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
• 27th May 2005

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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
• 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

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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

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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,
  STF

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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)
• 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

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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
• Dereks remaining funds used to extend Micha
  Bayers contract at Glasgow
• Micha originally only 18 month contract

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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

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Exploitation via projectsctd

• 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 via projectsctd

• Genetics and Healthcare Initiative
• Five (23) 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,

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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

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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?

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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 specs from GGF

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