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BRIDGES Dr Richard Sinnott Technical Director National e-Science Centre |||

BRIDGES Dr Richard Sinnott Technical Director National e-Science Centre ||| Deputy Director (Technical) Bioinformatics Research Centre University of Glasgow 16 th May 2005. computers. software. Grid. sensor nets. instruments. Shared data archives. colleagues.

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BRIDGES Dr Richard Sinnott Technical Director National e-Science Centre |||

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  1. BRIDGES Dr Richard Sinnott Technical Director National e-Science Centre ||| Deputy Director (Technical) Bioinformatics Research Centre University of Glasgow 16th May 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. HPC(x) Edinburgh Glasgow Newcastle Lancaster Belfast York Manchester Leeds White Rose Grid Sheffield Daresbury Lab Leicester Core National Grid Service Midlands Cambridge Oxford Hinxton UCL RAL Cardiff Reading Imperial Bristol Southampton NeSC in the UK NeSC CSAR

  4. Glasgow e-Science Hub • E-Science Hub • Externally • Glasgow end of NeSC • Involved in UK wide activities • ETF, STF, … • Involved in numerous life science/security related projects (more later) • Public visibility of NeSC • responsible for NeSC web site • Internally • Focal point for e-Science research/activities at Glasgow • Work closely with foundation departments • Department of Computing Science • Offer full course on Grid Computing to advanced MSc students • First batch of students completed in December 2004 • Department of Physics & Astronomy • Also working closely with other groups including • Bioinformatics Research Centre • Electronics and Electrical Engineering • Biostatistics • Sir Henry Wellcome Functional Genomics Facility • Clinical/Medical • …

  5. 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, …

  6. + 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)

  7. 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

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

  9. Database Growth • DBs growing rapidly!!! • Biobliographic (MedLine, PubMed…) • Amino Acid Seq (SWISS-PROT/UNI-PROT, …) • 3D Molecular Structure (PDB, …) • Nucleotide Seq (GenBank, EMBL, …) • Biochemical Pathways (KEGG, WIT…) • Molecular Classifications (SCOP, CATH,…) • Motif Libraries (PROSITE, Blocks, …) http://www.genome.jp/dbget/db_growth.gif

  10. 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 • Make it all easy to use! • Scientists should not have to be Linux script experts, • …nor set up/configure complex Grid software or follow complex procedures for getting, using Grid certificates, • …nor have detailed understanding of low level data schemas for all data sites, • … etc etc

  11. BRIDGES Tissues Cell Organs Protein functions Protein Structures Organisms Physiology Gene expressions Populations Nucleotide structures Cell signalling Nucleotide sequences Protein-protein interaction (pathways)

  12. Overview of BRIDGES • Biomedical Research Informatics Delivered by Grid Enabled Services (BRIDGES) • NeSC (Edinburgh and Glasgow) and IBM • Two year project funded by DTI - started October 2003 • Supporting project for Cardiovascular Functional Genomics (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

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

  14. Grid Security • Grid security • Single sign-on based on (X.509) digital certificates • CA in RAL • local CA’s possible also • Services (and clients) have APIs for fine grained security • “I know who you are and here is your local account” • Provides for authentication but need authorisation • “I know who you are and here is what you are allowed to do on my resource” • Various technologies for authorisation including PERMIS, CAS, VOMS, … • PERMIS is leading fine grained authorisation implementation! • Lead by Prof David Chadwick, University of Kent (www.permis.org) • Supports GGF SAML AuthZ interface • Generic way to link Grid services with authorisation infrastructure

  15. Security Authorisation • PERMIS allows to • Define roles for who can do what on what • Policy = { Role x Target x Action } • Can user X invoke service Y and access or change data Z? • Policies created with PERMIS PolicyEditor (output is XML based policy)

  16. Security Authorisation • PERMIS tools then used to associate roles with specific users and sign policies • Policies stored as attribute certificates in LDAP server • BRIDGES authorisation • Authorisation of computational resources • Policies defined for: • Condor pool (default for unknown users) • ScotGrid (if local account exists for that trusted user) • National Grid Service (if known and trusted user) • Note solution does not require users have their own Grid certificates • Authorisation of data sets • Policies defined to restrict data sets scientists/others can get access to

  17. Demonstration

  18. Other NeSC Glasgow Projects • Joint Data Standards Survey • 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

  19. 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!

  20. Glasgow Edinburgh ScotGrid Condor pool Blue Dwarf Dynamically established VO resources/users Delegated VO policies Edinburgh Education VO policies Glasgow Education VO policies Shibboleth PERMIS based Authorisation checks/decisions DyVOSE Phase 2/3

  21. 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

  22. VOTES • Virtual Organisations for Trials and Epidemiological Studies • 3 year MRC (£2.9M) 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

  23. 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, …

  24. GHI SBRN BRIDGES VOTES DyVOSE JDSS Tissues Cell Organs Protein functions Protein Structures Organisms Physiology Gene expressions Populations Nucleotide structures Cell signalling Nucleotide sequences Protein-protein interaction (pathways) Numerous other proposals submitted looking at other parts of this picture!

  25. 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? • …

  26. Questions? www.nesc.ac.uk

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