BRIDGES Status Report Dr Richard Sinnott Technical Director National e-Science Centre ||| Deputy Director Technical Bioinformatics Research Centre University.

BRIDGESStatus Report

Dr Richard SinnottTechnical Director National e-Science Centre

||| Deputy Director Technical Bioinformatics

Research Centre University of Glasgow

[email protected] NeSC Review

11th October 2004

Overview

The teamReview goals of Bridges project

Brief summary of technical approach

Outline achievements thus farPlans for the future

Project ParticipantsThe 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

High blood pressure affects 25% of adults in western societiesCardiovascular Functional Genomics (CFG) project investigating this through physiological models of hypertension in ratBridges is a supporting project to CFG and will provide Grid infrastructure to facilitate scientific researchCFG 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

Glasgow Edinburgh

Leicester Oxford

London

Netherlands

Publically Curated Data

Private data

Private data

Private data

Private data

Private data

Private data

CFG Virtual Organisation Ensembl

MGI

HUGO

OMIM

SWISS-PROT

… DATA HUB

RGD

SyntenyService

blast

+

Information Integrator

OGSA-DAI

Magna Vista Service

Achievements

Web site and project portal establishedhttp://www.nesc.ac.uk/hub/projects/bridges

Engaged with CFG consortiaLots of new requests from CFG on how existing tools can be taken forward

Scenarios for linkage between tools

Local life science data repository developedLinked 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 setsMagnaVista tool developed to allow discovery and analysis of genomic data sets

These will all be demonstrated

Achievements …ctd

Results are being widely knownDissemination important

Conferences Seminars Commercial interest

Influencing standards developmentGGF AuthZ

Feedback to relevant groupsInvolved in GGF Life Science Grid Research Group

DisseminationPublications:

UK e-Science All Hands Meeting 2003 (poster)Invited paper to Life Science Grid Conference, Kanazawa, Japan 2004UK 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 2005Life 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 …ctdVirtual Organisations for Trials and Epidemiological Studies

3 year MRC funded project (£2.6M) expected to start imminentlyPlans 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

Clinical Virtual Organisation Framework

IMP

CVO-2 (e.g. for

recruitment)

Used to realise

GPs

Lei- Nott GLA

OX

Disease registries

Hospital databases

Transfer Grid

CVO-1 (e.g. for data collection)

Clinical trial data sets

Exploitation …ctdJoint 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 …ctdDynamic Virtual Organisations for e-Science Education (DyVOSE) project

– More later…

Future plans

Continue to support CFGNew applications, refine existing applications, extensions to repositorySecure 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…?

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Questions?