2008. Restriction fragment length polymorphism of mitochondrial DNA and Phylogenetic relationships among five species of Indian freshwater turtles. J. Applied Genetics. 49: (2): 167-182. Rohilla MS and Tiwari PK.2009 Morphological and Enzyme Polymorphism in Indian Freshwater Flap shell Turtle Lissemys punctata punctata. (Acta Herpetologica In press). Sharma Swarkar, Rai Ekta, Singh Shweta, Sharma Prithvi Raj, Bhat Audesh K., Darvishi Katayoon, Bhanwer AJS, Tiwari Pramod Kumar and Bamezai Rameshwar N.K.. 2009 The autochthonous origin and a tribal link of Indian Brahmins: evaluation through molecular genetic markers (J. Hum. Gen. In press). Shrivastava, Meghna, Patro, Nisha, Kamendra Kumar & Patro, I.K, Age related changes in pain sensitivity differ in male and female rats. Proceedings Nat. Acad. Sci. (India), Accepted.
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.
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. Several
Future activities We are planning to extend training to all biology students in the Campus on Bioinformatics. And develop databases on aspects listed above.
Additional details
Name of the Coordinator: Prof. Ishan Patro Postal Address: Head, School of Studies in Neuroscience & Coordinator Bioinformatics Centre, Jiwaji University Gwalior 474011. Phone Number: 0751-2442789, 2231816, 2231616 Fax No.:2231816 Email: [email protected], Website: www.jiwaji.edu, www.neuroscienceju.com
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Kakatiya University, Warangal Coordinator: Prof. A. Sadanandam Important activities at bioinformatics infrastructure facility Bioinformatics Infrastructure Facility (BIF) was established in the department of Biotechnology, Kakatiya University, Warangal A.P., in order to train teachers teaching biological sciences at UG and PG level. Under Kakatiya University jurisdiction, there are 4 districts with more than 100 degree and PG colleges which have introduced bioinformatics, in their course curriculum. Recently, Andhra Pradesh State Council for Higher Education (APSCHE), Hyderabad has revised the B.Sc. biology syllabus introduced bioinformatics subject, so that students will be get first hand information on this topic and learn the tools involved. The BIF has purchased bioinformatics software called CLC Combined Workbench software from CLCBio Private Limited, Hyderabad for running Bioinformatics training programmes for College teachers and Research scholars. Another Bioinformatics Software, Biological Operating Systems (BOS) developed by Helix Genomics Private Limited, Hyderabad is also available in BIF. Teaching faculty of the Departments of Biological Science, Kakatiya University use BIF regularly. They access internet facility to keep abreast of latest developments in Biotechnology and Bioinformatics, which is useful to complement their class room teaching. Research scholars have regularly used BIF to access information on genomics and proteomics sites which are on public domain. They have also undertaken literature survey for their research work. M.Sc. Biotechnology students have used BIF and have submitted small project reports on bioinformatics. In order to impart bioinformatics skills to teachers involved in teaching biology, a National Conference on “Frontiers in Bioinformatics and Biotechnology” was organized on 3rd and 4th January 2008, in the department of Biotechnology, Kakatiya University. Around 250 participants were benefited by this national conference. Delivering keynote address, Prof.A.R.Reddy, Vice Chancellor, Yogi Vemana University, Kadapa, A.P. emphasized the importance of “Rice Genomics and Bioinformatics”. Dr.Saurav Raghuvanshi, University of Delhi South Campus, New Delhi spoke on the advances in “Genome Annotation Strategies”. Dr.K.V. Radha Kishan, CEO, GVK Biosciences Private Limited, Hyderabad gave an excellent lecture on “Designing New Drugs using Computer Aided Protocols”. Mr.Rami Reddy of Rational Labs Private Limited, Hyderabad delivered a talk on the use of “Computer Aided Drug Design Methods and Structural Bioinformatics for Discovering Novel Drug Candidates for Diabetes and Arthritis”. Dr.Rakesh Mishra of CCMB, Hyderabad spoke on “Comparative and Functional Genomics of Non-Coding Genome”. A lecture on protein-protein interaction was delivered by Dr.Sheker Munde of CDFD, Hyderabad. Speakers from Ocimum biosolutions, Hyderabad delivered as talk on Miroarray technology Omprakash Mittapalii, Hyderabad spoke on “Comparison of Gene Expression in Salivary Glands of three Major Insect Pests of Cereals”. Other speakers from, IISC Bangalore and BARC, Trombay delivered talks on “Biotechnology and Bioinformatics”. Several posters on “Bioinformatics” were displayed during the conference. Some notable posters titles are (1) Data Mining for Simple Sequence Repeats from ESTs in Sesame, (2) Phramacophore Identification and Virtual Screening for Cannab- inoid Receptor-2-Inhibitors, (3).Homology Modeling and Docking Studies on DEACETYLASE 1, (4) Oncomarker DB: A Protein Biomarker Analytical Data Base Tool (5) Sequence Analysis and the Homology Modeling of N-Acetygalactosaminidase and (6) Homology Modeling of Protein Putative Thioredoxin from Streptococcus pyogenes.
Proposed activities during 2009-2010 1. Organizing Workshop A Workshop on “Bioinformatics Applications and Biological Data Analysis” for College Teachers will be organized from 5/3/2009 to 09/3/2009 at BIF Center, Department of Biotechnology, Kakatiya University, Warangal. Plenary lectures will be delivered by Dr.Shekar munde, CDFD, Hyderabad, Dr.Lalitha Guru Prasad, University of Hyderabad, Hyderabad, Dr.Murthy, IICT, Hyderabad and Dr.KV Radha Kishan, GVK Biosciences, Hyderabad. The workshop will focus on the following topics. Introduction to biological databases and uses, Types of Biological Databases, Import and export of molecular data, Viewing and editing sequences, Online database search, Sequence analysis of DNA, RNA & proteins, In silico prime design, Cloning restriction site analysis, Sequence alignment ,Phylogenetic trees, RNA structural analysis, Introduction to BLAST programme and working with NCBI blast and creating local databases.
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2. Summer training It is further proposed to organize another workshop cum training programme for one week for college teachers and research scholars during 2009 summer vacations on drug designing and drug targeting. 3. Studentship and Traineeship The DBT has allotted funds for Studentship and Traineeship during 2009-2010. We are in the process of conducting a walk-in-interview to select the incumbents from the departments of biological sciences. 4. Research Associateship Applications for Research Associateship (RA) to oversee the BIF facility are invited and accordingly interview will be conducted in due course.
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Kannur University, Kannur Coordinator: Prof. M. Haridas Summary of the progress made by the centre during 2008 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 and later, 6.7 lacs for the financial year 2008-09. 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 which 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.
Major Research activities in Biotechnology and its related fields at the department Extramurally funded research projects implemented during 2008 1. “Identification and modeling of targets of an Endocrine disruptor: Bisphenol A” of DBT, Govt. of India for Rs.13 lakhs, PI: Dr. C. Sadasivan 2. “Bioactive Compounds from Marine Cyanobateria” of Ministry of Earth Sciences, Govt of India, Rs 24 lacs, PI Dr M Haridas
Other areas of ongoing research a. Identification, Characterization and pharmacokinetic studies of anti inflammatory phytochemicals/marine cyanobacterial chemical and their derivatives biotransformed by fermentation. b. Development of inhibitor to â-lactamase from phytochemicals. c. 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. d. Modeling of inhibitors to enzymes associated with blood coagulation such as thrombin using molecular modeling tools. e. Peptide modeling/synthesis and study of their functionally important secondary structures/critical role of individual residues
Area of specialization of the Bioinformatics Centre: Structural Bioinformatics Major activities of the centre during the year 2008 The center was established with the facilities listed below. The focus of 2008 was to establish research in the area of strength (structural bioinformatics). During the period, three publications could be brought out as a result of the activity of the centre (listed below). Creation of a database on secondary metabolites is conceived since the major research activity of the department is in developing leads for anti inflammatory drugs (Five preliminary patent applications related to the above activity have been submitted to the Patent Cell of the Kerala State Council for Science, Technology and Environment, Thiruvananthapuram). The creation of the data base is progressing. Part of the data base is attached to this document*. Dr M Haridas, coordinator of the BIF attended the Coordinators meet at Mysore (Feb 3-4, 2008). Six MSc Bioinformatics students outside Kannur University have been guided for their MSc research project works and they have used only the Kannur University BIF facility for their MSc research work. The titles for their dissertations are listed below and publications are being developed from them.
M. Sc. Research project works in Bioinformatics carried out in the Department, at the BIF 1. ‘Designing more hydrophobic analogues of misgurin peptide with increased activity – A molecular dynamics study’ (2008) by Sajida A. A., Safi Institute of Advanced study, Vazhayoor, Malappuram 2. ‘Computer aided discovery of new anti-inflammatory agents from marine cyanobacteria’ (2008) by Shemi Abdulla Chalil, Safi Institute of Advanced study, Vazhayoor, Malappuram 3. ‘Molecular dynamics simulation studies of an antimicrobial peptide, misgurin and its substitution analogues’ (2008) by Sumayya P. A., Safi Institute of Advanced study, Vazhayoor, Malappuram
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4. ‘Role of oxidoreductase enzyme as an antioxidant – A study using bioinformatics tools’ (2008) by Sugeetha K.V., School of Biotechnology, Amrita Vishwa Vidyapeetham, Kochi 5. ‘Sequence and Structural Analysis of Beta-Lactamase: A class of enzyme associated with antibiotic resistance’ (2008) by Anju radhakrishnan, School of Biotechnology, Amrita Vishwa Vidyapeetham, Kochi 6. Desiging more hydrophobic analogues of misgurin peptide with increased activity – A molecular dynamics study (2008) by Sajida A. A., Safi Institute of Advanced study, Vazhayoor, Malappuram
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 (2 Mbps) With INFONET SERVICE of UGC 4. Photocopying machine, LCD Projector, Telephone and FAX b) Scientific Software packages Insight II, Discover Studio, Affinity, SPDBV, AMBER 9, VMD and ArgusLab for molecular modeling and computational biology and CCP4 and many free soft wares. c) Databases and other information resources Fungal Database : Provided by Bioinformatics Centre, Tropical Botanical Garden and Research Institute, Thiruvananthapuram, Kerala, India. 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 and two research assistants have been appointed, instead.
Types of services provided So far, the centre is not in a position to provide any service on demand.
Educational activities with details of placement Teaching in the department has been completely modified with the Bioinformatics facility
Papers published or presented in the conferences with references 1. Divya G. Nair, P. N. Sunilkumar and C. Sadasivan, ‘Modeling of Factor XIII Activation Peptide (28-41) V34L Mutant Bound To Thrombin’ (2008), J. Biomolecular Structure and Dynamics, 26, 387-394. 2. P. N. Sunilkumar, Divya G Nair, C. Sadasivan and M. Haridas, ‘Disruption Mechanism in the Helix of SPF Peptide by Interchanging E5 and K10 Residues: Inference from Molecular Dynamics (2009), J. Biomolecular Structure and Dynamics, 26, 491-496. 3. D. Naveenchandra, Abhilash Joseph, P. N. Sunilkumar, C. Sadasivan and M. Haridas (2009). Biotransformed berberine expels water from active site of PLA2 for inverted binding as a stronger inhibitor, J. Biomolecular Structure and Dynamics (communicated).
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) “Modeling and Molecular Dynamics Simulation of Peptide-Membrane Interaction and Wetlab Validation of 21- Residue Peptide , Misgurin, Its Analogs and Its Hybrid Sequences”. Rs.3,692,700, PI Dr. M. Haridas, Co-PIs: Dr. C. Sadasivan and Dr. A. Sabu (Pending with DBT).
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b) “Bioprospecting of Actinobacteria for anti-inflammatory drug-leads”. Rs 55 lacs as part of a multi centred project proposal of Kerala State Council for Science, Technology and Environment, to approach the DBT.
Details of training/workshop organized and total no. of user trained A two day national workshop is being organized during the third week of Feb, 2009.The theme of the workshop is “WETLAB-DRYLAB DIALOGUE”
Activities for 2009 To complete the database of secondary metabolites and other research activities
Additional details
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
Email: [email protected], [email protected] Phone: 04902347394, Fax: 04902345317
Name of Contact Person: Dr. C. Sadasivan, Reader Email: [email protected]
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Karnataka State Women University, Bijapur Coordinator: Dr. Shiva Kumar Madagi At the outset I take this opportunity to thank DBT for its generous support in-terms of funds and guidance in setting up bioinformatics centre at this KSW University, Bijapur. Further I would like to bring the following points in the report. 1. This KSW University of Bijapur is established in the year 2003. 2. The PG Dept. of Bioinformatics is established from 2007-08 onwards 3. The dept. is running MSc. (BioTech) and MSc. (BioInfo.) 4. This dept. of the university has received funds in the month of July 2008 to setup Bioinformatics Centre. 5. Soon after receiving funds from DBT I have requested the university authority to provide a separate room of size 30 x 30 ft. to setup the centre. Accordingly university has given me the required room with facilities like electrification, networking and air-conditioning etc. 6. Since the dept. is in the new campus which is 15 km away from the city was not having broadband facility, the ET Lab of the old campus is made available for accessing internet. Now, BSNL has agreed to extend cabling up to the new campus and therefore broadband facility will be available very soon. 7. One high-end server, another of medium range server and 10 desktops (HP Make) having required configuration as per the DBT direction are purchased and installed in the lab. 8. One more lab of 10 desktops is also available with networking and necessary softwares. 9. The biorinformatics centre established under the DBT funds will be functional within a month. 10.The facility available at this centre is brought to the notice of teachers and research scholars of life-science/ computer science who are working in the neighboring institutions. 11.It is planned to conduct short-term training programmes / workshops to the teachers of life-science and PG students in batches immediately after its inaugural. 12.At the end I thank the DBT, Dr. Gulshan Wadwa, Principal scientific officer and all co-ordinators for inviting me to the 20th annual meeting. At the same time kindly forgive me for not attending meeting because of my pre-engagements in the activities of our university convocation scheduled on 7th Feb. 2008.
Dr. Shivakumar Madagi Chairman Bio-Informatics, Karnataka State Women University, Bijapur
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Karnataka University, Dharwad coordinator: Prof. B. B. Kaliwal Summary of the progress made by the center from its inception Established Bioinfamatics Lab facility and shortly planning to oraganise workshop
Major research activities in Biotechnology and its related fields Toxicology, Medical Microbiology and Epdemiology of microbes.
Area of specialization of the center The details of Research areas undertaken in next five years is as fallows 1. Studies on antioxidative properties of staphylococcal pigments. 2. Epidemilogical studies on antibacterial resistance of staphylococcus aureus from clinical samples. 3. Studies on staphyloccal bovine mastitis: Epidermiology, Diagnosis and Vaccine development. 4. Studies on phytochemical and pharmacological investigations of medicinal plants. 5. Studies on production and characterization of Thermostable and alkalophilic alkaline protease from Bacillus Sp. JB99 under solid state fermentation. 6. Studies on antifungal, antibacterial, antioxidant properties of serratia marcescens pigment. 7. Studies on the evaluation of insecticide methomyl toxicity in Albino mice. 9. Biotechnological evaluation of pesticides in mice. 10.Immobilized Escherichia coli (E.coli)-A model for toxicity testing of pollutants. 11.Study of the production of L-Asparaginase an anti tumor agent from filamentous Fungi. 12.Biotechnological Production of Citric acid using different substrates by Aspergillus niger ATCC 26550 through submerged fermentation. Major activities of the center during the year 2007-08 The technical procedure for calling quotations and purchase of servers, computers was made for the establishment of Bioinfamatic center.
Infrastructure facilities in the Bioinfarmatics center • Computer and communication facility-server, Desktop computer (LAN are being set up) Scanner-1, Printer-2, Xerox machine-1 • Scientific software package (windows XP are purchased. Database and other information resource-Need to be done. Details about staff members working in the center Dr (Smt) R. D. Sanakal, Teaching assistant Ph.D in Life science with PGDCA Handling Bioinfarmatics.
Types of services provided: Being planned. Educational activities with details of placement M. Sc Biotechnology and Microbiology, almost all students are well placed in various MNCs and National and International research and educational Institutes.
Collaborative works/initiatives under process.
Papers published or presented in the conferences with reference 8 papers published in International Journals
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Initiation of R & D activities in Bioinfamatics Yet, to be initiated.
Impact shown by the center on the growth of Biotechnology and allied areas There is an improvement in the process of acquiring the latest skills in biotechnology and related subjects; hence both the postgraduate & research students are being benefited. Further there is also improvement in the quality of Research papers being published.
Future activities To provide training for Students, teachers and Research personnel in Bioinfamatics and Biotechnology.
Additional details
Name of the Coordinator: Prof. B. B. Kaliwal Postal Address: Postgraduate Department of Studies in Biotechnology, Karnatak University, Dharwad Phone Number: 91-0836-2779533(O) Mobile: 9449278648 Email: [email protected] Website: www.kud.ernet.in Name of contact person: Prof. B. B. Kaliwal
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Kumaun University, Nainital Coordinator: Dr. Veena Pande The Department of Biotechnology Kumaun University Nainital, established in the year 2000 with the support of Department of Biotechnology, Govt. of India has developed as an important academic centre of Uttarakhand state. At present activities of Department are focused on quality teaching programme at M.Sc. level including the Ph.D progrmme as well as execution of major research projects in selected areas. Biotechnology is an emerging discipline with far reaching consequence for human civilization. The Centre is engaged in research related with the Microbial Diversity, Genetic Diversity and Biotechnological application of Mycorrhizal fungi of Uttarakhand. Bioinformatics is a multidisciplinary subject and therefore the research and students are to be trained continuously to upgrade their knowledge and skills in this area. The Biotechnology Information System Network (BTISnet) of Department of Biotechnology is making all of its effort towards the effective utilization of various applications of bioinformatics and computational biology for accelerating biology and biotechnology R & D and teaching activities.
Overview of the centre The Centre has been established in the year of 2006-07 by the support of Department of Biotechnology, Govt. of India.
Achievements: (2008-09) • Department of Biotechnology, Kumaun University is ranked amongst Top 20 public Biotech schools by Biospectrum Biotech School Survey 2008 (Vol.6, issue 1, Jan 2008). • Completion of Project entitled “Genome Diversity in the tribal population of Kumaon Region” in collaboration with Dr. Lalji Singh, Director, CCMB, Hyderabad, sponsored by CSIR New Delhi. P.I. Dr. Veena Pande Head & Coordinator. • Development of Centre website (In-House) • Development of Database on Ectomycorrhizal Diversity of Kumaun Region. • Development of Database on Medicinal Plants of Indian Himalaya Region. (In- Progress) Major Infrastructure Facility • Computer & Communication facility- High end server – 1, Proxy Server – 1 Desktop Computers – 10, Laptops – 3 Multi media projector – 2, Scanner – 2 Printers (high end) –4 (LaserJet), 1 (inkjet) UPS – 5 KV (1), 2 KV (3), Xerox Machine – 1 • Scientific Software packages- Windows Office 2007, Windows XP, Red Hat Linux, HCL BIO-PACK, Geneious, CLC workbench etc. • Internet facility at a speed of 512 Kbps (BSNL). HR Development in Bioinformatics Workshop/Training: A three day workshop on “Application of Bioinformatics to study Genetic Diversity” was organized from September 2-4, 2008 for faculty and research scholar of our own & different Universities.
Collaboration Industry Interactions: Indian Glycol, Kashipur Interactions with Other Institutions / Centres: • CCMB, Hyderabad. • VIPKAS,Almora . • DARL,Pithoragarh . • G.B.Pant Institute of Himalayan Environment& Development Kosi. • G B Pant University, Pantnagar . • R M L Awadh University, Faizabad .
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• Directorate of Cold Water Fisheries Bhimtal. • Defence Institute of Bio Energy Research, Goraparao, Haldwani. Future Plans • To conduct some basic trainings for Graduate & Post Graduate students of near by colleges. • The Completion of Database on Medicinal Plants of Indian Himalaya Region & Development of more databases related to important flora and fauna of this region • The Centre is planning to offer some short term courses/ Hands on training in Bioinformatics for Faculty and Research Scholar. • Comparative Genomics & Proteomics study of Ectomycorrhizal & Microbial Diversity of the Himalayan Region. Research Publication Comparative Homology Modeling of Cold shock Protein in Pseudomonas fluorescens. (Communicated)
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Lady Doak College, Madurai Coordinator: Dr. (Mrs.) Shenbagarathai Summary of the progress made by the centre from its inception Bioinformatics lab was established in 2006 and upgraded into excellent infrastructure with 25 desktops with Intel core 2 Duo processor with one high end and one medium end server. The internet speed is of 2 Mbps leased line connection. The workshops and symposiums organized aimed to help the participants to be aware of the advanced usage and the importance of Bioinformatics. This is to accentuate the goal of the BIF centre “Biology teaching through Bioinformatics”. So far two workshops and three symposiums have been organized for teachers, UG, PG students and research scholars. The symposiums were organized to focus on students and researchers from the field of life science. A special workshop for School teachers was organized to enable them to develop competence in the field of Bioinformatics in order to deliver the same to the higher secondary students effectively. This center act as a Bioinformatics hub for the teachers and students (UG/PG/M.Phil/PhD) belonging to the various departments such as Biotechnology, Zoology, Botany, Chemistry, Physics and PG Diploma in Biomolecular Modeling and Dynamics to carry out their regular practical lab exercise, project and research work. In addition, the students from other colleges are also utilizing this facility for their project work, research etc.
Major research activities in Biotechnology and its related fields at your institution Biopolymer • Downstream and upstream processing of PHA from indigenous Pseudomonas sp LDC-5 and its mutant • Physio-chemical characterization of Poly Hydroxy Alkanoates(PHAs) • Insilico analysis of PHA synthase gene with available data in various databases. • Comparative study on PHA synthase genes of Pseudomonas sp. Medical Microbiology • Characterization Study on cytolytic proteins from nontoxic isolates of Bacillus thuringiensis sp. • Study on cry toxins from Bt isolates. • Study on HIV patient coinfected with TB. Area of Specialization of the centre - Microbial Biotechnology Major activities of the centre during the year 2008-09 The Workshop for school teachers was organized specially to highlight the concepts of Bioinformatics in the school level. Teaching materials (PPT files and hand outs) were given to them to enhance their competence in Biology teaching. Follow up action has been made to strengthen their teaching in the Bioinformatics labs.
Infrastructure facilities in the Bioinformatics Centre a. Computer & Communication facility 25 systems from DBT – BIF and 11 from UGC Innovative with internet facility at a speed of 2Mbps leased line connection b. Scientific Software packages GCG Wisconsin package, Discovery Studio 2.0, Geneious Pro Ver.3.5.6, Amber Packages, SPSS tables (Ver 16). Details about staff members working in the centre
All the candidates were selected based on merit and interview performance.
Types of services provided • Theoretical and practical training on Bioinformatics is provided to all the students from the Department of Sciences (Physics, Chemistry, Botany, Zoology, Biotechnology, Microbiology).
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• Providing internet facility for the students for their Bioinformatics work, Web based retrieval and analysis of data. • Summer courses are organized for students from various colleges and institutions on Bioinformatics. • Extended to students from various institutes like Bishop Heber College, Trichy, Karunya University, Coimbatore. Initiative to validate the outcome of bioinformatics resources The workshop for school teachers was of great help to teachers to enable them to understand the basic concepts on Bioinformatics. A follow up has been made with the teachers and students for further improvement and to update the same in the concerned area.
Collaborative works/ initiatives Dr. K.B. Ramachandran IIT, Chennai. Dr. Sankiliyandi, Kalasalingam University. Databases/ Software packages developed Development of local database for immunoinformatics – Completed Microbial database – In Progress Papers published or presented in the conferences with reference • A. Mahalakshmi, K. Sujatha and R. Shenbagarathai (2008). Molecular modeling and characterization of Bt and Bt LDC-9 cytolytic proteins. Journal of Biomolecular modeling and Dynamics. 26(3). • K. Sujatha, A. Mahalakshmi, Daniel K. Y. Solaiman, R. Shenbagarathai (2009). Sequence analysis structure prediction and functional validation of PhaC1 / PhaC2 genes of Pseudomonas sp. Ldc-25 and its importance in PHA accumulation.(In press) Initiation of R&D activities in Bioinformatics • Molecular modeling and comparative analysis of parasporin models. • Full length sequencing of Pseudomonas putida LDC-5 • Cloning and expression of PHA genes in heterologous system. • Site directed mutagenesis of cry proteins and its functional analysis. Details of Training/ Workshop organized and total no. of user trained • No of Training / Workshop: 5 • No of user trained: 285 Impact shown by your centre on the growth of biotechnology and allied areas. • Number of Papers Published - 6 • Number of papers published with the help of our centre - 2 • Manpower trained – 1085 Future activities a. Development of R&D activities in the field of Bioinformatics for the production of Biopolymers and Biopesticides (Parasporin). b. Hands on training and workshop for the school students on Biotechnology and Bioinformatics in order to motivate them to choose life science courses for their future studies. Additional Details Name of the Coordinator: Dr. R. Shenbagarathai Postal Address: Department of Biotechnology, Lady Doak College Madurai – 625002 Phone Number: 0452-2535575 Fax No: 091-452- 2535575 Mobile: 9443738168 Email: [email protected], [email protected] Name of Contact Person(s): Dr. R. Shenbagarathai Email: [email protected]
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Madras Christian College, Chennai Coordinator: Dr. D. Arul Samraj Facilities added Out of 7 lakhs released under equipments for the year 2008-2009, 21 terminals, 3 printers, 1 digi cam were purchased. Geneious pro 4.5 also added.
Staff members
Databases developed Offline database on Scope of Biology and distributed to all the participants of the workshop conducted for Biology Teachers of Hr. Sec Schools. Offline database on Campus Fauna is in progress.
Papers published or presented in the conferences with reference • R.W Alexander Jesudasan, Significance of Insect Genomics in Agro ecosystems. Proceedings of National workshop on Molecular modeling and Protein Docking, Feb 25-29, 2008, Eds. M. Balakrishnan & R.C Srivastava, SDIC, Central Agricultural Research Institute , Port Blair, Andaman &Nicobar Islands,18-25. • Christy Jancy Joy P., Lorraine Gifta S., Arul Samraj D., Priyakumari Joyce C. Integrating computational methods for prediction of protein structure and function in an endangered butterfly species Doleschallia bisaltide Cramer (Nymphalidae:Lepidoptera); National Seminar on Endemic and Endangered Species of the Nilgiris, Aug 21- 22, 2008, Government Arts College, Udhagamandalam, The Nilgiris,Tamil Nadu. • Lorraine Gifta S.,Santa Ram A., Christy Jancy Joy P., Arul Samraj D. Priyakumari Joyce C. Genetic diversity of Racemusta Genotypes using RAPD markers in Conservation of Coffee Germplasm; National Seminar on Endemic and Endangered Species of the Nilgiris, Aug 21-22 2008, Government Arts College, Udhagamandalam, The Nilgiris, Tamil Nadu. • S.A Vidhya and R.W Alexander Jesudasan, GBIF-A Reservoir of Biodiversity Data and the need for the hour. National Seminar on Endemic and Endangered Species of the Nilgiris, Aug 21- 22, 2008; Government Arts College, Udhagamandalam, The Nilgiris,Tamil Nadu. • Lorraine Gifta S., Santa Ram A., Christy Jancy Joy P., Arul Samraj D. Priyakumari Joyce C. Comparative assessment of DNA fingerprinting techniques (RAPD and ISSR markers) for genome analysis of Racemusta genotypes. Proceedings of The National Conference on Computational Biology, NCCoB ’08, Aug 22-23, 2008, Eds. Dr.Jannet Venilla, Department of Bioinformatics, Karunya University, Coimbatore, Tamil Nadu. Pg. 27. • Christy Jancy Joy P., Lorraine Gifta S., Arul Samraj D., Priyakumari Joyce C. Comparative study on Hsp70 protein on Bemisia tabaci and Trialeurodes vaporariorum. Poster presentation Proceedings of The National Conference on Computational Biology, NCCoB ’08, Aug 22-23, 2008, Eds. Dr. Jannet Venilla, Department of Bioinformatics, Karunya University, Coimbatore, TN. Pg.33 • Christy Jancy Joy P., Lorraine Gifta S., Arul Samraj D., Priyakumari Joyce C* Structure and function prediction of Wnt protein in an endangered butterfly species Doleschallia bisaltide Cramer (Nymphalidae: Lepidoptera), communicated to “Insiloco Biology.
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Workshop Conducted • “Introduction to Bioinformatics” for Biology Teachers of Higher Secondary Schools – 27 Teachers of 14 schools participated. • Science Faculty of MCC – March 2009 New programs • Bioinformatics optional under M. Phil Zoology. • New syllabus of Bioinformatics at U.G and P.G level of Zoology major students. • Bioinformatics at P.G level for Botany major students. Review Meetings • Executive Committee Meeting was held on Sep.20, 2008. • Periodic meetings of the Science Faculty and Bioinformatics Committee. M Phil Dissertations under the guidance of Dr. R. Moses Inbaraj • Pratheeba F G 2008 Relationship study and expression of StAR protein gene in the brain of Labeo rohita. • Sundari G 2008 Expression of the gene encoding 3â-Hydroxysteroid, dehydrogenase in the brain of an Indian Carp, Labeo rohita. • Saravanan N 2008Steroidogenic Enzyme 3á-HSD gene expression in the brain of an Indian major carp, Labeo rohita (HAM) • Uma T 2008 Identification and expression of the steroidogenic enzyme encoding CYP17 gene in the brain of an Indian carp, Labeo rohita • Sarumathy P 2008 Expression of steroidogenic enzyme P450 scc in the brain of Indian Major carp, Labeo rohita. M Sc dissertations under the guidance of Dr. (Mrs.) C. Joyce Priyakumari • Arun sivan 2008 Comparative proteomic analysis in the study of ecdysis in two insect pests. • Padmavathi G 2008 Analysis of putative-odorant binding protein precursor pheromone in ten Solenopsis sp. using bioinformatics tools. • Boby Thomas 2008 In silico analysis of two salivary gland proteins of mosquito. Future activities under Studentship/ Traineeship/ MSc. & MPhil dissertation • Structure prediction of juvenile hormone receptor protein in Insects. • In silico studies of genes and proteins of few nitrifying and denitrifying bacteria • Database on Reptiles of the scrub jungle of Madras Christian College campus. • Computational analysis of single nucleotide polymorphism in mammals. • Analysis of sequences of kairomones in polyphagous insects • M. Phil program in Bioinformatics (awaiting approval of University of Madras) • Ph.D. program for the Research Assts. Contact Details
Coordinator: Dr. D. Arul Samraj, Madras Christian College, Chennai 600 059, Phone No.: (+91) 9444 284670; Email: [email protected] Website: mccbioinformatics.htmlplanet.com Contact Person(s): Dr. (Mrs.) C. Joyce Priyakumari, Associate Coordinator, Bioinformatics centre of BTISnet, Madras Christian College, Chennai 600059. Phone No.: (+91) 9444 149280; Email: [email protected]; [email protected]
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Maharani Lakshmi Ammanni College for women, Bangalore Coordinator: Dr. M. B. Nagaveni Summary of the progress made by the centre from its inception A symposium titled “Features and Future of Clinical Research” at J.N. Tata Auditorium, Indian Institute of Science, Bangalore on April 22, 2008. A four day workshop from Sept. 18 – 21, 2008 on “Microarray, Microarray data analysis and Systems biology” in collaboration with Institution of computational Biology (IOCB). IOCB and DBT-BIF centre, MLACW jointly organized workshop on ‘Role of system biology and algorithms in drug discovery process” from 26-28, December 2008 A. Upgradation of the BIF centre- purchase of proxy server to host web server B. Purchased Discovery studio 2 C. BIF has given free access to use its facility to create awareness about bioinformatics among pre-university students, by conducting workshops D. Using BIF, our colleague, Mr. Sushil Kumar Middha has won Schrodinger prize for poster presentation at international bioinformatics symposium held at Hyderabad Univ, Hyderabad.
Major research activities in Biotechnology and its related fields Database creation and few Ph.D. programs.
Area of specialization of the center: Biotechnology and biochemistry Major activities of the centre during the year 2008 BIF centre has successfully conducted 1 symposium and 2 national workshops on bioinformatics related topics.
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, Discovery studio 2 (all are commercial packages and free ware Hex,RasMol,Qmol etc. ) c. Databases and other information resources: PFam (Protein database)
Details about staff members working in the centre Mr. Sushil Kumar Middha: Bioinformatician Mrs. Aruna H.K. : Bioinformatician Mrs. Saraswati B. : Bioinformatician Ms. Usha T. : Bioinformatician Mr. Venkatesh : Bioinformatician . (All are appointed on permanent basis since 2006)
Types of services provided Faculty members and students have used BIF for carrying out their various research activities
Educational activities with details of placement Students are placed in companies like Jubilant Biosys, Accenture, Molecular Connectius, Quintiles, Empower, Clinigene (Biocon group), Biowares, Apsara Innovation center- as bioinformatician, data management professionals etc. and project trainee at IISc (Cell Biology & Molecular Biology Dept.). One of the students has joined IISc as Ph.D. student
Initiative to validate the outcome of bioinformatics resources Database creation is under completion.
195 Bioinformatics Infrastructure Facility (BIF) for Biology Teaching Through Bioinformatics (BTBI)
Collaborative works/initiatives (a) With Chan Re diagnostics lab, Bangalore a project on data mining of immunological work (b) With IOCB database designing is planned (c) With Bioiware for conducting work shop in future.
Databases/software packages developed: Under completion
Papers published or presented in the conferences with reference Communicated
Initiation of R&D activities in Bioinformatics Under completion
Details of Training/workshop organized and total no. of users trained: 200 A symposium titled “Features and Future of Clinical Research” at J.N. Tata auditorium, Indian Institute of Science, Bangalore on April 22, 2008. A four day workshop from Sept. 18 – 21, 2008 on “Microarray, Microarray data analysis and Systems biology” in collaboration with Institution of computa-tional Biology (IOCB). IOCB and DBT-BIF centre, MLACW jointly organized workshop on ‘Role of system biology and algorithms in drug discovery process” from 26-28, December 2008 (a) Free training to Pre-univ. students to create interest towards life sciences (b) Diloma and certificate course students comprising both UG and PG students are utilizing this facility.
Future activities National workshop on PCR & bioinformatics tools during March 2009.
Additional details
Name of the Coordinator: Prof. M.B. Nagaveni Maharani Lakshmi Ammanni College for Women, Malleswaram, Bangalore- 560 012 Phone Number: 26692137 Mobile: 9886205533 Email: [email protected]
Name of Contact Person: Mr. Sushil Kumar Middha Email: [email protected]
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Maharani's Science College for Women, Bangalore Coordinator: Mrs. Kavitha B. 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 One National workshop on ‘Techniques in Molecular Biology and Bioinformatics’ for faculty was also organized in collaboration with Institute of Computational Biology (IOCB) and Aristogene Biosciences, Bangalore. Training programme for Undergraduate and postgraduates students and faculty is been provided. Access for browsing for research material is being provided for M.Phil, Ph. D & Post doc Students. The facility is being used by the faculty of our college and neighboring colleges.
Major research activities and Area of Specialization Microbiology & Bioinformatics being the major research area, a database on ‘Airborne fungal allergens in indoor environment’ has been prepared and launched. A database of Ribosome inactivating proteins from plant origin and Structural and functional analysis of airborne fungal allergens is in progress.
Major activities of the centre during the year 2007-08 Website of the facility www.mscwbif.org was launched in October 2008 Three workshops for students on ‘Basics of Bioinformatics was conducted for students. One national workshop on Techniques in Molecular Biology and Bioinformatics’ was organized for teachers in Oct 2008. Hands on training were given to the faculty during the workshop. Over 92 students and 16 teachers have been trained in the field of Bioinformatics.
Details about staff members working in the centre
The faculty of the Microbiology Department are involved in the activities of the facility along with one RA
Future plans Training for students and staff will be continued Database of Ribosome inactivating proteins from plant origin and Structural and functional analysis of airborne fungal allergens will be completed.
197 Bioinformatics Infrastructure Facility (BIF) for Biology Teaching Through Bioinformatics (BTBI)
Contact 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 Email: [email protected] Website: www.mscwbif.org
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Maharashtra Animal & Fishery Science University, Nagpur Coordinator: Dr. Arun S. Ninawe The centre was sanctioned by the Department of Biotechnology and the grants were received (Rs.20 Lacs) In newly constructed Library building separate block of 1450 sq. ft. was marked for the purpose and renovated for the centre. It had reception, server room, office, Wifi zone (10 Computer terminals) and office for coordinator and P.I. All the floor space had carpet flooring with Air conditioning of all the space. Wifi zone has conference facility with sufficient sitting arrangement and LCD Projector/Screen. All the related facilities as servers, scanners, copies and printers were purchased. Round the clock electricity supply is ensured with generator and UPS back up. For smooth functioning following working committee was formed. Dr. Dr. A. S. Ninawe Vice-Chancellor: Coordinator Dr. P. S. Lonkar, Director of Extension & Training: P.I. Dr. M. D. Kothekar Prof. Of Animal Genetics & Breeding: Member Dr. A. R. Chauhan Asst. Prof. of Surgery: Member Shri. C. S. Lawtawar Stenographer: Member All the members of the group are well versed with the computer and are already working with Information and Communication Technology cell, besides their own activities. The centre was inaugurated by Hon’ble Minister for Animal Husbandry, Dairy and Fisheries, Government of Maharashtra on 15/12/2008 Later a meeting of 15 faculty members of Maharahtra Animal and Fishery Sciences University (From Constituent Colleges) was called on 19/12/2008 and they were enlightened about the centre, objectives and facilities. Faculty members willingly asked for training initially for handling the website of University, Learning object Repository with retrieval and sites of bioinformatics. It is planned to have such training from January 2009 after training of the some member of the committee at Aligarh and Pune. This would later be a regular feature. In collaboration with Yashwant College of Bioinformatics, Parbhani, a training programme is planned from March 2009 for the faculty on Bioinformatics. The faculty would later be assigned future training programmes. Initially a 3 days Seminars/Workshop is being organized at Nagpur, in April 2009. Looking towards the support by the University, enthusiasm of the staff (especially young ones), large number of Departments in highly specialized fields of Veterinary, Dairy and Fishery and Other traditional Universities in the vicinity, the centre is bound to be self sustainable in near future with sufficient receipts through training programmes and facilities. Activities of the Commonwealth of Learning, Canada sponsored Information and Communication Technology Project on Open and Distance Learning of MAFSU (TechMODE) would act as a supporting unit with the Bioinformatics centre. Purchase of books and software is in progress.
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Manipur University, Imphal Coordinator: Prof. N. Irabanta Singh After the 1st BTInet Interactive meet for bioinformatics centers of North Eastern States held at Sikkim State Council of Science & Technology, Gangtok (12-13 Nov., 2008) the following progress have been made for the Manipur University BIOINFORMATICS INFRASTRUCTURE FACILITY (BIF) Centre. A separate room for Bioinformatics Infrastructure Facility has been earmarked in the newly constructed Life Sciences, building. Internal electric wiring has been completed. A name plate for the facility has been fixed at the entrance of the room and labeled as Bioinformatics Infrastructure Facility (Funded by DBT, GOI), Department of Life Sciences, Manipur University, Imphal – 795003. During June, 2008 supply orders of the following items viz., Server (High end); Server (Medium) for Proxy (1) and File Server (1); Desktop Machines with OS; Printer (Colour); Scanner; Window Server; Red hat Linux Server; MS Visual Studio 2008; SQL Server; MS Office 2007; Norton Antivirus have been made. Now, all the items have been received and installed. Computer table and chair for installation of PC and seating arrangement of the trainees have been purchased and displayed in the concerned room for bioinformatics Infrastructure Facility, Department of Life Sciences, Manipur University. Networking components (Active & Passive), UPS- APC/Emerson ONLINE UPS Systems Capacity: 6KVA, 230VAC, with power management software etc. have also been purchased and installed. The sanction order letter for release the second installment of Rs. 5.00 lakh (Rupees five lakh only) have been received by the Coordinator and the Registrar, Manipur University. Further, the centre needs manpower for looking after the equipments installed. Hence, a proposal is put up to DBT, Govt. of India for sanction of the following manpower. 1). RA/TA – 1 post 2). Data processor – 1 post 3). Attendant- 1 post The proposed activity during 2009-2010 will include organizing a workshop on the application of bioinformatics in preserving microbial biodiversity of North East India.
Name of Coordinator: Prof. N. Irabanta Singh Department of Life Sciences Manipur University, Imphal Email: [email protected], [email protected]
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Manonmaniam Sundaranar University, Tirunelveli Coordinator: Dr. K. Veluraja Facilities Available at the centre Hardware 1. Two Higher End Servers with LINUX Operating System 2. Six higher end Desktop systems with graphics card Support 3. Laser printer 3390n – All one mono 4. 24 hours Internet facility Softwares 1. Molecular Mechanics Software - AMBER 2. Molecular Dynamics Software – NAMD 3. Visualization Software – VMD 4. Gaussian 03 5. Plotting Software – GNUPLOT 6. Intel Compilers for FORTRAN and C++ 7. Graphics Software Molscript, Raster3D Databases 1. Complex Carbohydrate Structural Databases (CCSD) 2. A database for Sialic acid containing oligosaccharides 3. DSDCAR – Three Dimensional Structural Database for Carbohydrates is under progress. Research Interests of the Centre 1. Three Dimensional Structural Database for Carbohydrates 2. Protein – Carbohydrate Interaction 3. Molecular Modelling and Drug Design 4. Molecular Dynamics Simulation 5. Sequence Analysis Academic Activities of the Centre 1. A value added Certificate Course in Bioinformatics is introduced with 72 hours of teaching (Theory and Practical). Practical classes are conducted in the fields of programming and sequence and structural analysis. Seven students in first batch have completed the course. With the intake of 12 students, the second batch of the course is ongoing. Invited Lectures by experts in the subject are arranged for the students of the course. 2. One day training program was conducted to 40 students of “Centre for Marine Science and Technology, Manonmaniam Sundaranar University”. 3. Extra Departmental Optional Course students who have chosen Biophysics are given training in Bioinformatics Centre. 4. One student from Department of Environmental Sciences is carrying out his M.Sc project in the centre through the student fellowship offered. 5. Research scholars of the Biophysics lab are extensively using the servers and desktops for their Molecular Dynamics Run. 6. A National Seminar entitled “National Seminar on Structural Bioinformatics – NSSB2009” is conducted on January 29-30, 2009. 7. Process is going on for the purchase of the Molecular Modelling software “Schrödinger” for the Bioinformatics Centre.
Student Projects carried out at the centre One M.Phil student and two M.Sc students did their project work in the Bioinformatics Infrastructure Facility in the field of sequence analysis.
201 Bioinformatics Infrastructure Facility (BIF) for Biology Teaching Through Bioinformatics (BTBI)
Student Projects ongoing Currently One M.Phil and two M.Sc students are doing their project in this facility. The Research scholars are doing their research in Biophysics and bioinformatics are extensively using the machines for their research projects.
Proposed activities of the Centre for 2009-2010 1. To carry out Molecular Docking and Drug Design Projects 2. Extensive Molecular Dynamics Simulation for Sialic acid containing Oligosaccharides to create a Three Dimensional Structural Database. 3. Creation of Oligosaccharide Database
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Maulana Azad National Institute of Technology, Bhopal Coordinator: Dr. K. R. Pardasani 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 from this session i.e. July 2007. MANIT also intends to start B.Tech and M.Tech 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.
Major research activities in Biotechnology and its related fields The institute plans to develop a versatile research team in the following areas of computational biology- 1. Datamining 2. Thermal modeling of cancer 3. Modeling gene expression 4. Modeling and analysis of Biological sequences. 5. High performance computing for bioinformatics 6. Computational phylogenetics 7. Neuroinformatics. 8. Machine learning models in Bioinformatics Area of specialization of the centre: Computational Biology Major activities of the centre during the year 2008-09 1. Organized National workshop on Bioinformatics from 10-14 March, 2008. 2. Organized National workshop on Cheminformatics from 15-19 March, 2008. 3. National Training Programme on Bioinformatics for one month From 15 may-19 June ,2008 4. National Training Programme on Bioinformatics for one month from 23 June-22 July, 2008 5. EU-India grid workshop in applications of computational biology from 5 May-9 May , 2008 6. AICTE Staff Development Programme on Tools and Techniques in bioinformatics during 19 May-29 May 2008. Infrastructure facility in the Bioinformatics Centre A. Computer & Communication facility: 24 PIV computers along with one medium server ,5 laser printers Desk-jet printer , 1 photocopier and scanner one server high end (Procurement under process) B. Scentific Software Packages: At present we use online and free software ‘s like BLAST ,CLUSTAL - W, PHYLODENDRON, RASMOL, PRIMER 3, EMBOSS, Autodoc, Hex, Moldoc, Chemsketch, Hyperchem, VMD ,Compudrug, Pymol, SPDBV, BIOEDIT, PHYLIP,TINKER, GCG AND ACCELYRS, WEBCUTTERS etc. C. Database and other information resources : The online databases like NCBI, EMBL, PDB, CATH, SCOP, EXPASY,UNIPROT, GENBANK etc are accessed through internet Details about staff members working in the centre There are 14 Research Fellows working in the area of Bioinformatics. Mathematical and Computational Biology: Name of staff Designation Specialization Period of working Dr. K.R.Pardasani Professor & Head Computational Biology,Dataminig 24 years Dr. Namita Shrivastava Assistant Professor Computational Genomics, Integral Transforms 20 years Dr. Madhvi Shakya Head Department Biomathematics, Biocomputing 19 years Mrs. Usha Chouhan Lecturer Computational Phylogenetics 8 years Mr. Chandan k. Verma Lecturer Modelling, Gene expression 10 years Types of services provided I) Training programmes/ workshops in the area of bioinformatics to provide exposure to basic skills of
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bioinformatics to the students of biotechnology/ lifesciences , physical sciences and IT, from other institutes of our region and country. II) Guiding research for Ph.D Ddegree and in educational Programmes like B-Tech & M.Tech in the area of Bioinformatics. iii)Consultancy. iv) Development of software and databases. 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. Three MTech candidate have joined for PhD programme in different institutions . One candidate has been awarded PhD degree in bioinformatics and he got Post doctoral fellowship at Tel Aviv University, Israel. One more candidate has submitted her PhD Thesis.
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. Collaborative works/ Initiatives We have developed collaborations with institute like – Bhopal Memorial Hospital and Research Centre, Bhopal JALMA, National Institute for Leprosy and other Mycobacterium Diseases, Agra to create databases for their data International collaborations (Initialised) Dr. Tulpupco, Department of Bioinformatics, Tel Aviv University, Israel Databases / Softwares packages developed We have developed softwarepackages for: 1. Haplotyping 2. Molecular Cutter 3. Codon usage analysis (under procurement)
Papers published or presented in the conferences with reference Paper published- 6 Presented in conference –10 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 background of mathematics, biotechnology, computer 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 molecu- lar markers etc with their role in genomic and proteomic network, drug designing, diagnostics and therapeutics.
Details of Training / Working organized and total no. of user trained SN Training / workshops No. of participants 1. Organized national workshop on Bioinformatics from 10-14 March, 2008 105 2. Organized national workshop on Cheminformatics from 15-19 March, 2008 100 3. National training programme on Bioinformatics for one month from 15 May-13 June, 2008 40 4. National training programme on Bioinformatics for one month 23 June-22 July, 2008 12 5. EU-India grid workshop in applications of bioinformatics from 5 May-9 May, 2008 78 6. AICTE staff development programmeOn Computational models Tools and Techniques in bioinformatics during 19-29 May,2008 20 Impact shown by your centre on the growth of biotechnology and allied areas Among all the NIT’S, MANIT, Bhopal has taken lead by starting B.Tech, M. Tech and PhD programmes in the area of bioinformatics . Also MANIT has taken lead among all NIT’S in organizing short term training programmes in the area
204 XXth All India Coordinators’ BTISnet Meeting February 03-04, 2009 of bioinformatics since July 2004. The institute has developed collaborations with the institute 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 area of mutual interest . One candidate has been awarded PhD degree in Bioinformatics and he got Post doctoral fellowship at Tel Aviv University, Israel. One more candidate has submitted her PhD Thesis. A good number of candidates from different institutes come to our institute for Project/ Training.
Future activites 1. Proposed National workshop on Bioinformatics during March 16 – 20, 2009. 2. Proposed National workshop on Cheminformatics March 23 - 27, 2009. 3. International symposium on Computational and System biology during December 18 - 28,2009 Additional Details
Name of the Coordinator: Dr. K. R. Pardasani Postal Addess: Professor and Head Department of Mathematics Dean Research & Development MANIT, Bhopal Phone Number : 0755-2671633 Mobile : + 91 – 9425358308 Email: [email protected] ,[email protected] website: www.manit.ac.in Name of contact person: Dr. K. R. Pardasani
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Mizoram University, Aizawl Coordinator: Dr. N. Senthil Kumar The Bioinformatics facility has been established in the Department of Biotechnology, Mizoram University, Aizawl sponsored by DBT, New Delhi towards the promotion of Biology Teaching through Bioinformatics (BTBI) (Order No. BT/BI/ 12/042/2007 dt. 11 Feb. 2008 of DBT, New Delhi). The facility has been equipped with the following latest hardware configuration of desktop machines, High and medium end servers and Printers of HP make: Sl. No. Particulars Qnty 1. HP DX 2480 Intel core2Duo, E4600 10 Nos. 2. Medium end server - ML 350G5 1 No. 3. High end server - Proliant ML 370G5 1 No. 4. HP Laser Jet – 2015N 1 No. 5. HP Deskjet printer-L7380 1 No. 6. Toshiba E166copier / A3 scanner 1 No. 7. Software- Winproxy ver 6.0 1 No. 8. Antivirus package Norton-Multi tier with automatic updates (for 10 users) 1 No. 9. Uniline 1KVA online external battery (1 hr back up) 1 No. Basic infrastructure such as independent accommodation, electricity and furnitures needed for establishing BIF have been already made. Proposed activities for the year 2009-10 The importance of the region at the global stage can be vouched from the fact that the region lies within the Indo-Burma mega diversity hotspot. In order to conserve and utilize the rich bioresource, a proper documentation and maintenance of database through bioinformatics tools is the need of the hour. In Mizoram University, under the school of Life Sciences, the Department of Biotechnology, Botany and Zoology have initiated studies on the bioresource of Mizoram region. The Bioinformatics centre will strive to strengthen the research and developmental activities relating to other areas of biosciences. The following agendas have been identified as priority activities of the Bioinformatics centre for the year 2009 -10: • To conduct training and workshops for Master students, researchers and teachers. • To conduct bioinformatics awareness programs for the school students. • Development of bioresource database (Biodiversity Informatics) for flora and fauna of Mizoram, Northeast India. • To initiate various innovative projects in the frontier areas of science, supported by National and International agencies.
Additional details
Dr. N. Senthil Kumar Coordinator (DBT-BIF) Reader, Dept. of Biotechnology Mizoram University, Aizawl, Mizoram – 796 009 Phone Number : 0389 – 2330859 / 2330861 Mobile No. : 09436352574 Email : [email protected]
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Narendra Deva University of Agriculture & Technology, Faizabad Coordinator: Dr. K. N. Singh Overview of the center The Project “Bioinformatics infrastructure Facility (BIF) for the Biology Teaching through Bioinformatics (BTBI) was sanctioned on 7th September 2007 to Department of Plant Molecular Biology & Genetic Engineering, Narendra Deva University of Agriculture & Technology, Kumarganj, Faizabad (U.P.)
Name of centre Bioinformatics facility
Area of specialization Plant Molecular Biology with specific reference to Biotic and Abiotic Stress and transformation
Name of co-coordinator Prof. K.N. Singh, Prof. & Head, Department of Plant Molecular Biology & Genetic Engineering
Name of teaching staff Not yet appointed
Resource created during 2008-2009 • BSNL Broad Band connection with 2MBPS speed • IBM Server high end for database/Application with Intel Xeon Quad Core Processor (4 processors) • IBM Server medium for proxy & file server with Intel Xeon Quad Core Processor (2 processors) • Ten Lenovo desktop computers with core 2 Duo Processor & 19" TFT Monitor. • One 3 KVA UPS for computers & One 2KVA UPS for Servers for continuous power supply.
Major research activities • Used Fingerprinting tool-ClustalW, Map maker and • Biological databases utilization for primer designing, hypothetical gene searching etc. • Searching information through pubmed and other sites. HR development in Bioinformatics Training conducted for ten Participants (Asstt. Professor and SRF) on title “Introduction to Bioinformatics with hands on Internet Browsing and data Searching” from 9 to 10th January 2009. The resource persons are invited from Lucknow & Kanpur.
Impact made Motivated students and young faculties of Agriculture to use bioinformatics tools and support for better research and teaching providing training and demonstration.
Future plan a. Organise training and symposia periodically b. Make information package for local needs especially farmers. c. Data base for Aonla and rice varieties of poorvanchal areas.
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National Institute of Pharmaceutical Education and Research, Chandigarh Coordinator: Prof. P. Rama Rao 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 (PPARa,g,d), Glycogen Synthase Kinase (GSK3), DHFR, hERG, acetylcholineesterase, etc. The therapeutic areas of interest are Diabetes, Malaria, Leishmaniasis, Tuberculosis, 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.
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, 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 Major activities of the centre during the year 2008-09 (i) Workshop on pharmacoinformatics was conducted during 13-15 March 2008. (ii) A 21 days summer school in “Molecular Modeling and Informatics in Drug Design” from June 30 to July 18, 2008. (iii) A symposium on Bioinformatics was conducted as a part of an “International Conference on New Developments in Drug Discovery from Natural Products and Traditional Medicines” SAS Nagar (19th Nov. 2008).
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 Databases & other information resources available from NIPER. CCSD (Chemoinformatics) GCG (Bioinformatics) Details about staff members working in the centre 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.Gopi Mohan, Asst. Prof. in Pharmacoinformatics – specialization, pharmacoinformatics, structural biology, elec- tronic structure analysis, toxicoinformatics, etc.
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.
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
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Ph.D. students are using this facility. All the students of the previous batch of M.S. Pharm. (Pharmcoinformatics) who graduated in July 2008 have found placements. 60 % are in industry, 40% joined academic research.
Initiative to validate the outcome of bioinformatics resources Computational designed drugs have been synthesized and biologically evaluated and found to be promising. 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. Databases/ Software packages developed Alzhemier’s disease database: From Genome to Drug Papers published or presented in the conferences with reference i) Design of Benzene-1,2-diamines as Selective Inducible Nitric Oxide Synthase Inhibitors: A Combined De novo Design and Docking Analysis S.M. Francis, M. Sharma, A. Mittal, P. V. Bharatam J. Mol. Model. 2008 14 215-244 ii) Modeling and Informatics in Drug Design P. V. Bharatam, S. Khanna, S.M. Francis Chapter 1 in Preclinical Development Handbook: ADME and Biopharmaceutical Properties (Ed.) S.C. Gad, John Wiley 2008, 1-46. iii) High-throughput In vitro screening and In Silico analysis to design Structurally Diverse AChE Inhibitors. Shikhar Gupta, Adyary Fallarero, Mikko J. Vainio, P. Saravanan, J. Santeri Puranen, Päivi Järvinen, Mark S Johnson, Pia M. Vuorela, C Gopi Mohan; INTERNATIONAL CONFERENCE ON DRUG DISCOVERY FROM NATURAL PRODUCTS AND TRADITIONAL MEDICINES (DDNPTM-08) “New developments in drug discovery from natural products and traditional medicines” from Nov.16-20, 2008. iv) Mahendra Awale & C Gopi Mohan, Molecular Docking Guided 3D-QSAR CoMFA Analysis of N-4-Pyrimidinyl-1H- indazol-4-amine Inhibitors of Leukocyte-specific protein tyrosine kinase. Journal of Molecular Modelling, Vol. 14(10), p(937-947), (2008). 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. An industrial project on CYPs and site of metabolism with Eli Lilly.
Details of Training/ Workshop organized and total no. of user trained Workshop on Pharmacoinformatics : 13 – 15, March 2008 : 45 teacher participants from pharmacy colleges. Symposium on Bioinformatics during International conference on Natural Products: 19 Nov. 2008 : ~200 participants 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 2008-09 with the collaborative effort.
Future activities Research focus on drug design using pharmacoinformatics, including structural bioinformatics, molecular docking, pharmacophore mapping, electronic structure, metabolome informatics and toxicoinformatics, etc. Site of metabolism studies. Workshop to be conducted in March 2010 in Pharmacoinformatics
Additional details
Name of the Coordinator: Prof. P.V. Bharatam, 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
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National Institute of Technology (NIT), Rourkela Coordinator: Dr. Gyan Ranjan Satpathy The Bioinformatics Infrastructure Facility has been working at the Department of Biotechnology and Medical Engineering at National Institute of Technology, Rourkela, Orissa for last two years. The department of Biotechnology and Medical Engineering at N.I.T., Rourkela is started July 2007, offers B.Tech and M.tech degrees in both Biotechnology and Medical Engineering disciplines. Currently we have seven faculty members engaged in various research activities. Our collective research interests are Animal Cell Culture, Cells and Tissue Engineering, Bio-preservation of Cells and Proteins, Stem Cell for organ and ligament development, Biomaterial Engineering etc. Most of the research activities are in the initial stage. Bioinformatics Infrastructure Facility caters very effectively to the development of this interdisciplinary department having multi-faceted research interests. The aim of the centre is to create human resources in the field of bioinformatics. Currently the facility is used for both research and teaching. We have installed various important softwares and tools for teaching and research purposes. We are teaching our students the practical application of these tools along with the theory behind it. Our M.Tech students are taking a great deal of interest in Bioinformatics research. Four M.Tech. students from 2007-2008 batch had successfully completed their one year dissertation in the facility and four more from current (2008-09) batch are working towards their project work in different areas of bioinformatics. This year one student have joined in bioinformatics related Ph.D program, he will do all his research activities in our bioinformatics infrastructure facility. In this relatively short period of time the centre has established a strong base in Insilco drug and vaccine design, molecular dynamics simulation and biological database management. The students have communicated four research papers in various scientific journals and more are likely to be communicated for publication in near future. Some of the papers and oral presentations produced by the facility are given below. 1) Molecular modeling and docking studies of some novel derivatives of N-phenyl-2-(pyrimidin-2-ylsulfanyl) acetamide as anti SARS protease inhibitors Journal: International Journal of Chemical Sciences 2) Design and study of N-phenyl-2-(pyrimidin-2-ylsulfanyl) acetamide derivatives as inhibitors against SARS virus Journal: Asian Journal of Chemistry 3) Molecular Dynamics Simulations Of Sequentially Varied Human Immunodeficiency Virus-1 Tat P16 Isoform Consensus Protein Structures Sripad Chandan Patnaik, Gyana Ranjan Satpathy Journal of biomolecular structure and dynamics (Under review) 4) “Target identification and drug design for human pathogen Chlamydophila pneumoniae -in silico analysis”, E Harikishan Reddy, Gyan R Satpathy, Online Journal of Bioinformatics Oral Presentation In silico Prediction of Lead Molecules for Migraine Using Blind Docking and Identifying the Active Amino Acids Contributing To the Protein-Ligand Interaction. Akalabya Bissoyi, Gyan R Satpathy, Chinmay Mahapatra
Symposium National Symposium on recent advances in insislico Drug designing December 5-6, 2008 in NIT Raipur The centre has also facilitated students to attend symposium and workshops at different places. Two of the current students had attended the “National workshop on structural bioinformatics” at Birla Institute of Technology, Mesra. Another student had attended the workshop on microarray data analysis at institute of computational biology, Bangalore October and University of Hyderabad, December 1-15. The workshops helped in training the students in various recent techniques. We are seriously planning to conduct a workshop on a current bioinformatics topic for the local college students and researchers. According to the course curriculum of the department we have Bioinformatics Laboratory courses at B.Tech and M.Tech level, the infrastructure facility is conducting them gloriously. The bioinformatics classes and labs are carried out in the facility. The facility is serving its fruitful purpose to an elite institution like National Institute of Technology, Rourkela.
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Looking back to its successful period as a research and training facility and the location at an organization of national repute I would explore the possibility of upgrading the facility to sub-DIC from BIF so that it can serve its purpose more appropriately. I want to convey my gratitude for granting funds for establishing Bioinformatics Infrastructure Facility at Department of Biotechnology and Medical Engineering, National Institute of technology, Rourkela. I hope with the assistance of the Department of Biotechnology, Govt. of India we will be successful in fulfilling the purpose of establishing the facility and will lend our honest part in teaching and research of bioinformatics.
Additional details
Name of Coordinator: Gyana Satpathy Professor and Head, Department of Biotechnology and Medical Engineering, N.I.T., Rourkela, Orissa 769008, INDIA. Phone: 0661-2462261 (O), 0661-2463261 (H), +91 94375 79091 (M) Email: [email protected]
211 Bioinformatics Infrastructure Facility (BIF) for Biology Teaching Through Bioinformatics (BTBI)
North-East Institute of Science and Technology, Jorhat Coordinator: Dr. R.L Bezbaruah Introduction North-East Institute of Science & Technology (NEIST), Jorhat is the only CSIR laboratory in the entire North Eastern Region of India to provide R & D inputs for the effective use of material resources of the region as well as to develop indigenous technologies based on the natural wealth of the region for improving the economy in the rural area. Under these mandates, the Biotechnology Division of the Laboratory has been exploring microbial diversity in NE Regions to be used for biocontrol, induction of resistance to control different pests and diseases, plant growth promotion, fermentation, biotransformation, bioremediation etc. The addition of the Bioinformatics Infrastructure Facility (BIF) at NEIST, Jorhat will boost up the research activities of the institute.
Bioinformatics Infrastructure Facility The Department of Biotechnology, Govt. of India vied sanctioned no. BT/BI/12/042/2007 dated 11/02/2008 sanctioned Rs. 20 lakhs for this facility at NEIST, Jorhat. The first installment Rs. 15 lakhs was received on 06/05/2008 by this institute. Already NEIST has got ten computers, two servers, two laser printers, one scanner, one UPS and broadband internet connection. The BIF room with the computers is in working condition.
On going activities of the BIF 1. Arranging lectures for students & scientists of NEIST. 2. Arranging lectures for college students. The lectures and presentations delivered are: a) “Sequence Analysis and Alignment – Introduction to Biological Sequence database, BLAST, ClustalW, Jalview and CLC Workbench” on 28th May, 2008 b) “Central Dogma of Molecular Biology (Gene Expression) – Animated Video” on 27th June 2008. (14 undergraduate biotechnology students of Pandu College, Gauhati attended the lecture) c) “Introduction to Bioinformatics” on 3rd July, 2008. (14 undergraduate biotechnology students of Pandu College, Gauhati attended the lecture) d) “Protein Exploration (Molecular Visualization Tools) – Software’s Displaying Protein Data Bank (PDB) files” On 22nd August, 2008 e) “Lac operon and Trp operon” on 4th September 2008 f) “Chemical Informatics – ChemOffice 2008, Chemical and Ligand Databases, Bio Activity Prediction” on 31st October, 2008. 3. Publishing bioinformatics newsletter form June, 2008 onwards – 8 issues already published. 4. Provide Bioinformatics solutions to the scientist of NEIST, Jorhat such as: a) Sequence analysis and phylogenetic analysis for Aspergillus elegans strain SM01 using EBI ClustalW Server and Jalview b) Comparative study and restriction Site analysis for Pseudomonas aeruginosa strain RRLJH2 using CLC Sequence Viewer c) Plotting plasmid using pDRAW32. d) PCR primer designing for Sesbania rostrata using primer 3 web server e) Chemical structure drawing and biological activity predication of 2-methylheptyl isonicotinate and octyl isonicotinase using ChemOffice2008 – ChemDraw and PASS (Prediction of Activity Spectra for Substances) Future Activities 1. To provide hands on training on bioinformatics to the students and scientists of NEIST, Jorhat. 2. To provide lectures on bioinformatics and biotechnology topics to the graduates and post graduate students of the nearby institutes. 3. To provide training program on scripting languages like PERL, programming languages like C, front end tools like Visual Basic for developing bioinformatics applications. 4. To upgrade the center with most modern techniques and software’s. 5. To collaborate in research activities with other North-East Bioinformatics Centers.
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North Eastern Regional Institute of Science & Technology, Nirjuli Coordinator: Dr. S. Sureshkumar Singh Department of Biotechnology, Govt. of India had approved the proposal for establishment of Bioinformatics Infrastructure Facility (BIF) at NERIST on February 14th, 2008 for promotion of Biology Teaching though Bioinformatics. In this regard, DBT had sanctioned a sum of Rs. 20 lakhs (Rupees Twenty lakhs) only towards the establishment of BIF at NERIST. An initial grant of Rs. 15 lakhs (Rupees Fifteen lakhs) only had been received by the Institute as first installment out of the total grant of Rs. 20 lakhs by April, 2008. With the approval and sanctioning of the BIF at the institute, the following activities have been taken up to establish and functioning of the facility at the institute. 1. The Institute (NERIST, a Deemed University under Section 3 of UGC Act 1965) has provided an independent accommodation (22 x 36 ft) on the ground floor of the Central Library Building of the Institute for establishment of BIF. 2. As per DBT guideline, an executive committee of six (6) members was constituted to look after the functioning and progress of the BIF. 3. Similarly, a purchase committee of five (5) members was also constituted to deal with the matters related to purchase of requirements for the BIF. 4. An Action Taken Report (ATR) was submitted to DBT by 30th June, 2008. 5. The procurement of the required minimum requirement (as per DBT guidelines) for establishment of the BIF is on progress and expected to be completed by February, 2009. 6. The first executive meeting of the BIF is scheduled to be held before the formal inauguration of the centre in the last week of February, 2009 Calendar of Trainings /Workshops in Bioinformatics during 2009-2010 1. First (1st)training/ workshop of the centre is scheduled to be held from 26-28th February, 2009 with title theme on “Applications of Computer and Internet in Biology Teaching and Research” 2. Second (2nd) training/ workshop of the centre is scheduled to be held from 6-8th August, 2009 with title theme on “Bioinformatics-Tools, Techniques & Applications” 3. Third (3rd) training/ workshop of the centre is scheduled to be held from 12-14th November, 2009 with title theme on “Bioinformatics Software-Database Development, Management and Applications” 4. Fourth (4th) training/ workshop of the centre is scheduled to be held from 4-6th February, 2010 with title theme on “Applications of Bioinformatics in Biological and Biochemical Research” 5. Fifth (5th) training/ workshop of the centre is scheduled to be held from 1-5th June, 2010 with title theme on “Vacation Training on Bioinformatics for Biology Teachers of School and Colleges” 6. Sixth (6th) training/ workshop of the centre is scheduled to be held from 7-9th October, 2010 with title theme on “Recent Advances in Bioinformatics II: Protein Structure and Sequence Analysis” 7. Seventh (7th) training/ workshop of the centre is scheduled to be held from 27-29th December, 2010 with title theme on “Recent Advances in Bioinformatics I: Nucleic Acid Analysis”
Name of Coordinator: (Dr. S. Sureshkumar Singh) Postal Address: DBT-Bioinformatics Infrastructure Facility (BIF) Ground Floor, Old Block Central Library Building North Eastern Regional Institute of Science & Technology (NERIST) (Deemed University), P.O. Nirjuli-791109, Arunachal Pradesh Mobile: 09436248307; 09436635137 Phone No: 0360 2257 401 to 415 (Extn. 6468/ 6251) Fax. No: 0360 2258533; 2244307; 2257872 E-mail : [email protected]; [email protected] Website: http://www.nerist.ac.in
213 Bioinformatics Infrastructure Facility (BIF) for Biology Teaching Through Bioinformatics (BTBI)
North Orissa University, Baripada Coordinator: Prof. S. K. Dutta Summary of the progress made by the centre from its inception Bioinformatics, the convergence of information technology and biotechnology, which is the present day frontline discipline in science, has been attaining rapid developments in India. Bioinformatics Centre at North Orissa University was started in June 2007, as a part of National Bioinformatics network under the programme, Biotechnology Information System (BTIS) established by Department of Biotechnology, Government of India. This facility is providing bioinformatics support pertaining to the different research activity going on at NOU particularly functional genomics and proteomics. Apart from this, the total net working, web site management, mail server etc are fully dependent on this facility. The communication facility at the centre is strengthened by the 100 Mbps leased line internet connectivity from BSNL. The Centre conducts training programme in Bioinformatics for faculty working in the University and procures databases in the field of life sciences and related domains. A (2+2) credit course in Bioinformatics is offered to the Postgraduate students of Bioinformatics, North Orissa University.
Major research activities in Biotechnology The work carried out at Zoology Department includes Barcoding of Anuran, genomic library construction and cloning & drug designing of medicinal plants.
Major activities of the centre during the year 2007-08 a. The BIF got established in a near building which is also shared by the Biotechnology Department. b. Established a leased line connectivity of 100 Mbps speed at the Bioinformatics centre, from BSNL (Broadband). c. Meeting of Executive Committee Members was held 3 times. d. The centre purchased books and journals from the initial grant. e. The centre provided teaching to M. Sc. Bioinformatics students.
Infrastructure facilities in Bioinformatics Centre a. Scientific software packages: The centre has a good collection of commercial and public domain software’s covering a wide range of applications like sequence and structure analysis, molecular modeling and simulations, structure prediction and drug design. The software’s available are: Omiga, Rasmol, Qmol, Pymol, Genedoc, Bioedit, Isisdraw, Treeview, Mega, Clustal X, Gene pup, NTB Win, Sequin, DAMBE, PCCORD, Network, Python, Perl, AutoDock tools. Types of services provided a) Training programmes for faculty, technical staff, research scholar & students of NOU. b) Literature search by means of CD ROM and Internet. c) Offering courses in Bioinformatics to PG students. d) Support to R&D activities for PG student (projects) in Life sciences. Initiative to validate the outcome of Bioinformatics resources A national workshop on “Basic tools and Techniques in Bioinformatics and Biotechnology” will be held from 30-31 March, 2009, which will helpful for Scientists, faculties and research scholars of this university as well as other institutions. Main Thrust Area of the seminar are a) Functional Genomics & Proteomics b) Sequence Analysis c) Database and Software development in biotechnology Future activities Future activities would be to initiate Bioinformatics research in collaboration with Biotechnology, to create a digitized database of the existing data on Barcoding of Anurans. The Centre proposes to conduct training programmes for faculty, technical staff, research scholar & students. Other activities would be enabling of CD-ROM search facility, E print facility, development of teaching aids [practical manual] in Bioinformatics, Open journal accessibility for M.Sc students, and procurement of Books and Journals in Bioinformatics.
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Orissa University of Agriculture & Technology, Bhubaneshwar Coordinator: Dr. P. N. Jagadev 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 BTISnet” 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. i) During the previous years 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, besides 38 no. of PCs and GCG software of the PG Dept of Bioinformatics are available for the project work. ii) A new well furnished building had been constructed during the last year and the project has been shifted to the new building during November’ 08. iii)The Dept. of Bioinformatics has been accredited by the ICAR in 2008.
Major research activities in Biotechnology and its related fields 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 include sequence analysis, computational biology and development of biological databases besides offering a two years regular course with an 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.
Area of Specialization of the Centre: Biotechnology and Bioinformatics. 4. Major activities of the centre during the year 2007-08: During the year 2007-08 thirty Post-Graduate students (Bioinformatics) have done their dissertation project works in the areas of database development, Molecular Modeling and Drug Designing etc. for their M.Sc. degrees.
Infrastructure facilities in the Bioinformatics Centre A. Computer & Communication facility: Forty-eight PCs with 2048 kbps internet connectivity and two numbers of high-end servers and one medium end server with operating system are available. B. Scientific Software packages : GCG Wisconsin package, java, LINUX, UNIX, XL stat, Antivirus packages . C. Databases & other information resources: Oracle 10G, Microsoft SQL Server, Ricebase, Fusabase.
Details about staff members working in the centre
* The absorption status of the above staffs is on contractual basis.
Types of services provided The centre has provided the facilities of computer lab and twenty four hours internet facilities to the post-graduate students and teachers/scientists of the sister departments like Biotechnology, Pathology, Horticulture, Soil Science and
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Biochemistry, Plant Breeding and Genetics etc. for their dissertation and research work, besides rendering the computational knowledge to them.
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 interviews. During the previous years our students have been working at JVK Bio Science, Hyderabad, Mahatma Gandhi Institute of Medical Sciences, Wardha, RCM, Bhubaneswar, GIET, Gunupur, Orissa, Berhampur University, Orissa NEHU, Shillong, SVINMS, Tirupati, SGIPGMS, Lucknow etc.
Initiative to validate the outcome of Bioinformatics resources Actions have been taken to validate the Bioinformatics resources. For example a booklet was developed incorporating the abstract of the theses research works of students’.
Collaborative works/initiatives During the year 2007-08, students had done their dissertations at different reputed institutions and laboratories like, ITRC, Lucknow, WB University, Kolkata, Biotech Park, Lucknow, GVK Biosciences, Hyderabad, Satya Informatics, secunderabad, MGIMS, sevagram, wardha, NEHU, Shillong, NIMHANS, Bangalore, JNU, New Delhi for their partial fulfilment of M.Sc. Bioinformatics degree.
Databases / Software packages developed One CD-ROM database on rice genotypes available at OUAT research station is developed.
Papers published or presented in the conferences with reference i) Paper entitled “A tool-cum-database for identification of grnus Xanthomonas causing plant diseases” accepted for poster presentation in InCoB (Seventh International Conference in Bioinformatics) held at Taipei, Taiwan during october 20-23, 2008. ii) Paper entitled “Ricebase: A database of rice genotypes of Orissa” accepted for poster presentation in InCoB (Seventh International Conference in Bioinformatics) held at Taipei, Taiwan during october 20-23, 2008. iii)Paper entitled “ Tuberoculosis vaccinogenomics database: an immuno-informatics approachfor rational peptide vaccine design using Mycobacterium tuberoculosis H37RV proteins” accepted for poster presentation in InCoB (Seventh International Conference in Bioinformatics) held at Taipei, Taiwan during october 20-23, 2008.
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 tools for bacterial plant pathogens, database on rice genotypes of Orissa and Fusarium are developed in the department of Bioinformatics.
Details of Training/ workshop organized and total no. of user trained A two days National Workshop-cum Training was successfully organized from 14-15 March, 2008 with 26 numbers of participants and 8 Nos. of Resource Person from different R &D organizations and Institutions of National repute.
Impact shown by your centre on growth of biotechnology and allied areas Our centre is helping the students of this university and other Universities for their dissertation and works in the biotechnology and allied areas.
Future activities i) To organize hands on training, workshops and seminars 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 food crops.
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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: 0674-2565760/2565761, 09861128437 Fax: 0674-2397424/ 2397780 Email: [email protected] [email protected] Name of Contact Person: Dr. Sashikala Beura, Associate Professor Dept. Horticulture, OUAT, Bhubaneswar-751003, Orissa. Email: [email protected]
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Presidency College, Chennai Coordinator: Prof. S. Rajarajan An interactive and interesting online website www.bifcpresidency.tn.gov.in had been launched in March 2008 to provide online information on the activities the centre. A unique database on antibiotics of microbial origin had been prepared and made available for free online use and reference through the centre’s website from March 3,2008. So far 900 Institutes/Scientists have visited and benefited by the database. A 7-day (04.08.2008 to 11.08.2008) National Workshop on the Application of Bioinformatics on the discovery and Development of Drug was organized . The target group for the workshop was Post Graduates and Final Year P.G students. Twenty two Post Graduate delegates from all over India had participated in this important workshop. Dr. T.MadhanMohan, Adviser, DBT, Government of India had inaugurated the workshop. Dr.P.Gautham, Head, Centre of Biotechnology, Anna University delivered the key note address on “ Molecular Modeling and docking studies of some drugs like biomolecules”. A memorandum of Agreement was signed between Department of Virology, King Institute of Preventive Medicine and Bioinformatics Infrastructure Facility Centre of DBT, Presidency College on 04.08.2008 in the presence of Dr.T.Madan Mohan, Adviser, Department of Biotechnology (DBT),New Delhi for the development of efficacious vaccines with the application of Bioinformatics. Prof. S. Rajarajan, Coordinator attended the International Conference of Bioinformatics (InCoB 2008) at Taiwan on October 20,2008(with the financial assistance from DBT) and presented a paper entitled on “A Comprehensive And An Update Antibiotic Database On Essential Features Of Antibiotics Of Microbial Origin With Special Emphasis On Bioinformatics” in the Technology Track session. One hundred and thirty-seven (137) M.Sc, 19 M.Phil and 31 Ph.D students have been benefited by this centre. Ten teachers have been able to get funded project, utilizing the centre. Two candidates, under newly sponsored studentship and traineeship program have been absorbed. To meet the demand of increase in the users of the BIFC, Five more Think centre Desktops-M series: M58p,Part: A14, Operating system: Genuine Window Vista Business,1GB RAM, Mother Board: 8E400, Processing speed: 3.1 Gigabytes, Graphic 3100,DVD recorder, optical system with three years parts and labour warranty were installed along with computer furniture, a printer, 4KVA UPS and 1.5 ton A/C. Many students inclusive of two students from other states (Kerala) were benefited by the centre in their M.Sc projects on Bioinformatics. Activities of bioinformatics infrastructure facility centre of dbt, presidency college, Chennai during the year 2009-2010. The centre will be equipped with five more computers as the strength of the users consistently increase and many institutions prefer to send their students to train and do their project on Bioinformatics at this centre. The centre hopes to have a video conferencing system with the help of DBT to share its knowledge and expertise of Bioinformatics in Biology in general and in drug discovery & development in particular in an interactive manner with the students & teachers of prevailing and upcoming institutions of greater Chennai and to benefit the college teachers in semi urban and remote/rural areas. On the database front, development of database on semi synthetic and completely synthetic antibiotic will be completed and will be made available on online in 2009. A 10- days workshop for under graduates in science on the “General Application of Bioinformatics in relation to Biology will be conducted to inspire them to opt for Bioinformatics in their higher studies during May 2009.
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Rajiv Gandhi University, Itanagar Coordinator: Prof. A. K. Das The Bioinformatics Infrastructure Facility (BIF) Centre was established in the year 2007 with financial assistance of Rs. 20 lakhs from the Department of Biotechnology, Govt. of India. The centre is providing the infrastructural facilities to the students, young lecturers, research scholars and faculty of Life Sciences to expose and accrue the benefit of application of computer and information science (Bioinformatics) in the field of biological sciences. The Centre has well established Bioinformatics infrastructures with the following equipments Hardware: Server HP ML 350G5 1 No Server HP ML 370 G51 No Desktop system with OS 10 Nos HP Printer Desk Jet D4268 1 No HP Printer Laser Jet P3005dn 1 No HP Scan Jet G2410HP 1 No HP Scan Jet G3010HP 1 No Software: Visual audio 1 No Red Hat Linux Ent edi. 4 1 No MS Office 2007 1 No Bioinformatics Software Swiss-PdbViewer Rasmol MolMol Clustal W Phylodraw CN3D ArgusLab Mega2, etc The above systems are housed in a completely dust free and air conditioned room which is accessed by the Ph. D. scholars and M.Sc. students of the university. The centre is providing lectures and practical training to the M. Sc students of Botany and Zoology for the bioinformatics part of their syllabus.
Conduct of three days Workshop The Centre had organized a three days workshop tiled “Bioinformatics for the Biologists” during 3-5 March 2008 aiming at training young faculty members and Ph.D. Scholars of the region. Subject experts were invited from North Eastern Hill University, Shillong, Tezpur Univers ity, Tezpur and IBSD, Imphal. Besides, resource persons were also requisitioned from our own University. Participants were enlightened with Computer basics and computational biology, data base and data mining as well as use bioinformatics tools in establishing phylogenetic relationships. As many as thirty one participants attended the three days workshop. The centre had organized a lecture on “Application of Bioinformatics” by Dr Alok Dhawan, Senior Scientist, ITRC Lucknow
Future programs Training and workshops: Training and workshops will be conducted (at least twice in year) covering the following broad subjects: • Computer basics and application in bioinformatics • The role of computational biology • Algorithms and tools for phylogenetic analysis • Genome and Proteome Analysis • Bioinformatics in environment and Biodiversity • Data base and Data mining
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Database of flora and fauna Preparation of digital data base of flora and fauna of Eastern Himalayan region is another priority of Bioinformatics Centre. The centre has started the work on database development on the different flora and fauna of the Himalayan Biodiversity Hotspot. The Centre of Biodiversity, Rajiv Gandhi University could generate considerable amount of field data relating to fish and insect diversity including butterflies of the region. Similarly considerable amount of specimens are collected covering higher plants, macro fungi and soil microbes. As regard to higher plants considerable amount of information could be generated about the use pattern of plants by the indigenous communities. Such ethnobotanical and ethnomedicinal knowledge base about the plants could be important source for some potent drugs. Hence, digitalization of all those data could be of immense utility.
Awareness among school children The centre is also providing awareness programme to the school going children on the conservation of Bioresources by using audio visual like short movies, documentary films and print media. The centre also provides computer basics and computational biology, web surfing and data retrieval etc to acquaint themselves with the latest trend in life sciences and to make them interest in the subject.
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St. Anthony’s College, Shillong Coordinator: Dr. M.A. Laskar The Bioinformatics Centre (Bioinformatics Infrastructure Facility) at St. Anthony’s College, Shillong has been established with the grant (first release) received from the Department of Biotechnology, Government of India. The BIF, named as “Bioinformatics Centre”, is located in a 500 sq. ft room located in the main building of the College and can be accessed easily by all authorized users. Adequate measures have been taken by the College authorities to ensure round-the-clock security of the BIF. The Infrastructure that exists in the Bioinformatics Centre is detailed below:
Hardware: A. Networked Computer System: The BIF has a networked computer system in which a main server and a proxy server are connected by LAN to 27 clients. The servers and the clients have been assembled by qualified technicians of the college. The configuration of members of the network system is given below. i. Main Server: Processor: Intel QUAD Core 2 Duo 2.4 Ghz Xeon. Mother Board: Intel S5000VSA. Memory: Zion 2GB ECC (4 nos.). Seagate HDD 160 GB SATA. AOC 17" CRT flat monitor, Sony DVD writer. ii. Proxy Server: Processor: Intel Core 2 Duo 2.4 Ghz. Mother Board: Intel DG 31 PR. Memory: Zion 2 GB DDR 667 MHz (2 nos.). Seagate HDD 80 GB SATA. AOC 17" CRT flat monitor, Sony DVD writer. iii. Clients: Same as proxy server, except, memory: Zion 2 GB DDR 667 MHz (1 no.). B. Printers etc: One each of: Dot Matrix Printer (Epson LQ 1150 II). Laser Printer (HP 2650, Colour). Scanner (HP Scanjet G3010). Audio Speaker System: Creative SBS A500 5.1 channel. Head Phones: iball ( 15 nos). Web cam: Logitech (4 nos).
Internet Connection: A direct telephone line leased from BSNL was provided by the College. Broadband connection (512 kbps speed, unlimited data download volume) has been procured from BSNL. The ADSL Modem (Siemens C2110) was purchased outright as part of the package.
Software: A. Systems software: The academic license provided by Microsoft Corporation to St. Anthony’s College, Shillong for Windows Server 2003 (for main server), ISA 2006 server (for proxy server) and Windows XP, has been extended to the BIF. B. Application Software for Biology Teaching: i. Geneious Pro. Ver. 4.5.2 (Biomatters, New Zealand): This software will be used to teach students/trainees the basic concepts of bioinformatics. Trainees will learn how to carry out sequence alignments, search for ORFs, motifs and transcription factor sequences, study protein 3D structure and to design PCR primers. They will also learn how to conduct in silico reverse transcription and mutation studies. Geneious Pro will be used extensively in the training programmes that are to be started in the near future. The target groups for the training programmes will be life sciences teachers and students of undergraduate and postgraduate levels. Care will be taken to include applicants from other educational institutes in Shillong and rest of Meghalaya. Special training sessions for applicants from rural areas of the state are also planned. Twenty four Single User Academic Perennial Licenses have been procured. ii. NTSYS pc ver. 2.02r (Applied Biostatics Inc., USA): One Single User Academic Perennial License has been purchased. This software will be used to teach students how to analyze and interpret multivariate data generated from molecular markers-based wetlab studies on biodiversity of plants and animals. The post-graduate students of Biotechnology of the College will utilize it more often. Training programmes will also be conducted for people who teach and\or carry out research in molecular phylogeny and biodiversity. iii. FelxX (Biosolveit, Germany): This software was purchased to provide opportunity to students to deepen their understanding of protein-ligand interactions and to gain first-hand experience on virtual screening of compound libraries and identification of hit molecules. Such training will increase the employability of students, especially in corporate houses involved in development of prescription drugs. FlexX will be used to train the postgraduate
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students of Biotechnology of the College and the other groups as mentioned in the section for Geneious Pro. One Single User Academic License has been purchased for three years. Books and Journals Ten titles in the areas of Bioinformatics and Information Technology have been procured. Subscriptions have been made to seven journals that are in the areas of Life Sciences and Bioinformatics and published in India by NISCAIR (3 titles), Indian Academy of Sciences (3 titles) and Bioinformatics Institute of India (1 title). The modalities of training programmes (as indicated above under the head ‘Software’) are being prepared. Schedules of such programmes, reports on these and feedback from participants will be communicated to the Adviser, DBT, GOI. The above report was prepared and communicated by Dr. M.A. Laskar, Coordinator, Bioinformatics Centre, St. Anthony’s College, Shillong (Meghlaya)
Contact details
Dr. M.A. Laskar, Dept. of Biotech. St. Anthony's College, Shillong Contact no. 9463118118, 0364 2211955
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St. Aloysius College, Mangalore Coordinator: Fr. Denzil Lobo SJ Objective of the Bioinformatics Centre The Bioinformatics centre aims to deep and broader the understanding of Bioinformatics and train all the Teaching Faculty, Research Scholars and students in and around Karnataka with hands on experience on the same which will help them in using the appropriate tools and software’s to support their research work.
Work Done in 2008 Infrastructure: • A Fully furnished Lab with 20 personal Computers • 1 Cannon LBP3360 laserhot Printer • Ethernet 10/100 base network.
MOU Signed: An MOU was signed with Sai’s Biosciences Research Institute, Chennai Seminars / Workshops Conducted: • A National Workshop on Bioinformatics was conducted on July 10th 11th & 12th July 2008 • A National Workshop on Bioinformatics & Bio sequence Analysis was conducted on 5th, 6th, 7th November 2008 Student Projects: • The Post Graduate Bioinformatics are doing their Projects in our Labs. • Diploma Classes: • Regular Diploma Classes are conducted for the Undergraduate Students of the college for an hour along with hands on Practical training.
Forth coming planes for the year 2009-2010 • Workshop on “Bioinformatics- A Green Field for Research” Dated- 19th, 20th, 21st February 2009. OBJECTIVE: To Promote the awareness of Bioinformatics tools for Genomic and Proteomic analysis and Hands on Training in Basic Bioinformatics Tools and Software’s. METHODOLOGY: Lecture, Demonstration and Practical sessions with hands on Training. LEVEL OF PARTICIPANTS: Undergraduate students Form any life Science background. • Workshop on “Bioinformatics in Genomics and Proteomics” 16th, 17th 18th April 2009. OBJECTIVE: To provide the researcher’s hands on training on various use of bioinformatics Tools and their applications in genomics and Proteomics METHODOLOGY: Lecture, Demonstration and Practical sessions with hands on Training. LEVEL OF PARTICIPANTS: M.Sc., Ph.D Students and Teachers of College and universities. Paper presentation on “Genome and proteome Analysis”21st August 2009. OBJECTIVE: To provide a platform for the upcoming researchers to exhibit their talents and present their research papers. LEVEL OF PARTICIPANTS: B.Sc., M.Sc., And Research Students.
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St. Edmund’s College, Shillong Coordinator: Mr. J.M Sen, Head, Deptt. of Biotechnology
Bioinformatics is conceptualizing Biology in terms of molecules and applying “informatics techniques” (derived from disciplines such as applied mathematics, computer science and statistics) to understand and organize the information associated with these molecules, on a large scale. It explores new ways for approaching biological problems and aims at the comprehension of basic principles of Biology. Bioinformatics interacts strongly with modern structural, molecular and environmental biology, as well as with pharmaceutical and medicinal chemistry. Nowadays, the field is rapidly developing worldwide; several important goals have already been accomplished, while large investments from various sources are continuously attracted. Bioinformatics occupies a central position in the recent developments of Life Sciences, with the soundest example being the analysis of data derived from all genome sequencing efforts, including the Human Genome Project. The major advancements in Molecular and Structural Biology during the last decades, along with the development of large-scale genome technologies and the need to study complex biological systems, have led to the exponential growth of the biological information produced. As a direct consequence, a need has emerged to develop algorithms and computational tools, as well as to adapt existing technologies, in order to store, manipulate, analyze and display biological data. The Principal and the staff of department of Biotechnology heartily welcome the BTIS NET facility conferred to the college by DBT. This facility would render valuable services to the science students as they have project work during the final year of the degree and by this facility they could avail vast resources that are available online. This facility would also facilitate the teaching staff to carry on their research. Since this facility is at the juvenile stage but still the coordinator are henceforth looking forward to make this to develop databases of biological significance, organizing workshop for students and teachers, use of best possible teaching kits available for students etc.
Phone: 9863025415: Email: [email protected]; [email protected]
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Sant Gadge Baba Amravati University, Amravati Coordinator : Dr. Prasad A. Wadegaonkar Summary of the progress made by the centre from its inception Bioinformatics infrastructure Facility has been 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 and is being upgraded to 512 kbps. 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. Two training programs have been organized and facility is being used regularly by students, researchers and faculty for open access, books, video lectures and journal on various subjects.
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 under 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), identification and characterization of Phoma using RAPD-PCR and ITS rDNA sequencing (UGC sponsored) and 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) for production of secondary metabolites using bioreactors and search for Apoptosis inducts in herbs (UGC sponsored). Mr. A.K. Gade is working on biosynthesis of silver nano-particle and Mr. S.D. Kove is carrying out metagenomic studies of Lonar crater (UGC sponsored).
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 Photocopier (Cannon) Lease Line 256 kbps Scientific Software packages GenoCluster, Geneious, Bio-edit, ClustalW, GeneDoc, RasMol, TreeView, ACD/Chemsketch, Fermisym, Polymath.
Types of services provided BIF has collection of books in PDF format on Bioinformatics, Genetics, Molecular Biology, Biochemistry, Immunology etc. and other teaching resources in flash animations, which are loaded on server and made available to students through LAN. LAN based E-portal has been developed which provides links to more than 200 hours video based lectures on Bioinformatics, Biochemistry, Molecular Biology, immunology etc. These links are also made available on www.bioinformaticscentre.schools.officelive.com. BIF has also provided Internet access to DST FIST Computer facility, classroom and laboratories of the faculty members.
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.
Databases/ Software packages developed Database of Melghat Flora Database of Phytochemicals (On going) Database of Industries India involved in phytochemicals (On going) Initiation of R&D activities in Bioinformatics Comparative genomics of Clostridium Sp. Comparative analysis of protease inhibitors from plant origins.
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Details of Training/ Workshop organized and total no. of user trained Training Program on Bioinformatics in Data Analysis of Genes and Proteins was organized from September 5-7, 2008. Total 15 participants were trained during the period. During the training period special lectures were delivered by Dr. Indira Ghosh, Dean Information Technology, JNU, New Delhi. Along with participants, over 150 students, research scholars and teaching faculty attended the lectures. Prof. B.C. Harinath and Prof. S.P. Modak delivered invited talk which was attended by faculty, researchers and students of Biotechnology, Botany and Zoology Departments.
Impact shown by your centre on the growth of biotechnology and allied areas Eleven PG students and Research scholars, who used the computational facility of BIF, have been selected and represented the university in Inter-University Research Festival “Awishkar 2008”, at SGB Amravati University, Amravati. Three participants ranked first position in various categories.
Contact Details
Nname of Coordinator: Dr. Prasad A. Wadegaonkar Bioinformatics Infrastructure Facility Sant Gadge Baba Amravati University Amravati 444602, Maharashtra Phone Number: 0721-2662207 ext 267 Mobile: 09422157263 Email: [email protected], [email protected] Web address: www.bioinformaticscentre.schools.officelive.com
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Sardar Vallabh Bhai Patel University of Agriculture and Technology, Meerut Coordinartor: Dr. Raghvendar Singh Summary of the progress made by the center from its inception The Bioinformatics Center (BIC) at Sardar Vallabh Bhai Patel University of Agriculture and Technology has been setup in September, 2006 with the support of Department of Biotechnology (DBT), Ministry of Science & Technology under the Biotechnology Information System Network (BTIS) program. The Center is specialized in the field of Biotechnology and has been catering the need of teaching, training and research using bioinformatics tools related to different departments of college of Biotechnology of the university and other nearby organizations.
Major activities of the center during the year 2008-09 Inauguration of the Center Project trainings to the graduate and postgraduate Students Training on Bioinformatics tools and its application in Biotechnology Collaborative research projects Participation in seminars and symposia on Biotechnology Strengthening of the Infrastructure facility Teaching of bioinformatics courses to the B.Tech and M.Tech (Biotech) students Organizing international seminar in biotechnology and bioinformatics Infrastructure facilities in the Bioinformatics Center Computer & Communication facility Server (High end) Server (Medium end) Desktops Intel Pentium Dual Core 2.8 GHz Laser Printer (Network) HP 3600N Desk-Jet Printer HP 1020 Notebook Hp LCD Projector Internet facility Toshiba Photocopier Machine Scientific Software packages Lasergene 7.2 DNA sequence analysis software, BioEdit, Geneious Pro, Treecon, Modeller,
Types of services provided Teaching of graduate and postgraduate course in bioinformatics Scientific literature search and retrieval Students project training in bioinformatics Students research work in bioinformatics Biological database development Educational activities with details of placement Students of B.Tech- Biotech are being periodically trained through offering six month bioinformatics course M.Tech in Biotechnology has been started The project training is given to four students Initiation of R&D activities in Bioinformatics The following research proposals are being developed for post-graduate students In-silico study of Lactoferrin In-silico analysis of Lectins and their comparative study with major milk proteins. Molecular Modeling of Leptin Receptor and Binding with C-reactive protein In silico analysis of citrus yellow mosaic virus (CMBV) infecting Rangpurline In-silico characterization of Tomato leaf curl virus DNA A isolates retrieved from NCBI database
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In-silico characterization of Cotton leaf curl virus DNA â isolates retrieved from NCBI database Future activities Establishment of Agri-Information center for quick transformation of advance agricultural technology for the farmers of western U.P. To organize long-term training programmes and national/international symposium on Bioinformatics and Biotechnology To develop Bioinformatics training manuals Update and Modify facilities and website of the center To provide Traineeship and Studentship to the research scholars Modernization of the present Infrastructure facility 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 To prepare the information resources on research advances on wheat, rice, vegetable, dairy husbandry and beneficial microbes Advance Diploma and post graduate degree course will be started in Bioinformatics if approved. Additional Details
Name of Coordinator: Prof. Raghvendar Singh, Bioinformatics Center, College of Biotechnology, SVP University of agriculture & Technology, Meerut Phone Number: 0121-2411534, 2411565 Mobile: 09410816513 Email: [email protected]
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Sri Krishnadevaraya University, Anantapur Coordinator: Prof. Chitta Suresh Kumar Summary of the progress made by the centre from its inception The BIF has been set-up in August 2008 with and advisory committee having Prof. P. Gautam, Centre for Biotechnology, Anna University, Chennai as expert from the near by BTIS Centre. The BIF is catering the needs of all departments of Host institute and organizing the theory and practical course work as part of their Post Graduate studies in Biochemistry, Biotechnology, Microbiology, Botany, Zoology and Sericulture, Chemistry, Physics. In addition the DBT-BIF is also proposed to offer PG Diploma in Bioinformatics and Drug Design. The first activity of the BIF was organization of National workshop on “Protein Modeling of Drug Targeted Proteins in Genomic Era” from Dec 26 -28th 2008. Recently another program “Bioinformatics Workshop for Pharmacy Students” has been organized during 3rd to 5th Jan. 2009.
Major research activities in Biotechnology and its related fields at your institution Genomic analysis of Mycobacterium tuberculosis for Protein targeted In Silico Drug Design Plasmodium falciparum genome analysis for development of anti-malarial drugs and vaccine development using in silico techniques Sequence analysis of genes involved in salt stress in ground nut and fox-tail millet Proteomic approach and studies on salt stress protein expression Area of Specialization of the centre : Molecular Modeling, Dynamics, Docking and Drug Design. Major activities of the Bioinformatics Facility (BIF) during the year 2008-09 The BIF organizes the course of Bioinformatics and Computational Biology to PG students of Biochemistry, Biotechnology, Microbiology, Zoology etc., of host as well as nearby institutes. The facility also provides support for retrieval of material for seminar presentations, online literature survey and data analysis, bioinformatics analysis and use of specialized molecular modeling and drug design software. In addition the DBT-BIF is also offering PG Diploma in Bioinformatics and Drug Design The BIF is helping M.Sc. and Ph.D. students of Bioinformatics in teaching, research projects and finalizing their dissertations/thesis. M. Pharmacy – Computer Aided Drug Design : The entire course work for 2 years of M. Pharmacy (Computer Aided Drug Design) offered by College of Pharmacy, Sri Krishnadevaraya University has been organized with the facilities at DBT-BIF. 2 National Workshops Organized at DBT-BIF.
Infrastructure facilities at BIF Computer & Communication facility: Server (High end) for Database/Application Server- 1 No., Server (Medium) for Porxy & File Server-1No, desk tops (including internet clients) -20, HP-printers -2Nos, Scaner -1, copier -1, LAN with dedicated BSNL – broad band & Reliance net. Scientific Software packages: Public domain software, MODELER, Open Eye, R package, HYPERCHEM, VectorNT, Autodock, Molecular visualization software, Bioinformatics programs. Databases & other information resources: Public domain databases.
Details about staff members working in BIF 1. Prof. Chitta Suresh Kumar, Professor of Biochemistry, since from August, 2008
Types of services provided The Centre is helping M.Sc. and Ph.D. students of Bioinformatics in teaching, research projects and finalizing their dissertations/thesis of host and nearby institutions Offering PG Diploma course in Bioinformatics and Drug Design to PG students. Supporting to R&D activities in the field of Bioinformatics of the host and nearby Institutes. Additionally the BIF is used by students who come for short term projects at S.K. University College of Engineering and College of Pharmacy, from other colleges and universities Educational activities with details of placement All the post graduate and diploma students were easily absorbed by the Pharmaceutical and Biotech Industries as they have excellent hands on training in using Bioinformatics tools.
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Initiative to validate the outcome of bioinformatics resources The research activities and regular training programs validate the outcome of bioinformatics resources of BIF. With the available infrastructure we identified drug targets in M. tuberculosis causing TB. Advanced training programs for doctoral students have been organized to undertake research in Bioinformatics. Implementation of Bioinformatics projects and employment of bioinformatics in biotechnology research is a good indicator of validation of BIF.
Collaborative works Centre for Biotechnology, Anna University, Chennai, CDFD, Hyderabad, IIct, Hyderabad, IISc, Bangalore are having collaborations with BIF at S.K. University and research scholars are utilizing the facility at both ends.
Databases/ Software packages developed On-line Bioinformatics resources were made available through our BIF website (www.bic-sku.org) which is aimed to ease the data analysis using various on-line bioinformatics tools on single platform in well organized form of user-friendly manner.
Papers published or presented in the conferences with reference to BIF
Initiation of R&D activities at Bioinformatics Facility Research activities carried out by the centre are as follows: 1). UGC, New Delhi sanctioned Major Research Project on Homology modeling of Mtb proteins and the program is actively going on. 2). M.Tech Project work on Homology modeling by G. Narasimhulu, Satyabhama University, Chennai.
Details of Training/ Workshop organized and total no. of user trained 2 workshops organized. 1). National Workshops Protein Modeling of Drug Targeted Proteins in Bioinformatics Era during 26-28th December, 2008 and 50 participants trained. 2). “Bioinformatics Workshop for Pharmacy Students” during 3-5th Jan. 2009. Thirty six students of M. Pharmacy students were trained in basic tools of Bioinformatics in sequence analysis. Impact shown by your BIF on the growth of biotechnology and allied areas Primary impact of this centre is the manpower training in Biotechnology at levels that includes undergraduates, postgraduates and research scholars numbering about 300, of Biochemistry, Biotechnology, Microbiology, Botany, Zoology and Sericulture, Chemistry, Physics disciplines of Host University and nearby Institutes.
Research Publications 1. Chaitanaya, M., Babajan, B., Anuradha C.M. and Chitta Suresh Kumar. Functional insites from protein model of glucose kinase from streptococcus pneumonia, Bioiformation (2009) (In press) 2. Rajasekhar Chikati., Babajan, B., Chaitanya, M., Surendra Bau, N., Suresh Kumar Chitta. and Anuradha, C.M. Computational studies on GMP reductase a potential drug target of Streptococcus pneumonia . J. Pharma. Chem. (2009) (In Press) 3. Rasool S. N, Jaheerunnisa S, Suresh Kumar Chitta and Jayaveera K. N (2008) Antimicrobial activities of Plumeria acutifolia J. Medicinal Plants 2(4), 077-080. 4. Anuradha, C.M., Chaitanya, M., Babajan, B., Rajesekhar, C. and Chitta Suresh Kumar (2009) Probing ligand binding modes of mycobacterium tuberculosis MurC ligase by molecular modeling, dynamic simulations and docking, Journal of Microbes and infections (Revision)
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5. Babajan, B., Chaitanya, M., Anuradha, C., Rajasekha, C. and Chitta Suresh Kumar (2009) New Approaches to design anti-tuberculosis drugs: theoretical modeling, docking and dynamics studies on Mycobacterium tuberculosis serine hydroxymethyltransferase in complex with PLP, Internet journal of Microbiology, (Revision)
Proposed Future Activities To offer M.Sc./Ph.D. in Bioinformatics programs from next academic year if financial support for staff is provided by DBT, New Delhi. To develop computational models/Multimedia interactive educational aids for easy understanding of the biotechnology and related topics To organize training programs on various advanced topics of Bioinformatics to update the skills and knowledge of Scientists and Researchers. Implementing R&D in Bioinformatics Training programs in Drug Discovery, Systems Biology. Hands-on Bioinformatics training for the students and staff of rural schools. Intensive efforts will be made once the center is fully established with faculty sanctioned and supported by DBT, New Delhi.
National Workshops during 2009-2010 National Seminar on “Trends in Biotechnology in Post Genomic Era” during 12th and 13th March 2009 in collaboration with College of Engineering and Technology, S.K. University, Anantapur. Workshop on “Prediction and Validation of Protein 3-D Structure by In silico tools” during Oct-2009. Workshop on “Chemiinformatics in design and optimization of lead molecules” during March-2010.
Additional Details
Chief Patron of DBT-BIF: Prof. P. Kusuma Kumari, Vice-Chancellor Coordinator of BIF: Prof. Chitta Suresh Kumar Postal Address: DBT- Bioinformatics Facility (DBT-BIF), Sri Krishnadevaraya University, Anantapur-515 003, Andhra Pradesh, India Phone No.: 08554-255644; Mobile:9849669899; Email: [email protected] Website: www.sku-bic.org Name of Contact Person: Prof. Chitta Suresh Kumar, [email protected]
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S. Kula Women’s College, Manipur Coordinator: W. Robindro Singh About the college The S. Kula Women’s College was founded by the Late Sharva Shree Sanasam Kula Singh of Yaiskul in 1981 and located at Kongkhampat of Nambol under Bishnupur District away from the hustle and bustle of city life and noisy roads , 15 Km. away from Imphal towards the south ,the S.kula Women’s College stands as a pearl of beauty in the wilderness, completely reorganized to confirm to the standards and requirements of a modern college .This Women’s Institution is an amalgamation of high standard in academics, couple with a no. of Job Oriented and personality development program designed to cater to the needs of the individual and society. The College is conferred the status of “Colleges with Potential for Excellence” by University Grants Commission. The College has campus Networking with LAN interconnecting all the computers in the campus .The college has adopted a total ICT based teaching-learning and evaluation process. The college is a multi-faculty institution opening Arts, Science and Commerce streams with B.Sc. Biotechnology and B.Sc. Food Processing Technology are advance faculty of the College and Bioinformatics Infrastructure Facility (BIF) is also setup under the sponsorship of the Department of Biotechnology, Government of India.
Important Activities 1. The Coordinator of Bioinformatics Centre, S. Kula Women’s College takes the classes of B.Sc. IIIrd year Biotechnology for Bioinformatics Paper. 2. All the Practical Records/ data of the Biotechnology, Botany and Zoology are also computerized and updated by the BIF, S. Kula Women’s College, Nambol, Manipu‘r. 3. One-Day awareness program on the Bioinformatics application was organized by the Centre at Nambol L.Sanoi College on dated 12th December 2008. 4. One-Day awareness program on the scope of the Bioinformatics was organized by the Centre at Thambal Marik College, Oinam on 13th December 2008. 5. One-Day awareness program on the Application of Bioinformatics was organized by the Centre at C.I. College, Bishnupur on 14th December 2008. 6. One-Day awareness Program on the Application of Bioinformatics was organized by the Centre at Mangolnganbi College, Ningthoukhong on 15th December 2008 . 7. One-Day awareness program on the importance of Bioinformatics was organized by the Centre at Nambol Leiren Girl’s Higher Secondary School ,Nambol on 16th December 2008. 8. One-Day awareness program on the importance of Bioinformatics was organized by the Centre at Nambol Boy’s Higher Secondary School ,Nambol on 17th December 2008 . Proposed activities during the year 2009- 2010 1. Strengthening and up-gradation of Bioinformatics Centre, S. Kula Women’s College, Kongkhampat, Nambol with most modern techniques, software and other facilities. 2. To organize a National Seminar on the Application of Bioinformatics in Biodiversity. 3. To introduce the Short Term Certificate Courses like 3 months, 6 months and 1 year Courses. 4. To introduce an advance diploma Course. 5. To introduce Under graduate course like B.Sc. Bioinformatics. 6. To provide a standard format for collection data for endemic as well as endanger species of Manipur. 7. To make database of all endemic species of Manipur. 8. Phylogenetic analysis of all the endemic and endanger species of Manipur. 9. To develop software related to the teaching and research work for biosciences. 10. To set up Networking with some other external Institutes like IBSD, Central Agriculture University, DOEACC Centre, Imphal, etc.
S. Kula Women’s College Kongkhampat Nambol, Manipur Phone No.:-0385-2453242 & 2453319
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Sher-e-Kashmir University of Agricultural Sciences & Technology of Kashmir Coordinator: Dr. Nazir A Ganai Resources Created E-Learning Portal: The center has developed an e-learning portal in Veterinary Sciences using MOODLE on the intranet, as a cutting edge tool for teaching and learning. The subject –wise content is being now developed and uploaded into the program. LAN: A local area network has been established to connect 18 divisions at the Faculty of Veterinary Sciences with the Bioinformatics Laboratory and to give access to teachers to the e-learning server for building the teaching material. SheepManager- A web Based Server: This portal is under development. It is aimed to connect all the Sheep Research Farms in the State of J & K with the server, for management of the research data on sheep and goat breeding and its online analysis, and report generation. Software developed: FARMMAN 1.00 for e-management cattle / buffalo breeding research. The program helps to generate the reports in 25 customised formats for any period on the desired parameters at the livestock research farms MateSoft 1.00 – a tool for planning breeding / mating plans on the basis of inbreeding coefficient / pedigree relationships upto 7 generations. The main use of the program is to: • keep the inbreeding low at organized livestock research farms / captive farms • to produce progeny of desired level of inbreeding for research purposes
Major Research Activities in Biotechnology and related fields • Development of vaccine against virulent foot rot: A NAIP funded project under Basic and Strategic Research. • Value Chain on Pashmina: improving productivity and processing . A NAIP funded project under Basic and Strategic Research. • Genetic Characterization of FecB gene, and its introgression in local sheep to augment to production.: DBT funded • Molecular epidemiology of Dichelobacter nodosus –a major bacterial pathogen of virulent ovine footrot • Molecular epidemiology of ovine herpesvirus 2 infection– causative gent of sheep-associated malignant catarrhal fever. • Molecular Epidemiology and Characterization of Shiga Toxin-Producing Escherichia coli (STEC) • Studies on Rotavirus Infection in Kashmir Valley with Special Reference to Lamb and Calf mortality List of Peer Review Papers: 12 ( 2001-2008) • N. A. Ganai, H. Bovenhuis, J. A. M. van Arendonk and M. H. P. W. Visker: Novel polymorphisms in the bovine b-lactoglobulin gene and their effects on b-lactoglobulin protein concentration in milk Animal Genetics doi:10.1111/ j.1365-2052.2008.01806.x • TAS Ganai, Gupta S.C. : 16 Nucleotide Sequence variants of growth hormone gene of Karnah and Gurez breeds of Sheep (Kashmir) submitted to UniProtKB/Tr EMBL • N. A. Ganai and B.R. Yadav (2001). Genetic Variation within and among three Indian breeds if goat suing heterologous Microsatellite Markers. Animal Biotechnology, University of Illionois USA (12(2), 121-136 • Wani, S. A., Samanta, I., Bhat, M.A., Buchh, A. S. (2004). Molecular detection and characterization of Dichelobacter nodosus in ovine footrot in India. Molecular and Cellular Probes. 18 (5) : 289-291 • N. A. Ganai and B.R. Yadav (2003). Parentage Determination in Indian breeds of goat suing heterologous Microsatellite Markers. Presented at FAO/IAEA International Symposium on Applications of Gene-based Technologies for Improving Animal Production in Developing Countries in Vienna Austria, Oct 6-10, 2003 • N. A. Ganai and B.R. Yadav (2004). Characterization of three Indian breeds of goat suing heterologous Microsatellite Markers. Presented at 29th International Conference on Animal Genetics Meiji University Tokyo Japan Sep 11-16, 2004
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• Wani, S. A.; Bhat, M. A.; Ishaq, S. M.; Ashrafi, M. A.; Buchh, A. S. and Haq, M. (2003). Detection of a mammalian- like group A rotavirus in diarrhoeic chicken. Veterinary Microbiology. 94 (1):13-18. • Wani, S. A.; Bhat, M. A.; Samanta, I.; NishiKawa, Y. and Buchh A. S. (2003). Isolation and characterization of Shiga toxin-producing Escherichia coli (STEC) and enteropathogenic Escherichia coli (EPEC) from calves and lambs with diarrhoea in India. Letters in Applied Microbiology. 37 (2): 121-126 • Wani, S. A.; Bhat, M. A.; Nawchoo, R.; Munshi, Z. H. and Buchh, A. S. (2004). Evidence of rotavirus association with neonatal lamb diarrhoea in India. Tropical Animal Health and Production. 36 (1) : 27-32. • Wani, S. A.; Bhat, M. A.; Samanta, I., Nishikawa, Y. and Buchh A. S. (2004). Escherichia coli O116 associated with an outbreak of calf diarrhoea. Veterinary Record. 154 (16): 506-508. • Wani, S. A.; Bhat, M. A.; Samanta, I.; Ishaq, S. M.; Ashrafi, M. A. and Buchh, A.S. (2004). Epidemiology of diarrhoea caused by rotavirus and Escherichia coli in lambs in Kashmir valley, India. Small Ruminant Research. 52 (1-2): 145-153 • Niyaz Ahmed, J.R. Khan and N.A. Ganai (1999). DNA amplification assay for rapid detection of bovine tubercle bacilli in semen. Animal Reproduction Science,( Netherlands) 57:15-21
234 XXth All India Coordinators’ BTISnet Meeting February 03-04, 2009
Sri Padmavati Mahila Visvavidyalayam, Tirtupati Coordinator: Prof M. N. Reddy Summary of the progress made by the Centre Establishment of the Centre with the sanctioned Software & Hardware and other infrastructure Initiation of training to the students of various branches of Life Sciences in the University, in their Bioinformatics practicals and / project works also. Appointment of RA, Who is taking care of training of students and other activities of the Centre including development of some data bases. Selection of one Traineeship and one Studentship in the Centre who have just started their work. Staff members associated with the Centre 1. Ms. Subhalaxmi Nayak Research Assistant Major Activities of the Centre during the year 2008 – 09 (a) Procurement of different Hardware & Software items and Establishment of the Centre with the other Infrastructural facilities. (b) Recruitment of one RA to the Centre. (c) Selection of one Traineeship & one Studentship positions who just started their work. (d) Students of various departments in the University like Bioinformatics, Biotechnology, Microbiology, Pharmacy & Industrial Biotechnology are availing the facility for some practicals as well as Project works, assisted by the RA. Infrastructure Facilities Computer Hardware: High End Server - 1 No Medium Server - 1 No HP DX2280 Computers with LCD Monitors - 15 Nos HP LAPTOP 6710B - 1 No HP LASERJET PRINTER 300 SDN - 1 No. HP OFFICE JET K7108 - 1 No. HP SCANJET G2410 - 1 N0. CANON IR2016J COPIER - 1 No. 5.0 KVA online UPS system with 26 AH/12V/20 Nos., -1 No. Communication facility: a. Centre has purchased 250mbps BSNL Broadband connection b. Telephone with STD facility Scientific software Packages: i. Licensed Scientific Software: GCG Wisconsin Package, MATLAB (Purchase is underprocess). ii. Licensed System Software: Windows 2008 server with License 10 user, Red Hat Linux Enterprise Edition 4, Microsoft ISA server 2005 for proxy server, MS SQL Server std 2005, Licensed Application Software: MS Office 2007, MICROSOFT VISUAL STUDIO 2008 Professional Edition (.NET), Antivirus Package: Symantec Endpoint Protection 11.0 iii. Application Software: Macromedia Dreamweaver 8, Macromedia Flash 8, Selteco(Menu Maker, Banner, Flash Design), Adobe Reader 8.0, Adobe Photoshop 7.0, Adobe Page Maker 7.x, BioEdit, Clustal X, SeqVISTA, TreeV32, ActivePerl-5.8.8.819-MSWin, Bioperl, MySQL-Essential. Some software (RASMOL-2.7.4.2, Swiss PDB Viewer-4.0, and Cn3D-4.1) free for academicians has been installed. Databases and Other information Resources Internet based access to various biological databases. Bioinformatics Books purchased Subscription to Journals
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Databases/ Software packages developed Developed databases on SPMVV University, an aggressive weed Parthenium and one endangered Species endemic to Tirumala Hills - Cycas beddomei. Preparation of Website for the Centre is under process.
Impact shown by the centre on the growth of Biotechnology and allied areas Providing facility for Bioinformatics project works / practicals for students of Biotechnology and other branches of Life Sciences in the University.
Future Activities The Centre envisages — a) To initiate Research work in collaboration with researchers of different Departments. b) To Develop databases required for this locality and update of the existing ones. c) To Organize workshops, Guest lectures, Training programs for familiarizing the application of Bioinformatics in Biology teaching and learning activities for teachers, Scientists, Research scholars and students to accomplish the tasks in Bioinformatics. Additional Details
Postal Address: Bioinformatics Centre Sri Padmavati Mahila Visvavidyalayam (University for Women) Tirupati – 517502, Andhra Pradesh. Phone Number: 0877-6576759, (M): 09849085596 E-mail: [email protected]
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Shri Mata Vaishno Vevi University, Katra (J&K) Coordinator: Prof. V. Verma The bioinformatics infrastructure facility (BIF) Centre in the School of Biotechnology, Shri Mata Vaishno Devi University, Katra has been established with the kind help and support of the Department of Biotechnology, Govt. of India in 2007. The facility is headed by Prof. V. Verma, Dean, College of Sciences as the Co-ordinator of the BIF centre. During the last financial year the following equipment was procured and installed in the centre: a) High-end Server Sunfire x46oo M2. b) Entry-level Server Sunfire x2200 M2. c) Workstations Sun Ultra20 M2 (4nos). d) Desktop computers (Dell make, 10 nos). e) Scanner(HP make) f) Printer (HP make) g) Photocopier (Canon make) h) Colour printer (HP make) However, the university has financed the procurement of additional 20 nos of Desktop computers (HP make) besides the cost of the additional furniture, ACs, online UPS 5KVA and other requirements of the centre. The centre has also recruited the posts of one RA and one Trainee The BIF Centre was inaugurated by His Excellency Shri N N Vohra, IAS, the Governor of J&K state and Chancellor of University on October 8, 2008. The BIF Centre has started work ona web site construction for the Medicianl plants in J&K state, Bamboo species available in the country in general and the J&K state in particular. Besides, work on the proteomics of selected biomolecules is being initiated. The centre also p[roposes to hold a workshop in the last week of February, 2009 in collaboration with Department of Biotrechnology, University of Jammu, Jammu
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Sri Sathya Sai University, Prasanthi Nilayam Coordinator: Prof.S.Krupanidhi The Department of Biotechnology, Govt. of India has approved BIF to our Department of Biosciences, during the academic year 2008-2009. As one of the incipient steps to instill the awareness of informatics tools in biology, the members of the Board of studies in Biosciences of Sri Sathya Sai University, have recommended and approved to incorporate the course contents viz., Biological databases, Similarity Searches and Alignments, Multiple Sequence Alignment, Phylogenetics and Structural Informatics in a course entitled “Bioinformatics” for 24 hours and corresponding practical sessions in the second semester of 1st .M.Sc. and another course entitled “Biostatistics and Information technology” is also designed and implemented for 64 hours along with the practical component in the 3rd semester of 2nd B.Sc. Biosciences. The Executive Committee meeting was held on 25-10-08 in the Department of Biosciences, Prasanthinilayam Campus and as per the revised budget allocation, the following materials have been procured so far: 1) Computers: Intel Pentium core 2 DuoE4600, 2.4GHZ processor, 512 MB, 256MB Graphic card (8 No.); 2) IBM 3610 2U rack Server: (1 No); 3) LCD Projector; 4) HP Laserjet PCL 6-printer; 5) Software for running computers (MS Office, 2007, XP professional, etc, Norton Antivirus); 6) 5 KVA UPS 30 minutes back up; 7) HP photosmart D7368 A4 printer; 8) HP Deskjet D4368 printer (black & colour); 9) DS Libdock (accelrys software); 10) Red Hat Linux version 4; 11) Books and subscribed Online journal of Bioinformatics and 12) Furniture. The Department of Biosciences under the auspices of BIF is organizing a workshop during 20-21st February, 2009 on the topic entitled “Bioinformatics in the areas of Biomedical and Ecological Applications”. The members of the faculty in the Department of Biosciences have standardized the software tools such as PERL programme for the virtual observations of the salient features of DNA and a practical exercises book on “Introductory Workbook on Perl for Biology Students” comprising 14 exercises is communicated to the electronic source viz., “biology online”, which is an open access. The Entity Relationship (ER) models for Molecular Evolution and Health Informatics due to the Imbalance of Copper have been designed and published. The ER models are shown below. The consensus homology among interleukins constituting haematopoietic microenvironment is evaluated through2 BLAST search for their respective sequences and adopted online Clustal W programme to evaluate their molecular phylogeny and the same was published in “Online Journal of Bioinformatics”. The online Molinspiration software tool was adopted to evaluate whether Omega-3 s are drugs. All attributes except water solubility are satisfied suggesting that omega-3s by themselves are good lead neutraceutical drug candidates. The same was published as part of our article entitled “Is Algae Oil Fuel or Nutrition?” in Everyman’s Science Vol XLIII, (3), 164-168, 2008. 1. Name of the resources: Introductory Workbook on Perl for Biology Students 2. Application: The PERL programme for the virtual visualization of DNA features has been designed into 14 exercises and sent for publication in ‘Online biology’ which is an open source and would be accessible for everyone. 3. Target users: Students, Researchers and Teachers. 4. Website/Portal address for such resources: Google search - biology online
Prof. S. Krupanidhi Coordinator of DBT BIF Programme Department of Biosciences Sri Sathya Sai University Prasanthi Nilayam- 515 134 A P Email: [email protected]
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Sri Venkateswara Institute of Medical Science, Tirupati Coordinator: Dr. A. Umamaheswari Summary of the progress made by the centre since its inception Since its inception on 10th March, 2007, SVIMS Bioinformatics Centre focused on its main objective of promotion of Biology teaching through Bioinformatics. 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 through National level workshops, training programs, guest lectures by many eminent scientists working in the areas of bioinformatics and biotechnology and professionals from industry. The Centre has been offering M.Sc. and Ph.D. programs in Bioinformatics. Twenty eight students completed their M.Sc. dissertation work using Bioinformatics Infrastructure Facility. Forty students were awarded M.Sc. degree in Bioinformatics. Fifteen students during the academic year 2008-09 joined M.Sc. Bioinformatics course and two students registered for Ph.D. in Bioinformatics. The centre is open to the students, faculty and researchers of SVIMS to retrieve 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 departments. The Centre has taken up research activities in the areas of sequence analysis, molecular modeling, drug designing, medical informatics etc. Seven papers were presented in national and international conferences. Most of the students got placements in various leading research institutions and industries.
Area of specialization of the centre: Sequence Analysis, Molecular Modeling, Drug Designing and Medical Informatics. Major activities of the centre during the year 2007-08 • The Centre helped M.Sc. and Ph.D. students of Bioinformatics in teaching, finalizing research projects, and providing internet facility to students and staffs of the institute. • Organized a National Workshop on Drug designing on 24th – 26th, April 2008. • Organized a guest lecture on Computer aided drug designing by Prasad V. Bharatam • Appointed one Project Assistant, two Traineeships and two studentships. • The official website of SVIMS Bioinformatics Centre (http://svimsbic.org/) has been hosted. Infrastructure facilities in the Bioinformatics Centre A. Computer & Communication facility: SERVER (High end) for Database/Application Server, SERVER (Medium) for Porxy & File Server, 36 GB Server, Laptop, Desktop Machines (26 no. working on both windows and Linux OS), LCD Projector, HP Laser jet 2420 PCL6 Printer, Deskjet printer, Scanner (2no.), photo copier, 10 kva UPS, Wipro LQ DX Gold Printer, Canon Printer, Local Network Connection, 2 Mbps internet connectivity from BSNL Dataone Broad band internet. B. Scientific Software packages: Discovery Studio 2.0, AMBER10, AUTODOCK 4.0, DOCK6.2, MODELLER9v5, EMBOSS, PHYLIP, PAUP, PILE UP, TM4 Software Suite, Hex and Argus lab. Windows XP, Rad Hat Linux, Biolinux, Turbo C++, JAVA, Visual Studio professional 2005, Ms-SQL Server, Oracle 9i, Active Perl and MySQL. C. Database & other information resources Leptospiral Drug Target and docking interactions Database,BTIS library books Database,Dissertation Database Diabetes Database and e- Learning modules on Bioinformatics.
Details about Staff members working in the centre
Educational activities with details of placement The Centre has been offering M.Sc. and Ph.D. programs in Bioinformatics.
239 Bioinformatics Infrastructure Facility (BIF) for Biology Teaching Through Bioinformatics (BTBI)
Collaborative work/initiatives Collaboration is under progress with Mahatma Gandhi Institute of Medical Sciences, Sevagram to implement online Certificate course in Medical Informatics.
Papers published or presented in the conferences with references 1. Pradhan D., Umamaheswari A. and Subramanyam G., “Interaction strudy of putative drug target tryptophan synthase (TRPS) alpha chain of Leptospira interrogans with TRPS inhibitors” was presented (oral) and published (abstract) in proceedings of National Workshop on System Biology and its use at Bioinformatics Centre, University of Kalyani, West Bengal from 18th - 22nd Nov 2008. 2. Pradhan D., Umamaheswari A. and Subramanyam G., “In silico detection of binding mode of k-Hefutoxin with modeled human voltage gated potassium channel Kv1.2 receptor and L-carnitine” was presented (oral) and published in proceedings of CGPSYS 08 at IISc. Bangalore on 1st -3rd Oct 2008. 3. Priyadrshini I. V., Umamaheswari A. and Subramanyam G., “Homology modelling and Docking simulation of putative drug target Thiamine phosphate kinase of Leptospira interrogans “ was presented (poster) and published (abstract) in proceedings of CGPSYS 08 at IISc. Bangalore on 1st -3rd Oct 2008. 4. Umamaheswari A., Pradhan D., Priyadrshini I. V. and Subramanyam G., “In silico Putative Drug targets in Leptospira interrogans and Homology Modeling of UDP-N-acetylglucosamine 1-carboxyvinyltransferase Mur A” was presented (poster) and published (abstract) in proceedings of HUGO’s 13th Human Genome Meeting Hyderabad, India, on Sep 27-Tue 30 Sep 2008. 5. Madhusudhan M.V.G.N.S., Pradhan D., Umamaheswari A. and Subramanyam G., “Homology modeling of putative drug target translation initiation factor (IF-1) of Leptospira interrogans and docking studies with 6-aminohexanoic acid” was presented (oral) at National Workshop on Influence of Microbes on the earth’s environment and Inhabitants from 23rd-24th July 2008 at SPMVV, Tirupati. 6. Priyadrshini I. V., Pradhan D., Umamaheswari A. and Subramanyam G., “Homology modeling of 50s ribosomal protein L10: Putative common drug target among organisms causing infective endocarditis” was presented (oral) and published (full-length) in proceedings of National Workshop on “Recent trends in Biomedical Physics” at T.J.P.S., Guntur, A.P. 7. S. Jaya kishor, K. Dedeepya, D. Pradhan, A. Umamaheswari and G. Subramanyam., “3D computational modeling and docking simulations of 3-oxoacyl (acyl-carrier-protien) synthase III (FabH) from L. interrogans” was selected for poster in NDDC 2009 from Jan 21-24th at Sp Jain Auditorium,University of Delhi South Campus, Delhi. Initiation of R&D activities in Bioinformatics Current research activities focused on identification of drug targets for various human pathogens such as Leptospira, Mycobacterium and Endocarditis etc. Computerized protein modeling of identified targets and docking studies. The research activities were also extended towards developing databases, e-learning modules, Mirror sites, Medical informatics online course and developing databases related to Medical Informatics.
Details of Training/Workshop organized and total no. of users trained 1. A National Workshop on Drug Designing was organized from 24th – 26th, April 2008 - 64 participants. 2. The 2nd National Workshop on Perspectives trends in Bioinformatics will be organized from 11th – 13th February, 2009. Impact shown by the Centre Our centre is first of its kind to offer M.Sc. in Bioinformatics in Andhra Pradesh. The Centre has been able to achieve many targets towards training and manpower development in bioinformatics The Centre has helped various Universities/ Colleges for curriculum development & training.
Future activities • Strengthening of R&D activities in the areas of comparative genomics, Microarray technology homology modeling, molecular docking and Database development. • Developing Medical informatics Databases. • Development of databases for Drug targets and docking interactions for pathogens such as Leptospira, Mycobacterium, Endocarditis etc.
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• Development of teaching e-learning modules in Bioinformatics. • Strengthening and expansion of teaching and research programme.
Additional details
Name of the Coordinator: Dr. A. Umamaheswari Postal Address: Co-ordinator of BIF, Department of Bioinformatics, SVIMS University, Tirupati – 517 507, Phone: 0877 2287727 Website: http://www.svimsbic.org/ Name of Contact Person: Dr. A. Umamaheswari Email: [email protected]
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Tezpur University, Tezpur Coordinator: Dr. A. K. Mukherjee Brief description of Bioinformatics-related activities Use of BIF in teaching: M Sc Molecular Biology and Biotechnology 3rd semester students are using the facility for practical classes of the Course BT414 “Application of computer in Biotechnology”. Scholars and faculties of the Department are using the facility for their research work. The facility is also extended to students, scholars and faculties of other science and technology departments. M Sc Mol Biol & Biotech projects completed on Bioinformatics topics: 5
Research Petroleum Microbiology: A total of 75 bacterial strains were isolated from soil samples collected from oil well sites of Assam Asset. Twelve strains were found to efficient degrader of crude oil and its components like hexadecane, dodecane, polycyclic aromatics etc. Two bacterial consortia were formulated which could degrade contaminant crude oil. The same were handed over to the ONGC for large scale field evaluation. Ph D degree: 2 persons obtained Ph D degree on the above work Yeast genomics: Yeast strains from cultures used by tribal communities of North East India in their indigenous alcohol preparation have been isolated and identified. Biochemical and genome assessment of 23 yeast strains has also been done. Ph D degree: 1 person completed the research work Medicinal plants: So far 9 medicinal plants were assessed in respect of their chromosome number, karyo-type, genome size, active compound isolation and structure elucidation as well as anti-microbial efficacy. Ph D degree: 3 persons obtained the degree on medicinal plant research
List of ongoing Research Projects: Sl No Name of the project Funding agency Duration (yrs) Amount (Rs in lakh) 1 Bioremediation of contaminant crude oil.(collaborative project Tezpur Univ. & ONGC; PI: Prof. B. K. Konwar and Coinvestigator:Head, INBIGS, ONGC) ONGC 5from Oct., 08 to Sept., 2013 70.03
Research publications/presentations in 2008–09: 20 in national/international journals and conferences/ seminars. (3 of them on bioinformatics topics)
Library facility Important biotechnology journals available in the library: Cell, Trends in Biotech., Plant Cell Reports, Current Microbiology, Annual Review of Biochemistry, Critical Review of Biotech. and Nature UGC Infonet E-journals: Elsevier (34 Life Science Journals), Biosis, Science Online, Ingenta, IEEE/IEE (Single user), ASTP journals Available in CDs: Biological abstract and Annual Reviews
Computer facility available Silicon graphics, High speed computing system [SGI ALTX 350 Computer Server: 4* IA 64 Processors/LTO Backup HCL Gglobaline 4550 Server, Xeon 1.0 GHz, HP Net Server E60], Computer for each faculty, Computers for groups of Ph D Scholars University Computer Centre with 60 terminals for students Types of Biotechnology-related soft-wares available SPSS 8.0, Mathematica 3.0 and Genocluster
Manpower The Coordinator is assisted by 3 faculties (DR. S. K. Ray, Dr. M. Mandal and Mr. S. S. Satapathy: Lecturers), Computer Engineer (Mr. D. Sharma) and Lab Asstt (Mr. P. Mudoi).
242 XXth All India Coordinators’ BTISnet Meeting February 03-04, 2009
Appointment of RA: The DBT-sanctioned post of Research Associate (RA) is expected to be filled up by the first week of February 2009 through the interview scheduled on 30th January.
Teaching/Training programs on Bioinformatics Teaching: The University is going to start Integrated M Sc Bioinformatics program with 10 students from the current year (2009) under the Department of Molecular Biology and Biotechnology. The course syllabus has already been prepared. Faculties will be appointed on the basis of positions sanctioned under the 11th plan. Training: Two trainings were organized in the month of December 2008 for students, scholars and faculty members. (1) “Introduction to bioinformatics and its implications” dated 15th - 21st Dece 2008. (2) “Bioinformatics application in computational biology” dated 22nd - 28th Dec 2008. There were 20 participants in each training. Students, scholars, RO, RF and faculties from organizations like IIT, Guwahati; NERIST, Itanagar; ICMR, Dibrugarh; Tezpur University; Guwahati University; Dibrugarh University; Orissa; IBSD, Imphal; Manipur University; Rajiv Gandhi University, Itanagar; Uttar Pradesh participated.
Executive Committee Meeting The EC meeting was held on 22nd December 2008 and the following resolutions were adopted: 1. Bioinformatics laboratory in the new Biotechnology Building Sufficient space may be provided in the newly constructed Biotechnology building for housing the BIF with the minimum number of 30 computer terminals, 4 servers and sitting arrangement for the personnel along with furniture, telephone, fax etc. 2. Technical and maintenance support from the Computer Centre The Computer Engineer and other technical personnel of the university Computer Centre may be allowed to provide technical and maintenance support to the BIF. 3. Use of BIF for M Sc program in Bioinformatics The BIF was created for imparting teaching to M Sc Mol Biol and Biotechnology students; the same may also be extended to the proposed M Sc Bioinformatics program. 4. Creation of additional facilities in the BIF For imparting teaching to 40 students of two M Sc programs, Ph D scholars and faculties; there will be additional requirement of at least 20 terminals, one lap top, one laserjet color printer, a multimedia projector, one video camera (with all accessories) and two 5 KVA UPS (online). A proposal to this regard may be submitted to the Bioinformatics Section, DBT, Govt of India, New Delhi for funding. 5. DBT support for trainings The BIF has organized trainings to both internal and external candidates. The Bioinformatics Section, DBT, Govt. of India, New Delhi may be approached for obtaining regular and incidental funding for such trainings/workshops/ seminars etc.
Place: Tezpur University, Napaam Prof. B. K. Konwar Date: 22.01.09 Coordinator
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Tripura University, Tripura Coordinator: Dr. Sukanta Banik About the location Tripura University is located at Suryamaninagar at west district of Tripura. The distance from Singherbil (Agartala airport) to the University is about 22 km. However, the distance from the airport to Ujjayanta Palace (Agaratala City) is about 10 km.
About the Centre The Bioinformatics Centre of the University is placed at the second floor of Academic Building – Phase I. There are two laboratories in the centre- (a) Instrument Lab and (b) Study Lab. The centre organized its first workshop during 25-27 September 2008 entitled “Basics of Bioinformatics- a tool for Promotion of Biology Teaching”. The advertisement for such programme was done in the website of the University in June 2008. Therefore, with the followings the Centre organized its first workshop during 25-27 September 2008: 1. Total Participants: 42 Specialization Bioinformatics: 1 Botany 7 Fisheries Science: 1 Human Physiology: 3 Pharmaceutical Science: 1 Microbiology: 2 Zoology: 27 2. Resource Persons: 05 Professor P Chakrabarti, Bose Institute, Kolkata Dr T. Ghosh, Bose Institute, Kolkata Dr B De, Regional Institute of Pharmaceutical Science, Agartala Sri M Das, Women’s Polytechnique Institute, Agartala Sri D Majumder, Kolkata 3. Comment of the participants during Valedictory session: The participants greatly appreciated for overall facilities available from the Centre. The centre organized one seminar during 24 December 2008 entitled “An Introduction to Bioinformatics”. 1. Total Participants: 15 2. Resource Person: Dr M Das, University of Calcutta, Kolkata Future activities of the Centre 1. Training program for Undergraduate 2. Training program for Post graduate 3. Seminar and Workshop
244 XXth All India Coordinators’ BTISnet Meeting February 03-04, 2009
University of Allahabad, Allahabad Coordinator: Prof. Dwijendra K. Gupta 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 7th 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 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. The Bioinformatics Infrastructure Facility was recently inaugurated on 6th January 2009 by Hon’ble Justice Arun Tandon of Allahabad High Court and Prof. R.G.Harshe, Vice-Chancellor of Allahabad University
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, Prof .Shanthy Sundaram,Dr Avinash Pandey and Dr. Anjana Pandey . These projects have become operational as regards the procurement of the equipment is concerned.
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
Major activities of the Center during 2007-08 An International Collaboration is already in force between University of Allahabad (Prof. D.K. Gupta )and University of Cagliari ( Prof. Paul la Colla) for the third year.
Infrastructure facilities in the Bioinformatics Center A. Computer and Communication facility: We are 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. 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 Bioinformatics Centers as well as any softwares that we may develop in the meanwhile.
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 under its Non-Plan 8 faculty positions (Professor 1, Readers 2, and Lecturers 5)against which recruitment process has been started and these posts are likely to be filled soon. Presently, the core teaching faculty comprises of faculty drawn from different departments vide infra as well as guest faculty:
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).
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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. 6 . Dr.K.N.Uttam (specialty is Diatomic Molecular Spectroscopy).
Future activities 1. We are developing our website 2. We are seeking interaction with Bioinformatics institutions abroad for collaborative research proposals. This may include summer training of our students and researchers in these international laboratories in different areas of Genomics and Proteomics, Transcriptomics and Metabolomics. 3. We are starting a B.Sc. Bioinformatics Program at the University . Educational activities with details of placement The International Collaboration between University of Allahabad ( Prof. D.K. Gupta) and University of Cagliari ( Prof. Paul la Colla) is running in the third year. Besides, international collaborations with Italian universities at Turino, Bologna, Parma, Milano and Roma have started this year. 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.
Papers published or presented in the conferences with reference 1. Ashutosh Mani , Shanthy Sundaram and Dwijendra K. Gupta. (2008) Mitochondrial ATP synthase sub unit six of Mushrooms: Genes Genomes & Genomics (Vol.2). Bioscience Publications, India 2. Ashutosh Mani& Dwijendra K. Gupta (2008) An Evolutionary and Comparative Genomics Based Account of Y-box Proteins in Eukaryotes. Proceedings of the International Conference on Bioinformatics of Genome Regulation and Structure (BGRS’2008). June 22-28, 2008, Institute of Cytology and Genetics, Novosibirsk, Russia.(Accepted) 3. Ashutosh Mani & Dwijendra K. Gupta (2008) Y-Box proteins:A statistical approach towards comparative genomics based in silico study. International Conference of Gwalior Academy of Mathematical sciences. January 10-13, Anand Engineering College, Agra. 4. Ashutosh Mani ,S.Shanthy& Dwijendra K. Gupta (2008) Evolutionary study of Mitochondral ATP synthase subunit six of mushrooms Employing Bioinformatics Approach. Conference of International Aacademy of Physical Sciences. January12-14, Guru Ghasidas University, Bilaspur. 5. Ashutosh Mani, Shanthy S. and Dwijendra K. Gupta (2008) Mitochondrial ATP Synthase Subunit six of mushrooms are conserved during evolution: A Bioinformatics approach. Proceedings of National Workshop cum Training on“ Molecular Modeling and Protein Docking” At Bioinformatics Center, CARI, Port Blair February 25-28, 2008. 6. Dwijendra K Gupta*, Shailendra Srivastava*, Eva Smolenova**, A.Hasilik** and Shanthy Sundaram* (Sept. 2008 ) “Nanogold-IgY-Nanophosphor tagged approach for affinity retrieval of lysosomal membrane transporter proteins -A Proteomics based study on Lysosomal storage Diseases - in EMBO Conference “At the joint edge of Cellular Microbiology and Cell Biology” (Villars sur Ollon, Switzerland)
Details of Training/ Workshop organized and total no. of user trained The BIF was inaugurated early this month( 6.1.2009) because the preparation of BIFgot delayed due to circumstances beyond our control. So the training course/workshop as proposed in the Bioinformatics Calendar could not get underway. It is planned after March 2009.
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 now become operational after an 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, was completed. Also, the site where the Facility has now become operational could not be completed earlier for want of funds.
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Future activities As the facility is now become operational, the Workshop proposed to be organized here is being planned to a later date sometime after March 2009. 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 & Ex-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
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University of Calicut, Kerela Coordinator: Dr. P. R. Manishkumar Summary of the progress made by the centre 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 2007-08.
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 post graduate programme in Biotechnology having Bioinformatics in the course curriculum. The department is actively engaged in research in the area of Plant Biotechnology, Immunology, Cell and Molecular Biology / recombinant DNA technology.
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.
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 (Sim Vector), primer premier, and free down loadable software packages are available. · A few more software packages such as DS standalone, DS Charmm and Accelrys Gene have also been procured recently.
Details about Staff members working in the centre
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 members and research scholars. A total number of 25 participants have been given training in this area.
Impact shown by the 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.
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Future activities Steps are underway to conduct a training programme in Bioinformatics for the teachers, post graduate and research students in Biological Sciences by mid- February / March 2009. We intend to develop data bases of some important medicinal plants used in traditional medicine and those endemic to the state of Kerala. The data base would also cover information on collection of rare plants in the Calicut University Botanical Garden. A similar data base on microorganisms is also being planned.
Additional details
Name of the coordinator : Dr. P.R.Manish Kumar Reader and Head Department of Biotechnology, University of Calicut. P.O., 673 635 Kerala State Phone No.: 0494-2401972: Fax: 0494-2400 269, 0494-2400361 E-mail: [email protected]., [email protected]
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University of Hyderabad Coordinator: Dr. Anand K. Kondapi The Bioinformatics Infrastructure Facility, funded by the Department of Biotechnology, Govt. of India is well equipped facility maintained by the Department of Biotechnology, School of Life Sciences, University of Hyderabad, and Hyderabad. Since the research in the University of Hyderabad is presently focused on genomics, proteomics and drug discovery, the required infrastructure namely microarray data analysis and proteomics and drug synthesis, screening and evaluation is available in the University. Hence, the principle focus of the facility is to augment the teaching and research in Systems Biology and Drug Discovery. The facility is at present equipped with R-package, SAS Genomics (10 lic.), MAT Lab with statistics (5 lic) and bioinformatics (5 lic) tools, the systems biology tools will be procured in the current year. Other open source tools of systems biology are also available. The drug discovery platform at the facility include Tripos Sybyl 8.0 (3 lic.) with QSAR support, GOLD, Silver suite for docking, open source software for docking (Open Eye, Auto Dock), Molecular mechanics software (GROMACS), other visualization and homology modeling software. The facility is made available by students of all departments of School of Life Sciences of University. The students have access to high performance computational facility and Centre for Molecular Simulation and Design for regular training as well as project works. M.Sc in Biotechnology, Systems biology, Biochemistry, Animal Biotechnology, Plant Biotechnology, M.Tech Bioinformatics, M.Tech Medical Biotechnology and all PhD students are active users of the facility. The Bioinformatics Infrastructure facility at University was used by twelve students who had come from all over India of different institutes for doing their project work as a part of their curriculum. The genomics, proteomics and systems biology are emerging technologies that are being implemented in various Institutions and Universities. The data obtained in these technologies have lot of variability due to signal-noise ratio and population variability. Hence such a data need to be normalized and analyzed using various statistical tools. This is the main objective to conduct a training course and to train mid career scientists on the use of various advanced research techniques in the areas of Bioinformatics and Statistics and all the participants of the training course were encouraged to carry out the techniques themselves. The facility has organized short term training course “Bioinformatics Statistics School 2008” for 16 days, from Dec 1st to Dec 16th, 2008, for mid career scientists involved in undergraduate teaching in life sciences and biotechnology. The funds are provided by the Department of Biotechnology, Govt. of India, New Delhi for the organization of the training course. The University of Hyderabad jointly with C.R.Rao Advanced institute for mathematics, statistics and computer sciences conducted this short term training course.
The objectives of this course are 1. To familiarize in basic concepts of statistical methods in statistical methods in biological data analysis. 2. Implementation of statistical methods of genomics and proteomics data. 3. Hands on practice using various packages. This course had 30% theory and 70% practical classes, which were held in on-line interactive mode. All participants are trained such a way that they can implement back at home Institute. The winter school is conducted with close association of well known statistician Prof. C R Rao.
The proposed activities during the year 2009-2010 are 1. Conducting a summer training program for 25 B.Tech students for one month in May 2009 on Drug Discovery. 2. Upgrade the facility with software on modeling, drug design and systems biology and other infrastructure that will help developing an interdisciplinary research project in Bioinformatics and drug discovery. 3. Conducting a Bioinformatics Statistics School for College teachers. This will be done in collaboration with CR Rao Advanced Institute for Mathematics, Statistics and Compute Sciences. 4. 3 months projects for 16 selected candidates from different Institutes in the chosen areas of the candidates in systems biology and drug discovery.
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Additional details
Name of Coordinator: Prof. Anand K. Kondapi Laboratory for Molecular Therapeutics Department of Biotechnology School of Life Sciences University of Hyderabad Hyderabad 500046 India
Phone: (O)91-40-23134571; (H)91-40-23000654 FAX: 91-40-23101145 Email: [email protected], [email protected]
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University of Jammu, Jammu Coordinator: Prof. Manoj K. Dhar Summary of the progress made by the centre from its inception The Bioinformatics Centre at University of Jammu, was established during - 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 six months, the process for procurement of the hardware was completed. In the next phase several softwares were purchased and installed. The Bioinformatics lab was made 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 incorporated in the syllabus of M.Sc Biotechnology, Microbiology, and Biochemistry and is fully supported by the centre. 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 software, tools to assist in their research programmes. Major research activities in Biotechnology and its related fields The centre is focusing mainly on In-silico analysis using Bioinformatics software. The centre promotes Bioinformatics awareness. Research projects and interdisciplinary research in collaboration with wet lab Biotechnology research programmes are being carried out. Area of specialization of the centre: The main areas of specialization are Genome and Proteome Analysis. Major activities of the centre during the year 2008-09 a) Training programme for College and University teachers The Refresher course organized by the Academic Staff College, University of Jammu in collaboration with Department of Zoology, the teachers serving in various Govt. colleges of J & K State and few from University visited the Bioinformatics Centre. The Bioinformatics Centre focused on the major aspects of Bioinformatics and the staff of the centre delivered a detailed lecture on Bioinformatics and its vital role in Biological Science Research. b) Workshop for Lecturers (10+2) A six day workshop was organized by the School of Biotechnology in collaboration with the State Institute of Education. The workshop included the lectures and practical sessions in various areas of Biotechnology and Bioinformatics for the participants. c) Creation of awareness in Bioinformatics In order to create awareness about Bioinformatics, the coordinator delivered popular lectures in the Departments of Physics, Computer Sciences and Information Technology, Environmental Sciences, Botany and Zoology of the University of Jammu and also in the affiliated colleges. 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 dedicated internet facility and training to the students, research scholars for using the online and offline software, tools to assist in their research programmes. Infrastructure facilities in Bioinformatics Centre a) Computers : Fifteen (15) b) Servers : Two (High-End and Medium) c) Printers : Two (hp1020n, hp2600n) d) Scanners : Two e) Communication facility : Telephone connection, Jammu University Server f) Scientific software packages : Geneious PRO (Bioware, New Zealand), Discovery Studio (Accelerys,U.S.A), NTSys, PHYLIP, TREE VIEW, RAPDPLOT g) Databases and other information resources Databases acquired : Under process Journal : Science (AAAS)
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Details about staff members working in the centre
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. Creating awareness among undergraduate and post-graduate students and faculty regarding the basics of Bioinformatics and its applications.
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.
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.
Collaborative works / Initiatives: Under Process Databases/Software packages developed: Under Process 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 and one review paper is under process. TITLE OF THE PAPERS: 1. Using Bioinformatics tools to create a database of transcription factors binding sites. Mohit Kumar Sharma and V.B.Bajic 1. Bioinformatics Centre, Department of Biotechnology, University of Jammu 2. Institute for Infocomm Research, Singapore. 2. Cloning and functional analysis of carotenoid biosynthesis genes from carrot Khalid Zaffar Masoodi and Manoj K. Dhar Department of Biotechnology, University of Jammu, Jammu – 180006, India 3. Overview: Introduction to Bioinformatics Mohit Kumar Sharma and Manoj k. Dhar School of Biotechnology, University of Jammu, Jammu-180006,India
Initiation of R&D activities in Bioinformatics The centre promotes Bioinformatics awareness and fosters the growth of Bioinformatics and allied disciplines and catalyzes the initiation of Bioinformatics and interdisciplinary research in teamwork with wet lab Biotechnology researches. Research efforts are initiated which will provide insight into the In-silico analysis with main spotlight in biotechnology research.
Details of Training / Workshops organized and total no. of users trained The Centre conducted various hands on sessions for lecturers (10+2) 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 Lecturers(10+2) 40 Biotechnology 13 Biochemistry 7 Microbiology 8
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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 software available is being used for Phylogenetic analysis by several research scholars.
Future activities The focus will be on research activities in Bioinformatics and the centre plans to start the Certificate courses and Diploma courses on Bioinformatics. The Centre proposes to conduct three day workshop for University and college teachers during third week of February 2008. The other routine services of the Centre would be continued efficiently.
Additional details
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]
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University of Kalyani, Kalyani Coordinator: Dr. Alpana Seal Summary of the progress made by the centre from its inception The centre was inaugurated on 28th March, 07. 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 are going on in a regular basis. Scientific Software package GCG. DS Suite, Geneious Pro and other scientific program packages, free for academicians have been installed. The database CSD and in house database on DEHYDROGENASE (http://www.bifku.in/DBD/) is available. Since its inception three workshops has been arranged and another national workshop on “Evolutionary Biology” will be arranged in this financial year.
Major research activities in Biotechnology and its related fields Department of Biochemistry and Biophysics: ` 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. ` Molecular modeling of protease inhibitor interaction. ` Molecular Mechanism of Artificial Transformation of E. coli with Plasmid DNA. ` siRNA technology for knocking down a gene (in collaboration with SINP, Kolkata) Department of Molecular Biology and Biotechnology: ` Molecular Phylogeny of Indian Shad Tenualosha ilisha inferred using mitochondrial DNA partial gene sequences. ` Molecular Breeding of Rice with Special Reference to Marker Assisted Gene Pyramiding for Biotic Stress Resistant. ` An Investigation on Somaclonal Variance of certain Aromatic Plants using Biochemical and Molecular Approaches. ` 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. ` An exploration of in vitro somatic embryogenesis of two important medicinal plants and their biomodulatory mechanism. ` Identification of DNA markers associated with disease and pest resistant in Mulberry. ` A study on induction of somatic embryos and over-expression of SAM Decarboxylase in Limonium sinensis through transgenesis. Area of Specialization of the centre I. Molecular Modeling II. Computational Biology Major activities of the centre during the year 2008-09 ` National workshop on ‘Systems Biology and Its Use’ was arranged held during 18th-22nd November, ’08. ` Another national workshop on ‘Evolutionary Biology’ will be held during 17th-20th February,’09. ` Some local training programs have been arranged to introduce Bioinformatics in the neighborhood. ` Talks on Bioinformatics was delivered at undergraduate college for students of Physics/Chemistry ` Accelrys DS programme, Geneous Pro packages has been installed. ` Other free scientific programme packages (DOCK, AUTODOCK, GROMACS, MODELLER, HEX, PYMOL, MEGA-4, TREEVIEW, JALVIEW, PHYLIP, CHEMAXON etc.) have also been installed for use according to requirement. ` CSD was installed and updated. ` An in-house database on dehydrogenase was built and published on web (http://www.bifku.in/DBD/). ` Trying to interact with local hospitals and other local institutions to generate Medical & Pharmaceutical Databases and to start collaborative work. ` Appointment to two DBT funded studentship was given.
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Infrastructure facilities in the Bioinformatics Centre A. Computer & Communication facility: 1) Ten P (IV) Lenovo desktop Computers with 17" TFT monitors 2) One high-end (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: BSNL Broadband (2 MBPS) connection (annual). B. Scientific software packages: Operating System Softwares: As recommended by DBT. Scientific Software: 1) Acclerys GCG & DS package. 2) Shelx-97 package. 3) Geneious Pro 4.5.6 4) Some software free for academicians. C. Databases & other information resources: 1) Developed one database on the enzyme Dehydrogenase. 2) Cambridge structural database Details about staff members working in the centre 1) Shri Rajabrata Bhuyan, Research Assistant 2) Shri Gautam Kundu, Office assistant Types of services provided Teaching/training students. Project and Research workers are also using the facility.
Educational activities with details of placement Training students, arranging national workshops, initiated project work and research activities.
Initiative to validate the outcome of bioinformatics resources: We have initiated Collaborative works/ initiatives Initiatives has been taken to collaborate with nearby Institutions and other research institutes in Kolkata.
Databases/ Software packages developed Till now one database on dehydrogenase has been developed.
Papers published or presented in the conferences with reference: Diversity in Carbon Assimilation and Transfer of C4 traits into C3 Plant: M.K.Adak and D.N.Sengupta* Department of Botany, University of Kalyani, Kalyani 74 1235, West Bengal,* Department of Botany, Bose Institute, 93/1, A.P.C. Road, Calcutta 700 009, West Bengal, XVIII Annual Conference of Indian Association for Angiosperm Taxonomy and International Seminar on Multidisciplinary Approaches in Angiosperm Systematics, 11th – 13th October 2008 Initiation of R&D activities in Bioinformatics: Nothing started yet. Details of Training/ Workshop organized and total no. of user trained We have arranged one national workshop till now and trained sixteen participants in the current financial year. We will arrange another one in February,’09.Training of University students, researchers and project workers are also going on in regular basis..
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Impact shown 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 sixteen participants were trained. V. A database on dehydrogenase has been developed. Future activities: We plan to Research on: ` Modeling studies of membrane system. ` Structural Bio-informatics to develop novel drug molecules. ` Cluster and self assembly study. ` Protein – ligand interactions. 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. 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: http://bifku.in Name of Contact Person(s): Dr. Alpana Seal Email: same as above
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University of North Bengal, Siliguri Coordinator: Dr. Arnab Sen Since its inception in November 2006, we have marched forward steadily. The center has every modern facility of information and communication including necessary hardware and software. There were a number of publications in journals and posters presented in national and international conferences on the relevant areas.
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.
Area of specialization of the centre: Microbial genomics, molecular modeling, molecular phylogenetics Major activities of the centre during the year 2008-09 Three National Level Workshops on Bioinformatics were held from 18th-20th January 2008, 7th-9th March 2008 and 7th-9th November 2008. About 65 participants (students, research scholars and faculties) in total from different disciplines of biological sciences were provided training on databases, codon usage, molecular modeling, alignment tools and molecular evolution. Another has been planned from 12th-14th February, 2009. Four volumes of the official newsletter of the NBU Bioinformatics Facility “BIOINFOLINE” have been published. Our website www.nbu.edu.in/bioinformatics has been launched. The Coordinator Dr. Arnab Sen has an International collaboration with the University of New Hampshire, USA. He along with Prof. Louis S 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 bacterial genes on the basis of codon usage, molecular phylogeny and molecular modelling has been done.
Infrastructure facilities in the Bioinformatics Centre: Computer and communication 10 PCs with OS, One High end server and a Medium end server, One Toshiba make Laptop, One Laser printer (network), one Desk-Jet printer, One Canon make Photocopier, one Sony make LCD Projector, CISCO 1700 Leased line Router. Purchase of some more PCs, Servers and software are in process. 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, Fedora 7 Linux, 10 Quick Heal AVG Antivirus Package. Acclerys Gene Package, MAUVE, GRIL, GENOME BROWSER, BIOEDIT, CODONS, CODON W, MATLAB 5.0, MODELLER 9v4, CLUSTAL W, CLUSTAL X, DNAsp 4.0, MEGA 4.0, TREEVIEW, PHYLODRAW, CHIMERA, SPDBV, RASMOL, PHYLIP, PAUP, DAMBE, VMD, Jcat, Argus Lab, C++ and PERL. Other resources Dedicated 256 kbps Internet Leased line from BSNL, 4Mbps Line from Reliance and 2Mbps line from VSAT.
Details about staff members working in the center Serial No. Name of the Staff Designation Working Since 1 Saubashya Sur Research Associate February 2008 2 Subarna Thakur Traineeship Holder January 2009 3 Arvind Kumar Goyal Traineeship Holder January 2009 4 Tanmayee Mishra Studentship Holder January 2009 Types of service provided The center 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.
Educational activities with details of placement Three PhD students (S. Sur, U.K.Mondal and S. Thakur) are currently engaged in their research work utilizing the facility. Besides faculty members, students and research scholars from other departments, institutes and nearby areas utilize this facility.
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Collaborative work and initiatives The Coordinator Dr. Arnab Sen has set up International collaboration with the Department of Microbiology, University of New Hampshire, USA.
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. We are in a process of developing a plant identification database and bamboo database of North Bengal.
Papers published or presented in the conferences /workshops in the year 2008-09 · Sen A., S Sur, AK Bothra, LS Tisa, & UK Mondal. (2008). Homology modeling of Nif H proteins from Frankia EAN1pec. 15th International Frankia and actinorhizal plants meeting. Bariloche, Argentina. · Furnholm TR, A Sen, A Konisky & LS Tisa (2008). Frankia sp. strain EAN1pec Gene Expression in Response to Heavy Metal Stress. 15th International Frankia and actinorhizal plants meeting. Bariloche, Argentina. · Sur S, S Thakur, UK Mondal, AK Bothra & A Sen (2008). Homology modeling of Nif H proteins from Frankia. International Symposium on Microbial Biotechnology: Diversity, Genomics and Metagenomics. University of Delhi, Delhi, India. 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. Three PhD students (S. Sur, U.K.Mondal and S. Thakur) are actively pursuing their research work.
Details of Training/ Workshop organized and total number of user trained NBU Bioinformatics Facility organized three National Level Workshops on Bioinformatics from 18th-20th January 2008, 7th-9th March 2008 and 7th-9th November 2008. About 65 research scholars, students and faculties from different disciplines of biological sciences participated in the workshops. Another will be conducted from 12th-14th February, 2009. Frankia Genome sequencing project collaborating laboratory: The Coordinator of NBU Bioinformatics Facility, Dr. Arnab Sen has set up a long-term collaboration with Dr. Louis S. Tisa, Department of Microbiology, University of New Hampshire, USA. He along with Dr. Louis S. Tisa has been working towards the complete genome sequencing of five Frankia strains collected from different parts of the world.
Impact shown by the centre on the growth of biotechnology and allied areas Research publications from the Centre (2008-09) Sen A, S Sur, LS Tisa, AK Bothra, S Thakur & UK Mondal (2009) Homology modelling of nitrogenase iron proteins from three Frankia strains. Symbiosis (communicated) Thakur S, AK Bothra, S Sur, BS Bajwa & A Sen (2009). Molecular modeling of a NifH protein from Bradyrhizobium sp. ORS278. InSilico Biology (communicated) Mondal UK, B Das, TC Ghosh, A Sen, & AK Bothra (2008). Nucleotide Triplet Based Molecular Phylogeny of class-I and classII Aminoacyl t-RNA. Journal of Biomolecular Structure and Dynamics 26: 321-328. Sur S, AK Bothra, M Bajwa, LS Tisa & A Sen (2008). In Silico analysis of Chlorobium genomes divulge insights into the subsistence of the bacteria. Research Journal of Microbiology 3: 600-613. Mondal UK, S Sur, AK Bothra & A Sen (2008). Comparative analysis of codon usage patterns and identification of predicted highly expressed genes in five Salmonella genomes. Indian Journal of Medical Microbiology 26: 313-321. Sur S, M Bhattacharya, AK Bothra, LS Tisa & A Sen (2008). “Bioinformatic analysis of codon usage patterns in a free living diazotroph, Azotobacter vinelandii”. ‘Biotechnology’ 7: 242-249. Sen A, S Sur, AK Bothra, DR Benson, P Normand & LS Tisa (2008) “The implication on life style of codon usage patterns and predicted highly expressed genes for three Frankia genomes. Antonie van Leeuwenhoek” 93: 335-346.
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Future activities · Development of software for the analysis of DNA sequencing data and protein. · Annotation and analysis of five Frankia genomes whose sequencing has been undertaken. · Development of plant identification database and Bamboo database of North Bengal. · Bioinformatics analysis of nitrogen fixing and food pathogenic bacterial genomes. · Molecular modeling of some nitrogen fixing proteins and bacterial toxin proteins. · Publication of Newsletter and conducting various training programs/workshops and seminar/ conference in bioinformatics. Additional Details
Coordinator: Dr. Arnab Sen NBU Bioinformatics Facility, Department of Botany, University of North Bengal, Siliguri-734013 Phone: +91-353-6528172, Fax : 0353-2699106 E-mail: [email protected], [email protected] Deputy Coordinator: Dr. Asim K Bothra Chemiinformatics Bioinformatics Laboratory Department of Chemistry Raiganj (University) College, Raiganj-733134 Phone: 9474441570; E-mail: [email protected]
260 XXth All India Coordinators’ BTISnet Meeting February 03-04, 2009
University of Rajasthan, Jaipur Coordinator: Dr. S. L. Kothari Summary of the progress made by the centre from its inception (a) The sanction for the establishment of BIF was issued by DBT through its order number BT/BI/04/055/2001 dated 22.09.06. University in its Centre for Converging Technologies has provided independent accommodation 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 preparation has been completed. The university has provided one direct phone line. The executive committee has been constituted. One R.A has been appointed since 1.12.07. (b) Activities of the centre in one last year are as follows: · Workshop in Bioinformatics : Introduction and Application.(7th- 9th Feb, 2008) · Workshop in Biotechnology and Bioinformatics (25th-26th September, 2008) · National Workshop on Biological Sequence Analysis. (9th- 10th January, 2009) · National Workshop on Introduction to Bioinformatics. (11th – 12th January, 2009)
Major research activities in biotechnology and its related fields at your institution (a) The institution has biotechnology and its related fields of study in the departments of Botany, Zoology, Biotechnology, Microbiology, Chemistry and Centre for Converging Technologies. 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 i.e, N – Nanomaterials & Nanotechnology B – Bioinformatics & Biotechnology I – Information & Communication Technology C- Cognitive Neuroscience (b) Two Ph.D students are working on Bioinformatics. (c) Bioinformatics is a part of the curriculum of the M.Tech programme of the Centre for Converging Technologies. Area of specialization of the centre: Converging Technologies Major activities of the centre during the year 2008-2009 Following four national workshops were held during this year: • Workshop in Bioinformatics : Introduction and Application.(7th- 9th Feb, 2008) • Workshop in Biotechnology and Bioinformatics (25th-26th September, 2008) • National Workshop in Biological Sequence Analysis. (9th- 10th January, 2009) • National Workshop on Introduction to Bioinformatics. (11th – 12th January, 2009). For college students. Infrastructure facilities in the Bioinformatics Centre A. Computer and Communication facility: 11 Desktop Computers, 2 Servers, 1 coloured printer and 1 black & white printer. B. Scientific Software packages. C. Databases and other information resources. Details about staff members working in the centre Ranjeeta Bonal R.A Bioinformatics One Year
261 Bioinformatics Infrastructure Facility (BIF) for Biology Teaching Through Bioinformatics (BTBI)
Types of services provided The 5- year integrated M.Tech course in CCT take the help of BIF.
Initiation of R&D activities in Bioinformatics Two Ph.D scholars are working in the subject area of Bioinformatics.
Details of Training/Workshop organized and total no. of users trained • Workshop in Bioinformatics : Introduction and Application.(7th- 9th Feb, 2008) No. of participants: 20 • Workshop in Biotechnology and Bioinformatics (25th-26th September, 2008) No. of participants: 26 • National Workshop in Biological Sequence Analysis. (9th- 10th January, 2009) No. of participants: 32 • National Workshop on Introduction to Bioinformatics. (11th – 12th January, 2009) No. of participants: 28
Future activities • Organization of workshops for teachers, researchers and university faculty. • Organization of National level seminars. • Lectures by eminent scientists. • Hands-on practical training for researchers. • Making R&D proposals in Bioinformatics.
Additional Details
Name of the coordinator Prof. S. L. Kothari Postal Address Centre for Converging Technologies, University of Rajasthan, Jaipur, 302004 Phone No. 0141-2700370, 2712489
262 XXth All India Coordinators’ BTISnet Meeting February 03-04, 2009
Vidyasagar University, Midnapur Coordinator: Prof. Bikas Ranjan Pati Summary of the progress made by the center from its inception Bioinformatics laboratory of our center is start to functioning since August’ 2007. From the inception of this centre our aim is 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 eight training programme in different aspects of Bioinformatics like Structural Bioinformatics, Computational Biology, Database & data mining, and Evolution & Phylogeny and trained more than 200 students. We also established a local area network in our department. We have procured 12 PC and few softwares and installed many from the internet, which are sufficient at this stage. One manpower (RA) has been recruited and research work initiated.
Major research activities in Biotechnology and its related fields Our faculties are actively engaged in research in different aspect of biotechnology. Major field of research are:- I. Microbial enzyme (amylase, tannase, xylanase, chitinase) production and scale up process. II. Production of microbial polysaccharides and antibiotics. III. Biofertilizer production and transfer of technology. IV. Anticancer substances from mashroom. V. Antioxidant and antidiabetic constitute from medicinal plants. VI. Development of new fish feed. Area of specialization of the center a. Microbial fermentation; b. Biofertilizer ; c. Medicinal plants; d. Mashroom polysaccharides; e. Fish feed Major activities of the center during the year 2008 - 09 In this session we have completed four short-term workshops for: • UG and PG students • College and University teachers • Ph. D. scholars Now we are starting some shorts of proteomics research work in our center. • We have published eight research papers (see item no. 12) Infrastructure facilities in the Bioinformatics Centre Computer & Communication facility Computer Hardware : Server high end, Server medium, IBM PCs (10 nos), Laptop (one), Assembled desktop (one), Printer-2 (laser and Desk Jet), Photocopier (one), Scanner (one), External HD (two) Communication facility: Twenty four hours internet facility and one dedicated telephone (no. 03222 – 274173) is available in this center. Scientific software packages ActivePerl 5.10.0, ii) Modeller9v5, iii) CLC 5.1.2 Sequence Viewer, iv) Codon W, v) Clustal W, vi) MEGA 4.0, vii) Red Hat Linux 5.0 OS, viii) Sigma plot 11.0 with enzyme kinetics. Databases & other information resources Some free software collected from the internet and used regularly – GenBank http://www.ncbi.nlm.nih.gov/Web/GenBank/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
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NCBI http://www.ncbi.nlm.nih.gov Ensemble http://www.ebi.ac.uk/embl/ DDBJ Http://www.ddbj.nig.ac.jp/ TIGR http://www.tigr.org/tdb/e2k1/ath1/ ASDB http://hazelton.lbl.gov/~teplitski/alt/ ExPASy Proteomics Server http://www.expasy.ch/ SWISS-MODEL http://swissmodel.expasy.org/SWISS-MODEL.html Some specific software could not purchase due to shortage of fund. We can procure it whenever next allotment is available. Details about staff members working in the center There is no permanent staff in our center. Following departmental faculty and staff are actively engaged in this center – Prof. B. R. Pati (Coordinator of BIF center) Dr. K. C. Mondal (Faculty, Microbiology Department) Dr. D. Banerjee (Faculty, Microbiology Department) Dr. P. Das Mohapatra (Faculty, Microbiology Department) Mr. Bipulesh Bhowmik [RA, BIF center] Mr. J. Chalak (Staff, Microbiology Department) Mr. Biplab Chakraborty, [Information scientist] BE (Computer Science) Types of services provided a. Data retrieval b. Sequence analysis c. Laboratory supports to our students for learning their course curriculum. d. Internet & e-journal facilities to the PG students, Ph D scholars and faculties. e. Computational facility to all users of the University. f. Short term training & workshops are given to different scientific communities. Educational activities with details of placement At present we are not able to provide any type of conventional course on Bioinformatics but short-term training are given in regular interval. However our students regularly utilize this center for their M. Sc. dissertation works.
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. But response of each participant is very good and they are satisfied with our course contents training offer. 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.
Collaborative works/ initiatives We are trying to develop our research in collaboration with Bioinformatics Centre, Bose Institute, Kolkata and Department of Biotechnology, IIT, Kharagpur.
Databases/software packages developed We are not able to develop any software / databases. We have only collected free and available softwares from the internet.
Papers published or presented in the conferences with reference Paper Published Kar S., Mandal A., Das Mohapatra P. K., Samanta S., Pati B.R. and Modal K. C. (2008) Production of xylanase by immobilized Trichoderma reesei SAF3 in Ca-alginate beads, Journal of Industrial Microbiology and Biotechnology, 35, 245–249.[Germany] Mandal A., Kar S., Das Mohapatra P. K., Maity C.,Pati B.R. and Modal K. C. (2008) Xylanase production under submerged fermentation by newly isolated Bacillus cereus BSA1: Parametric optimization of cultural conditions, Journal of Pure & Applied Microbiology, 2, 155-160. [India]
264 XXth All India Coordinators’ BTISnet Meeting February 03-04, 2009
Samanta S., Kar S., Jana M., Maity C., Das Mohapatra P. K., Pati B.R. and Modal K. C. (2008) Study of the potentialities of immobilized bacterial a-amylase on coconut coir, a smart carrier for biocatalysts, Biocatalysis and Biotransformation, 26, 1-5. [UK] Mandal S.M., Ghosh A.K., Pati B.R. and Das A. K. (2008) Detection of trivalent arsenic [As (III)] complex with DNA: a spectroscopic investigation, Toxicological & Environmental Chemistry, 1 - 6. [Germany] Maity C., Das Mohapatra P. K., Pati B.R. and Modal K. C. (2008) A simple gel detection method of microbial tannin acyl hydrolase (EC. 3.1.1.20), World journal of Microbiology &Biotechnology, DOI 10.1007/s11274-008-9935-8, Internet publication [UK]. Mandal A., Kar S., Das Mohapatra P. K., Maity C., Pati B.R. and Modal K. C. (2008) Purification and Characterization of an Endoxylanase from the Culture Broth of Bacillus Cereus BSA1, Applied Biochemistry And Microbiology, Accepted. [Russia] Das Mohapatra P.K., Mondal K.C. and Pati B.R. (2008) Effect of amino acids on tannase biosynthesis by Bacillus licheniformis KBR6, Journal of Microbiology, Immunology and Infection (JMII03-05-028), Accepted. [China] Mandal S.M., Pati B.R., Das A.K., Ghosh A.K. (2008) Characterization of a symbiotically effective Rhizobium resistant to arsenic: Isolated from the root nodules of Vigna mungo (L.) Hepper grown in an arsenic-contaminated field, Journal of General and Applied Microbiology, Accepted. [Japan] Papers presented in conferences The following research articles of our laboratory were presented in conferences: Dr. Keshab C. Mondal delivered lecture on “An investigation on the alteration of gastrointestinal flora after varying atmospheric pressure” in the International congress on “Life and Living in High Mountains” held at Delhi on 28-30th November 2008. Dr. Pradeep K. Das Mohapatra presented a paper entitled “Tannase production by Bacillus licheniformis KBR6: Optimization of submerged culture conditions by Taguchi DOE methodology” in the 3rd International Congress on Bioprocesses in Food Industries [ICBF 2008] in Osmania University during 6 – 8th November 2008 at Hyderabad. Dr. Sanjoy Kar presented a paper entitled “ Parametric optimization of production and extraction of xylanase from the newly isolated Trichoderma reesei SAF3 under solid state fermentation” in the 3rd International Congress on Bioprocesses in Food Industries [ICBF 2008] in Osmania University during 6 – 8th November 2008 at Hyderabad. Mr. Chiranjit Maity presented a paper entitled “Production of microbial tannase using tea leaf-extracts as solid substrate” in the 3rd International Congress on Bioprocesses in Food Industries [ICBF 2008] in Osmania University during 6 – 8th November 2008 at Hyderabad. Initiation of R & D activities in Bioinformatics Two M. Sc. students started project work in Bioinformatics in our center with active support of IIT, Kharagpur and Bose Institute, Kolkata.
Impact shown by your center on the growth of biotechnology and allied areas Our BIF center is becomes a nodal center for information collection and data processing in our University and our surrounding institutes. PG students and research scholars are regularly used our center. They collect the information from our high speed internet, search different databases, validate the data by our statistical software and make different types of graph through Sigma plot software.
Paper published 08 Paper presented in conference : 06 Manpower trained: 203
265 Bioinformatics Infrastructure Facility (BIF) for Biology Teaching Through Bioinformatics (BTBI)
Future activities a. Project has been sent to DBT on 21.11.2008 for Initiation of refresher course for college and university teachers on ‘Bioinformatics & Advance Biology’. b. Initiation of research in our center. c. Regular workshop and training on different fields of bioinformatics for UG & PG students. d. Purchase of software and appointment of a research associate. e. 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
266 XXth All India Coordinators’ BTISnet Meeting February 03-04, 2009
West Bengal University of Technology, Kolkata Coordinator: Dr. Raja Banerjee Summary of the progress The Dep t. of Bioinformatics was founded for PG teaching and research in the year 2005. The courses offered in Bioinformatics– I. M. Tech. in Bioinformatics, II. Post B.SC. Int. Ph.D in Bioinformatics. For details : www.wbut.ac.in, www.utechbiotech.org 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. 13.50 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), jointly organized by DBT and University of Pune. An MoU has been signed for DOEACC-B level programme for M.Sc.(Tech) in Bioinformatics.
Major Research Activities in Biotechnology and its Related Fields A number of ongoing research stresses on Microbial Biodiversity, Plant Biotechnology(heavy metal homeostasis in plants), Conformational analysis of short designed peptide motifs, metal binding small molecules used for therapeutic purpose, design of biomimic–bioactive molecules involving construction of minimalist version of sequences with predefined structure, Human Molecular Genetics and Human Cordblood Stem Cell. Grants were received from DBT, BRNS, ICMR
Areas of Specialization of the Centre: ZTUS – Zero Tolerance in Unlicensed Software Major activities of the centre during the year 2008-2009 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. Users from more than 125 countries other than India have downloaded approximately 112 TB in the first 15 days of January 2008. In India more than 100 TB of viewed data has been downloaded. Workshops Organized: Bioiformatics – 1. Five days hands on workshop cum seminar on Molecular Dynamics from 24th March to 28th March 2008 and Numbers of seminars were organized. 2nd Annual JC Bose Memorial lecture by Prof. B. Sanyal, honored by the French Govt. with Legion de honor (Feb 22nd 2008). Research Activities: Research has focused on the mechanism of action of chemical carcinogens in DNA; conformational analysis of short designed peptide motifs with design of biomimic – bioactive molecules involving construction of minimalist version of sequences with predefined structure; sequence analysis of a plant specific family of receptor like kinase proteins; developing a bioinformatics software suite with a graphical interface, molecular dynamics study on heteropolymerization of a biological pigment; pharmacophore modeling and database designing for comparative study. Projects Approved: Design of ‘anion recognition’ short peptide motifs : an approach towards designing ‘model scaffolds’ for binding by DBT,Govt of India to Dr. Raja Banerjree Publications in peer-reviewed Journals: Bioinformatics – 5, Biotechnology – 8 Infrastructure facilities in the Bioinformatics Centre: Computer & Communication facility Hardware – IBM X226, IBM X206, IBM Intellistation Z Pro, IBM x3650, TFT Monitors, 2 D-Link v92 Modem; Scientific Software – the laboratory runs primarily on Open Source and free 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.
267 Bioinformatics Infrastructure Facility (BIF) for Biology Teaching Through Bioinformatics (BTBI)
Details about staff members working in the centre Professor Rabi Majumdar, Advisor, Molecular Biophysics, 3yr Dr. Raja Banerjee, Reader, Spectroscopy & Structural Biology,3.5 yr Dr. Soumalee Basu, Lecturer, Computational Biology & Bioinformatics, 3.5yrs Mr. Subhrangshu Supakar, Project Officer, Pharm. & Bioinformatics, 3yr Ms. Aulie Banerjee, Project Officer, Botany & Bioinformatics, ~3yr Ms. Sujata Roy, Project Officer, Molecular Modelling, 2.5 yr Ms. Aditi Moulik Types of service provided The centre provides training programmes. Initiative to validate the outcome of bioinformatics resources:
Placement of students – 95% students are placed either in industry or academics. 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 USA-based company specialises in development of software related to Patent database signed an Agreement. Hinovation Research Centre Pvt.Ltd. is another incubatee. Besides, faculty members have collaboration with many premier national and international level institutes.
Initiation of R&D activities: see collaborative works. Details or training/ workshop organized and total no of users trained: 20 (see workshop) Impact shown by your centre on the growth of biotechnology and allied areas: in teaching and research Future workshops workshops have been planned and will be organized soon on Python, Molecular Dynamics, Workshop on Qt
Programs Setting up of High Performance Computational Platform for working on problems involving parallelized codes run on clusters. The areas of interest would include: Molecular dynamic analysis of protein-ligand interactions, Molecular modeling, Fluidity analysis of formulation involving proteins/drug molecules. Planned to purchase IBM 3450 Quad core server with 300 GB HDD, CPU(Quad core) X 2. 2GB RAM
Additional details
Name of the Coordinator: Dr. Raja Banerjee 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], [email protected] Website: www.wbut.net and www.utecbiotech.org Name of Contact Person(s): Dr. Raja Banerjee, [email protected] [email protected] Mr. S. Supakar, [email protected], [email protected]
268 Itanagar Dibrugarh
Sikkim Jorhat Tezpur Guwaha Kohima
Shillong
Silchar Imphal
Amritsar Tripura
Izatnagar Aizawl
Pantnagar
Sikkim
Siliguri
Kharagpur
Bhubaneshwar Mumbai
Goa Tirupa
Mangalore Kannur Kasaragod Chennai Pondicherry Coimbatore Port Blair Thrissur Thiruchiparpallli Calicut Madurai
Thiruvananthapuram
Centre of Excellence Distributed Informa on Centre Distributed Informa on Sub-Centre Bioinforma cs Infrastructure Facility (BIF)
Prof. Veena Tandon Phone No. : (0364) 2721241 / 2721242 Deputy Coordinator Fax No. : (0364) 2550150 Bioinforma cs Centre Email : [email protected], North-Eastern Hill University nehuniv.b snet @nic.in Shillong 793 022, India