NeSC Review 11 th October 2004

1. BRIDGESStatus ReportDr Richard SinnottTechnical Director National e-Science Centre||| Deputy Director Technical Bioinformatics Research Centre University of Glasgowros@dcs.gla.ac.uk NeSC Review 11th October 2004

2. Overview • The team • Review goals of Bridges project • Brief summary of technical approach • Outline achievements thus far • Plans for the future

3. Project Participants • The BRIDGES team • Project Leaders • Dr Dave Berry (NeSC Edinburgh) • Dr Richard Sinnott (NeSC Glasgow) • Developers • Dr Micha Bayer (NeSC Glasgow) • Derek Houghton (NeSC Glasgow) • Magnus Ferrier (NeSC Edinburgh)… left on 24th September • Principle Investigators • Prof Malcolm Atkinson • Prof David Gilbert • Steering Committee • Dr Ela Hunt • Prof Anna Dominiczak • Other Key People Involved • David White, Andy Knox, Colin Henderson (IBM) • Neil Hanlon, Rick Dixon, Donald Dunbar, Janice Paterson (CFG)

4. Bridges Goals • High blood pressure affects 25% of adults in western societies • Cardiovascular Functional Genomics (CFG) project investigating this through physiological models of hypertension in rat • Bridges is a supporting project to CFG and will provide Grid infrastructure to facilitate scientific research • CFG project partners are distributed but need to access and integrate various software and especially data resources Main aims of BRIDGES are to develop re-useable infrastructure to provide data federation incorporating appropriate security concerns

5. Information Integrator OGSA-DAI Magna Vista Service SyntenyService blast + Bridges Project

6. Achievements • Web site and project portal established • http://www.nesc.ac.uk/hub/projects/bridges • Engaged with CFG consortia • Lots of new requests from CFG on how existing tools can be taken forward • Scenarios for linkage between tools • Local life science data repository developed • Linked to data that can be federated and populated with data that cannot be federated (e.g. no programmatic access) • Includes shared data sets of CFG scientists • QTL DB, …microarray data coming

7. Achievements …ctd • GT3 based BLAST Grid service that provides access to and usage of high-throughput compute resources • includes access to large e-Science infrastructures at Glasgow (ScotGrid++) and local Condor pool • implements own meta-scheduler • SyntenyVista tool extended to allow Grid enabled visual navigation of genomic data sets • MagnaVista tool developed to allow discovery and analysis of genomic data sets • These will all be demonstrated

8. Achievements …ctd • Results are being widely known • Dissemination important • Conferences • Seminars • Commercial interest • Influencing standards development • GGF AuthZ • Feedback to relevant groups • Involved in GGF Life Science Grid Research Group

9. Dissemination • Publications: • UK e-Science All Hands Meeting 2003 (poster) • Invited paper to Life Science Grid Conference, Kanazawa, Japan 2004 • UK e-Science All Hands Meeting 2004 (paper, 2 posters) • Intelligent Systems for Molecular Biology (ISMB)/European Conference on Computational Biology (ECCB), Glasgow, Aug 2004 (poster) • Presentations/Seminars: • Seminar at University of Stirling, "Grids and Life Sciences", March 2004 • Life Science Grid Research Group, Global Grid Forum, Hawaii, June 2004 • HPCInform meeting, Strathclyde University, Glasgow, September 2004 • Life Science Grid Research Group Global Grid Forum, Brussels, September 2004 • Demos: • Life Science Grid Research Group, Global Grid Forum, Hawaii, June 2004 • Intelligent Systems for Molecular Biology (ISMB)/European Conference on Computational Biology (ECCB), Glasgow, Aug 2004 • UK e-Science All Hands Meeting, Nottingham, September 2004 • HPCInform meeting, StrathClyde University, Glasgow, September 2004 • Forthcoming events: • Condor week, Condor Activities at NeSC Glasgow, October 2004 • Demo at Supercomputing 2004, Pittsburgh, PA, November 2004 • Invited talk at the Shimadzu Research Laboratory, Manchester, October 2004 • Papers in progress for: • International Parallel & Distributed Processing Symposium, Denver, Colorado, April 2005 • Life Science Grid Conference, Singapore, May 2005

10. Exploitation • Beta-testers for Masala (new name for Information Integrator/DiscoveryLink) • BRIDGES results/experiences being directly used in (as basis for) numerous projects

11. Exploitation …ctd • Scottish Bioinformatics Research Network (SBRN) • Four year proposal (£2.5M) expected to start November 2004 • Funded by Scottish Enterprise, Scottish Higher Education Funding Council, Scottish Executive Environment and Rural Affairs Department • Involves Glasgow, Dundee, Edinburgh, Scottish Bioinformatics Forum • Aim to provide bioinformatics infrastructure for Scottish health, agriculture and industry • Infrastructure support at Dundee, Edinburgh and Glasgow to support first-rate research in bioinformatics at each academic institute • Infrastructure support at three institutes, to support inter-institutional sharing of compute and data resources through application of Grid computing • Outreach and training activities mediated by the Scottish Bioinformatics Forum

12. Exploitation …ctd • Virtual Organisations for Trials and Epidemiological Studies • 3 year MRC funded project (£2.6M) expected to start imminently • Plans to develop Grid infrastructure to address key components of clinical trial/observational study • Recruitment of potentially eligible participants • Data collection during the study • Study administration and coordination • Involves Glasgow, Oxford, Leicester, Nottingham, Manchester, Imperial

13. Exploitation …ctd • Joint Data Standards Survey (JDSS) • Started on 1st June and involves • Digital Archiving Consultancy (Philip Lord, Alison MacDonald) • Bioinformatics Research Centre, Glasgow (David Gilbert) • NeSC (Richard Sinnott, Denise Ecklund, Martin Westhead) • Identifying barriers to sharing of life science data sets • BRIDGES experiences • Often cannot query databases directly • Often not easy/possible to find schemas • Schemas/data structures change (often without warning … during demos!) • JDSS looking at reasons (technical, political, social, ethical etc) involved in difficulties in accessing and using public life science resources • Liasing with NDCC • Interview relevant scientists, data curators/providers • 8 month project with final report in January • Funded by MRC, BBSRC, Wellcome Trust, JISC, NERC, DTI

14. Exploitation …ctd • Dynamic Virtual Organisations for e-Science Education (DyVOSE) project • More later…

15. Future plans • Continue to support CFG • New applications, refine existing applications, extensions to repository • Secure storage of microarray datasets • Exploring OGSA-DAI solutions for data access and usage • Important initially to engage CFG scientists • Continue to work with David Chadwick (PERMIS) and Von Welch (Globus team) on improvements to AuthZ specifications at GGF and apply prototype solutions

16. Future plans …ctd • Feed BRIDGES experiences/software into other projects • SBRN, VOTES, … and new ones • Basis for future complete systems biology…?

17. Tissues Cell Organs Protein functions Protein Structures Organisms Physiology Gene expressions Populations Nucleotide structures Cell signalling Nucleotide sequences Protein-protein interaction (pathways)

18. Questions?