BRIDGESStatus Report

Dr Richard SinnottTechnical Director National e-Science Centre

||| Deputy Director Technical Bioinformatics

Research Centre University of Glasgow

ros@dcs.gla.ac.uk NeSC Review

27th May 2005

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

Information Integrator

OGSA-DAI

Magna Vista Service

VO Authorisation

blast

+ + +

Achievements

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

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

Driving forward bioinformatics focus of NGSData sets supported, applications required

Helping others via training at NGS induction and training events

Release of code to wider communityIncludes feedback/comments on how to re-use it

Numerous follow-ups/enquiries already

Achievements …ctd

GT3 based BLAST Grid service providing access to and usage of high-throughput compute resources

includes access to and usage of NGS, ScotGrid, Condor pools… implements own meta-scheduler with fine grained PERMIS-based

authorisation back-end– demonstration later

SyntenyVista tool extended to allow Grid enabled visual navigation of genomic data setsMagnaVista tool developed to allow discovery and analysis of genomic data setsGeneVista tool (portlet) offering subset of MagnaVista functionality (based upon user demands)

Includes PERMIS based authorisation back-end

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, STF

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)Paper at European Grid Conference, Amsterdam, February 2005Paper at Life Science Grid Conference, Singapore, May 2005Paper and poster at UK e-Science All Hands Meeting, September 2005

Presentations/Seminars:Seminar at University of Stirling, 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 Systems Biology workshop, Edinburgh, March 2005 PharmaGrid workshop, Edinburgh, March 2005

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 Supercomputing 2004, Pittsburgh, US [actually 25 demonstrations!!! :o(]Condor week, Condor Activities at NeSC Glasgow, October 2004 Invited talk at the Shimadzu Research Laboratory, Manchester, October 2004JISC Core Middleware, Loughborough, May 2005

Team Changes

Jos Koetsier replaced Magnus Ferrier as Grid Engineer in Edinburgh

Magnus left for a higher paid position in industry

Derek Houghton (DB Designer/developer) left for a higher paid 5-year position in Edinburgh

Working with Richard “Mouse Atlas” Baldock againDerek’s remaining funds used to extend Micha Bayer’s contract at Glasgow

Micha originally only 18 month contract

Exploitation

Via projects…Scottish Bioinformatics Research Network (SBRN)

Four year proposal (£2.5M) just started– 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 via projects…ctd

Virtual 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 via projects…ctd

Genetics and Healthcare Initiative Five (2+3) year proposal (£4.4M) expected to start imminently

Funded by Health Department and Department for Enterprise and Lifelong Learning

Involves Glasgow, Dundee, Edinburgh, Aberdeen– focus of genetics as applied to healthcare– first two years emphasis on providing a platform for research into the

genetic basis of common complex diseases in Scotland» Mental health, cardiovascular, … » Plan to establish 15,000 family-based intensively-phenotyped cohort

recruited from the East and West of Scotland– basis for neutralising heritable (genetic) risk factors in disease

surveillance, treatment optimisation, avoidance of adverse drug events and prediction of response to therapy, health care planning and drug discovery, …

Exploitation by others

Working with NGS on bioinformatics data sets and applications

Fair to say that we are driving this work in the UK

Showing/training people how to use NGS and how to develop applications using such facilities

BRIDGES case study lectures given at NGS training course BRIDGES system used by Neil Geddes to demonstrate NGS

Code released for multiple scheduler job submission systems

Alternative models of job submission without explicit user certificates

Based upon host certificatesMakes life simpler for users

Requires logging/accounting information is kept

BRIDGES being used to explore other security areas such as Shibboleth, e.g. in projects such as DyVOSE

Commercial Exploitation?

Email from Colin Henderson (IBM UK) to head of IBM clinical genomics US (Kareem M Saad) 17th May 2005

… It's actually very interesting to see what the guys at NeSC have achieved here. This is a great reference for IBM. The group are now looking to deploy some of their expertise and learning to longitudinal clinical trials, a project called VOTES which we supported. I just wanted to make you aware of this work and flag it as an innovative project in Clinical Genomics and Grid.

…Perhaps there might be an angle from somewhere in IBM to help us and the BRIDGES/VOTES team develop the relationship further, hence develop the reference further?

Future plans

Continue to support CFGNew applications, refine existing applications Modify delivery mechanisms (user issues with WebStart)

JSR168 portlets in GridSphere, WebSphere

Refine OGSA-DAIT solution for data access and usage

Integration of Grid based data access and security solution

Extending spec’s from GGF

Future plans …ctd

Feed BRIDGES experiences/software into other projects

SBRN, VOTES, GHI… and new ones Including one BBSRC bid with Cornell, Riken Institute made

through contacts at SC2004! ;o)

Basis for future complete systems biology…?

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Numerous projects/proposals submitted looking at all parts of this picture!

Questions?