NeSC Review 27 th May 2005

1. BRIDGESStatus ReportDr Richard SinnottTechnical Director National e-Science Centre||| Deputy Director Technical Bioinformatics Research Centre University of Glasgowros@dcs.gla.ac.uk NeSC Review 27th May 2005

2. VO Authorisation Information Integrator OGSA-DAI Magna Vista Service SyntenyService blast + + + Bridges Project

3. Achievements • Web site and project portal established • http://www.nesc.ac.uk/hub/projects/bridges • 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 • Driving forward bioinformatics focus of NGS • Data sets supported, applications required • Helping others via training at NGS induction and training events • Release of code to wider community • Includes feedback/comments on how to re-use it • Numerous follow-ups/enquiries already

4. 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 sets • MagnaVista tool developed to allow discovery and analysis of genomic data sets • GeneVista tool (portlet) offering subset of MagnaVista functionality (based upon user demands) • Includes PERMIS based authorisation back-end

5. 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, STF

6. 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) • Paper at European Grid Conference, Amsterdam, February 2005 • Paper at Life Science Grid Conference, Singapore, May 2005 • Paper 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 2004 • JISC Core Middleware, Loughborough, May 2005

7. 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 again • Derek’s remaining funds used to extend Micha Bayer’s contract at Glasgow • Micha originally only 18 month contract

8. 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

9. Exploitation via projects…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

10. 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, …

11. 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 certificates • Makes 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

12. 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?

13. Future plans • Continue to support CFG • New 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

14. 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…?

15. Tissues Cell Organs Protein functions Protein Structures Organisms Physiology Gene expressions Populations Nucleotide structures Cell signalling Nucleotide sequences Protein-protein interaction (pathways) Numerous projects/proposals submitted looking at all parts of this picture!

16. Questions?