BRIDGES Status Report Dr Richard Sinnott Technical Director National e-Science Centre ||| Deputy Director Technical Bioinformatics Research Centre University of Glasgow [e-mail]

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BRIDGESStatus ReportDr Richard
SinnottTechnical Director National e-Science
Centre Deputy Director Technical
Bioinformatics Research Centre University of
Glasgowros_at_dcs.gla.ac.uk

• NeSC Review
• 11th October 2004

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Overview

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

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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)

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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

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Bridges Project
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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

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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

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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

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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

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Exploitation

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

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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

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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

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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

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Exploitation ctd

• Dynamic Virtual Organisations for e-Science
  Education (DyVOSE) project
• More later

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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

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Future plans ctd

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

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