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Towards Grid-Based System Biology Dr Richard Sinnott Technical Director National e-Science Centre

Towards Grid-Based System Biology Dr Richard Sinnott Technical Director National e-Science Centre ||| Deputy Director (Technical) Bioinformatics Research Centre University of Glasgow 24 th February 2005. computers. software. Grid. sensor nets. instruments. Shared data archives.

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Towards Grid-Based System Biology Dr Richard Sinnott Technical Director National e-Science Centre

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  1. Towards Grid-Based System Biology Dr Richard Sinnott Technical Director National e-Science Centre ||| Deputy Director (Technical) Bioinformatics Research Centre University of Glasgow 24th February 2005

  2. computers software Grid sensor nets instruments Shared data archives colleagues Grids? E-Science? E-Research? • methodologies transforming science, engineering, medicine and business • driven by exponential growth in data, compute demands • enabling a whole-system approach

  3. Transition to WSRF/OGSA under discussion • Two UK OGSA Test Grid projects started in January • UCL, Imperial College, Universities of Edinburgh and Newcastle • Universities of Portsmouth, Reading, Manchester, Westminster and CCLRC • There are still issues to be resolved • OGSA definition and delivery • Standards OGSI, WSRF, … • …and Technologies GT3, GT4… • Hosting environments & Platforms • Combinations of services supported • Material and grids to support adopters HPC(x) Challenges/ Opportunities? • Previous work on UK e-Science Grid based on GT2 • Demonstrated broad set of applications across it • Monte Carlo simulations of ionic diffusion through radiation damaged crystal structures • Integrated Earth system modelling • BLAST on the Grid • Grid Integration Test Script Suite • … The next Grid software White Rose Grid Core National Grid Service NeSC in the UK NeSC Glasgow Edinburgh Newcastle Belfast Manchester Daresbury Lab Cambridge CSAR Oxford Hinxton RAL Cardiff London Southampton

  4. Life Sciences • Extensive Research Community • >1000 per research university • Extensive Applications • Many people care about them • Health, Food, Environment • Interacts with virtually every discipline • Physics, Chemistry, Maths/Stats, Nano-engineering, … • 450+ databases relevant to bioinformatics (and growing!) • Heterogeneity, Interdependence, Complexity, Change, …

  5. + links to plant/crops, environmental, health, … information sources Systems Biology? Tissues Cell Organs Protein functions Protein Structures Organisms Physiology Gene expressions Populations Nucleotide structures Cell signalling Nucleotide sequences Protein-protein interaction (pathways)

  6. Arabidopsis thaliana Buchnerasp. APS Yersinia pestis Aquifex aeolicus Archaeoglobus fulgidus Borrelia burgorferi Mycobacterium tuberculosis Man Caenorhabitis elegans Campylobacter jejuni Chlamydia pneumoniae Drosophila melanogaster Escherichia coli Neisseria meningitidis Z2491 Plasmodium falciparum Ureaplasma urealyticum Helicobacter pylori Mycobacterium leprae Pseudomonas aeruginosa mouse Bacillus subtilis Thermotoga maritima Xylella fastidiosa Rickettsia prowazekii Saccharomyces cerevisiae Salmonella enterica rat More genomes …... Thermoplasma acidophilum

  7. Distributed and Heterogeneous data Function Structure Sequence LPSYVDWRSA GAVVDIKSQG ECGGCWAFSA IATVEGINKI TSGSLISLSE QELIDCGRTQ NTRGCDGGYI TDGFQFIIND GGINTEENYP YTAQDGDCDV Gene expression Morphology

  8. Database Growth PDB Content Growth • DBs growing exponentially!!! • Biobliographic (MedLine, …) • Amino Acid Seq (SWISS-PROT, …) • 3D Molecular Structure (PDB, …) • Nucleotide Seq (GenBank, EMBL, …) • Biochemical Pathways (KEGG, WIT…) • Molecular Classifications (SCOP, CATH,…) • Motif Libraries (PROSITE, Blocks, …)

  9. Is Grid the Answer? • Some key problems to be addressed • Tools that simplify access to and usage of data • Internet hopping is not ideal! • Tools that simplify access to and usage of large scale HPC facilities • qsub [-a date_time] [-A account_string] [-c interval] [-C directive_prefix] [-e path] [-h] [-I] [-j join] [-k keep] [-l resource_list] [-m mail_options] [-M user_list] [-N name] [-o path] [-p priority] [-q destination] [-r c] [-S path_list] [-u user_list] [-v variable_list] [-V] [-W additional_attributes] [-z] [script] • Tools designed to aid understanding of complex data sets and relationships between them • e.g. through visualisation

  10. Access to and Usage of Data • Grid technology should allow to • hide heterogeneity, • deal with location transparency, • address security concerns, • … • Data Access and Integration Specification (DAIS) being defined by GGF • OGSA-DAI and DAIT projects key role in shaping these standards • Other commercial solutions • IBM Information Integrator, …

  11. Access to and Usage of HPC facilities • Consider whole genome-genome (2*3*10^9 bp) comparisons between two species • Current strategy essentially chops up one genome and fires searches for those fragments in the other then re-assembles results • messy approximate matching - re-assembly difficult • important correlations can be lost • to make this tractable so called junk DNA ignored • chopping may introduce artefacts or hide phenomena • Better to put both full genomes in memory and perform a useful complete comparison • Only possible with very high-end machines (available via grids) • Should not have to be script writer/Linux sys-admin to use these facilities

  12. Cognitive aspects of Data • Life science data can be “ugly” • Raw data sets messy • Requires significant effort to understand • Schemas/data models evolving • … • Tools needed to • Simplify understanding • Improve analysis • Navigate through potentially huge data sets • e.g. to find genes of interest in chromosomes of different species

  13. GHI SBRN BRIDGES VOTES JDSS DyVOSE Tissues Cell Organs Protein functions Protein Structures Organisms Physiology Gene expressions Populations Nucleotide structures Cell signalling Nucleotide sequences Protein-protein interaction (pathways)

  14. Overview of BRIDGES • Biomedical Research Informatics Delivered by Grid Enabled Services (BRIDGES) • NeSC (Edinburgh and Glasgow) and IBM • Started October 2003 • Supporting project for CFG project • Generating data on hypertension • Rat, Mouse, Human genome databases • Variety of tools used • BLAST, BLAT, Gene Prediction, visualisation, … • Variety of data sources and formats • Microarray data, genome DBs, project partner research data, … • Aim is integrated infrastructure supporting • Data federation • Security

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

  16. JDSS Project • Public data resources openness • Often cannot query directly • Often not easy/possible to find schemas • Joint Data Standards Study investigating this • Started on 1st June and involves • Digital Archiving Consultancy • Bioinformatics Research Centre (Glasgow) • NeSC (Edinburgh and Glasgow) • Look at technical, political, social, ethical etc issues involved in accessing and using public life science resources • Interview relevant scientists, data curators/providers • 8 month project with final report due imminently • Funded by MRC, BBSRC, Wellcome Trust, JISC, NERC, DTI

  17. DyVOSE Project • Dynamic Virtual Organisations for e-Science Education (DyVOSE) project • Two year project started 1st May 2004 funded by JISC • Exploring advanced authorisation infrastructures for security • … in Grid Computing Module as part of advanced MSc at Glasgow • Provide insight into rolling Grid out to the masses!

  18. Scottish Bioinformatics Research Network • Four year proposal expected to start imminently • Funded (£2.4M) 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

  19. VOTES • Virtual Organisations for Trials and Epidemiological Studies • 3 year MRC (£2.8M) funded project 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

  20. 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, …

  21. Systems Biology? • Once we have (securely) connected all relevant data sets and simplified access to and usage of HPC resources, wrapped your favourite bioinformatics applications as Grid services... • what questions would you like to ask? • How does a cell work? • Why do people who eat less tend to live longer? • How many people across Scotland had a heart attack in the last 5 years took drug X, and of those that did where genes A or B influenced by this drug? • Who has performed an experiment similar to mine and where their results similar? • …

  22. Questions? www.nesc.ac.uk

  23. Back-Up Slides www.nesc.ac.uk

  24. Bridges Portal

  25. MagnaVista www.nesc.ac.uk

  26. MagnaVista

  27. QTL upload

  28. QTL upload

  29. QTL browsing

  30. Grid Blast Client • Allows ‘genome scale’ blasting • Uses ScotGrid and idle compute resources of training lab Condor pool

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