BRIDGES Status Report Dr Richard Sinnott Technical Director National e-Science Centre ||| Deputy Director Technical Bioinformatics Research Centre University of Glasgow NeSC Review 11 th October 2004

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

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 24 th 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)

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

Bridges Project Synteny Service blast + Information Integrator OGSA-DAI Magna Vista Service

Achievements Web site and project portal established 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

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

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

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

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

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

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

Exploitation …ctd Joint Data Standards Survey (JDSS) Started on 1 st 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

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

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

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

Nucleotide sequences Nucleotide structures Gene expressions Protein Structures Protein functions Protein-protein interaction (pathways) Cell Cell signalling Tissues Organs PhysiologyOrganisms Populations

Questions?