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BRIDGES Status Report Dr Richard Sinnott Technical Director National e-Science Centre ||| Deputy Director Technical Bioinformatics Research Centre University of Glasgow ros@dcs.gla.ac.uk. NeSC Review 11 th October 2004. Overview. The team Review goals of Bridges project

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NeSC Review 11 th October 2004


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nesc review 11 th october 2004

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

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

Information Integrator

OGSA-DAI

Magna Vista Service

SyntenyService

blast

+

Bridges Project
achievements
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
achievements ctd
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 ctd1
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
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
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
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 ctd1
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 ctd2
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
exploitation ctd3
Exploitation …ctd
  • Dynamic Virtual Organisations for e-Science Education (DyVOSE) project
        • More later…
future plans
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
Future plans …ctd
  • Feed BRIDGES experiences/software into other projects
    • SBRN, VOTES, … and new ones
  • Basis for future complete systems biology…?
slide17

Tissues

Cell

Organs

Protein functions

Protein Structures

Organisms

Physiology

Gene expressions

Populations

Nucleotide structures

Cell signalling

Nucleotide sequences

Protein-protein interaction (pathways)