Centre for Bioinformatics Imperial College London Second Report 31 May 2004 Centre Director: Prof Michael Sternberg www.imperial.ac.uk/bioinformatics [email protected] Support Service Head: Dr Sarah Butcher www.codon.bioinformatics.ic.ac.uk [email protected] Centre for Bioinformatics - Imperial College London - Second Report - May 2004 1 Contents Summary..................................................................................................................... 3 1. Background and Objectives .................................................................................. 4 1.1 Objectives of the Report........................................................................................ 4 1.2 Background........................................................................................................... 4 1.3 Objectives of the Centre for Bioinformatics........................................................... 5 1.4 Objectives of the Bioinformatics Support Service ................................................. 5 2. Management ......................................................................................................... 6 3. Biographies of the Team....................................................................................... 7 4. Bioinformatics Research at Imperial ..................................................................... 8 4.1 Affiliates of the Centre........................................................................................... 8 4.2 Research............................................................................................................... 9 5. Teaching .............................................................................................................. 11 5.1 MSc in Bioinformatics.......................................................................................... 11 5.2 Wellcome Trust 4 year PhD in Bioinformatics..................................................... 11 5.3 Computational Bioinformatics ............................................................................. 11 6. The Bioinformatics Support Service.................................................................... 12 6.1 Introduction ......................................................................................................... 12 6.2 Management ....................................................................................................... 12 6.3 Hardware, Software and Databases ................................................................... 12 6.4 Support & Training .............................................................................................. 16 6.4 Research Projects............................................................................................... 16 6.5 Grants ................................................................................................................. 17 6.6 Courses............................................................................................................... 17 6.7 Financial Arrangements ...................................................................................... 17 7. The London Bioinformatics Forum...................................................................... 19 7.1 Mission of the London Bioinformatics Forum ...................................................... 19 7.2 Objectives ........................................................................................................... 19 7.3 Management ....................................................................................................... 19 7.4 Activities.............................................................................................................. 19 8. Seminar Programme........................................................................................... 20 9. Achievements and Plans..................................................................................... 22 9.1 Achievements...................................................................................................... 22 9.2 Plans ................................................................................................................... 22 Appendix 1 - Selected Publications........................................................................... 23 Centre for Bioinformatics - Imperial College London - Second Report - May 2004 2 Summary The mission of the Centre for Bioinformatics is to promote and co-ordinate world-class research and training in Bioinformatics within Imperial College London and to provide state-of-the-art Bioinformatics support to members of Imperial for their research. Our second report describes the activities of the Centre from 1st February 2003 to 31st May 2004 and documents our publications and grants for the calendar year 2003. Additional information can be found at www.imperial.ac.uk/bioinformatics. The main achievements of the Centre during this period are: • The provision across the College of a Bioinformatics Support Service with 230 registered users as of May 2004. • The successful role of the Bioinformatics Support Service in obtaining a £600K BBSRC grant for the application of E-science to provide support for microarray analysis. • The development of collaborative research projects between the Support Service and several research groups in the College. • The expansion of the Centre with the addition of 11 new Affiliates. • The publication by our Affiliates of more than 50 refereed papers in Bioinformatics during 2003. • The award during 2003 of more than £2 million of grant support for research and training in Bioinformatics. • The co-ordination of postgraduate teaching of Bioinformatics across the College. • The running of a seminar series that attracts an audience from the College and other organisations in the London area. • The establishment with colleagues from other London groups of the London Bioinformatics Forum. Centre for Bioinformatics - Imperial College London - Second Report - May 2004 3 1. Background and Objectives 1.1 Objectives of the Report This is the second report of the Centre for Bioinformatics and covers the period 1st February 2003 to 31st May 2004. The objectives of this report are: • To document the status of the Centre as of May 2004, particularly describing the contribution from our Steering Committee, External Advisors and the Affiliates. • To highlight the main developments over the period of this report. • To describe the activities of the Bioinformatics Support Service in terms of facilities provided and its uptake by users. • To report grants awarded and publications for the calendar year 2003. 1.2 Background • Bioinformatics can be defined as the use of computational, mathematical and statistical methods to organise, analyse and interpret biological information, particularly at the molecular, genetic and genomic levels. • Bioinformatics is central to the interpretation and exploitation of the wealth of biological data being generated in the post-genome era with the consequential major clinical and commercial benefits. • It is vital that Imperial has world-class research in Bioinformatics together with state-of-the-art facilities for all users. Since Bioinformatics research is located in all four Faculties, a clearly identifiable focus is required, in particular to co- ordinate multi-disciplinary research. In parallel, it is essential to provide biologists and clinical reseachers with state-of-the-art Bioinformatics to empower them to deliver world-class research. • To address these issues, in 2001 the Deputy Rector together with the Faculties of Life Sciences and of Medicine established the Centre for Bioinformatics and the associated Bioinformatics Support Service. • The Bioinformatics Support Service is located on the newly-refurbished third floor of the Biochemistry Building on the South Kensington Campus. This acts as the focus for the Centre with its links to the different Departments and Campuses of the College. Centre for Bioinformatics - Imperial College London - Second Report - May 2004 4 1.3 Objectives of the Centre for Bioinformatics The objectives of the Centre for Bioinformatics are to: • Co-ordinate the strategic development of Bioinformatics at Imperial across the four Faculties and at the different Campuses. • Develop new collaborative projects within and outside Imperial, particularly those that are multi-disciplinary. • Contribute to a broad College-wide view of Bioinformatics including the development of links with areas such as statistical genetics, chemometrics and image processing. • Have a strategic role in the provision of teaching and training in Bioinformatics. • Organise seminar programs and symposia on Bioinformatics. • Disseminate relevant software, databases and information to the UK and world scientific communities, both academic and industrial. • Facilitate the provision of state-of-the-art Bioinformatics support to members of Imperial by directing the Bioinformatics Support Service. 1.4 Objectives of the Bioinformatics Support Service The objectives of the Bioinformatics Support Service are to provide the following services to all Imperial Campuses: • In-house facilities for major Bioinformatics tasks, such as sequence database searching and microarray processing. • Access to appropriate commercial software and data. • Curated links to public domain sites providing additional services. • Expertise and training courses on the use of the above facilities. • Collaborative