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Can Grids Deliver the Vision for Future Hypothesis Driven Life Science Research?

Can Grids Deliver the Vision for Future Hypothesis Driven Life Science Research? Professor Richard Sinnott Technical Director National e-Science Centre University of Glasgow 9 th May 2006. Grids and e-Research. Classical characteristics HPC, data deluge, … More recent push

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Can Grids Deliver the Vision for Future Hypothesis Driven Life Science Research?

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  1. Can Grids Deliver the Vision for Future Hypothesis Driven Life Science Research? Professor Richard Sinnott Technical Director National e-Science Centre University of Glasgow 9th May 2006

  2. Grids and e-Research • Classical characteristics • HPC, data deluge, … • More recent push • Security, virtual organisations, usability, … computers software Grid sensor nets instruments Shared data archives colleagues

  3. E-Health Future Drivers • The big questions • Why do people who eat less tend to live longer? • Is there a genetic reason why Scotland has such a high incident rate of cardiovascular disease? How significant are social, cultural, occupational factors in this? • … • Tailored e-Heath • Wouldn't it be wonderful to know what measures you could take to stave off/prevent the onset of disease? • Wouldn't it be a relief to know that you are not allergic to the drugs your doctor just prescribed? • Wouldn't it be a comfort to know that the treatment regimen you are undergoing has a good chance of success because it was designed just for you?

  4. The Big Picture… Tissues Cell Organs Protein functions Protein Structures Organisms Physiology Gene expressions GRID Populations Epidemiology Nucleotide structures Cell signalling Nucleotide sequences Protein-protein interaction (pathways) SECURITY +social, lifestyle, occupational,environmental, …

  5. There are still issues to be resolved • OGSA definition and delivery • Standards OGSI, WSRF, … • Technologies GT2, GT3, GT4, EGEE, OMII… • What about the science drivers • What data sets, what services, accessed by whom, … • Longevity of systems…? • If I build a Grid infrastructure for you, do you promise not to change your requirements (completely!) HPC(x) Challenges/ Opportunities? 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

  6. Grid Projects & Experiences

  7. VO Authorisation Information Integrator OGSA-DAI Magna Vista Service SyntenyService blast + + + BRIDGES Project

  8. MagnaVista www.nesc.ac.uk

  9. BRIDGES Security • Used PERMIS (www.permis.org) to provide fine grained security (authorisation) • XML based policies digitally signed (tamperproof) and used to make authorisation decisions when users invoke services • (XACML based policies coming…) • Use SAML callouts to transparently link Grid service and policies • Data Policies • Only members of CFG can access all public and local warehoused data • Other guest users can only access remote genome databases • Security at DB level! • Computational Policies • CFG members can run BLAST across NGS, Glasgow clusters and Condor pools • Guest users only get access to the Condor pool • Users do not need their own X.509 certificates – all hidden behind portal!

  10. BRIDGES data • Originally planned that would have many different types of data with different security requirements • Public data: data from public sources • Processed public data: public data that has additional annotation or indexing to support the analyses needed by CFG • Sensitive data: data about individuals in the cohorts of patients and the data derived from animal experiments • Special experimental data: such as quantitative trait loci (QTL) or microarray data • Personal research data: data specific to a researcher as a result of experiments or analyses that that researcher is performing • Team research data: data shared by the team members at a site • Consortium research data: data produced by one site or a combination of sites that is now available for the whole consortium • Personalisation data:metadata collected and used by the bioinformatics tools pertinent to individual users • …but scientists reluctant to share their data!

  11. JDSS Project • Public data resources openness • Often cannot query directly nor easy/possible to find schemas (and they change… often!) • Joint Data Standards Study investigated this • Funded by MRC, BBSRC, Wellcome Trust, JISC, NERC, DTI and involved • Digital Archiving Consultancy • NeSC (Edinburgh and Glasgow) • Bioinformatics Research Centre (Glasgow) • Looked at technical, political, social, ethical etc issues involved in accessing and using public life science resources • Final report completed September 2005 and available at: • www.mrc.ac.uk/prn/pdf-jdss_final_report.pdf • (to also appear as a NeSC technical report)

  12. Grid Enabled Microarray Expression Profile Search (GEMEPS) • 1 year project (just) started 1st March 2006 • Funded by BBSRC • Involves Glasgow, Cornell University, US, Riken Institute, Japan • Aim to provide tools for discovery, comparison and analysis of microarray data sets • How does my data compare to others? • How do these experiments compare? • Can we improve the way we establish how genes in different species are linked? • … • Microarrays expensive and contain potentially important (valuable) data sets • Fine grained security essential (and willingness of researchers to collaborate)!

  13. Grid Enabled Microarray Expression Profile Search (GEMEPS) • Why bother…? • Major journals require experimental data to be published • Minimal Information About a Microarray Experiment (MIAME) standard • Does not provide sufficient information for scientist to repeat experiment, to compare results, … • Scientists often unwilling to spend time to provide additional meta-data • …experiences from BRIDGES • Scientists also now questioning sensitivity of microarray data results • Gene names and expression values vs ordering of gene expression values • Initial prototypes support both of these but issues of gene naming • entrez, unigene, go, … • Work on searching/mining of public repositories on-going • including GEO, arrayExpress, …

  14. Grid Enabled Occupational Data Environment (GEODE) • GEODE • Funded by ESRC lead by University of Stirling with NeSC Glasgow • Two year project aiming to develop Grid enabled portal for occupational data • includes integration of various existing classification scheme • Many occupational classification schemes exist • Used by different researchers/sociologists • Linkage to national and international census data sets • When is a plumber not a plumber? • When they are a water transport technician…? • How many plumbers had a heart attack in Scotland in the last 2 years?

  15. 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 • Prototypes available now building on SCIStore, GPASS, consent DB, existing trials repositories

  16. Distributed Data Framework Portal Grid Server Grid Server Data Server Data Server Access Access Access Authorisation Authorisation Security Security Security Access Matrix Access Matrix Policies Policies Policies Security Policies Security Policies Globus Globus OGSA OGSA - - DAI DAI Service Service Container Container User Authentication Glasgow Glasgow SCI Store 1 Remote Remote Other Other (SQL Server) Trust Trust GPASS SCI Store 1 Transfer Transfer Policies Policies Driving Driving (SQL Server) Grid Grid DB DB Nodes Nodes Local Local SCI Store 2 SCI Store 2 Consent DB Consent DB Trust Trust (SQL Server) (SQL Server) Policies Policies (Oracle 10g) (Oracle 10g) Local Local RCB Test RCB Test Local Local Local Local Trust Trust Trust Trust Trials DB Trials DB Trust Trust Policies Policies Policies Policies Policies Policies (SQL Server) (SQL Server)

  17. VOTES Data Federation Portal Beta Prototype

  18. VOTES Data Federation Portal Beta Prototype

  19. VOTES Data Federation Portal Beta Prototype

  20. VOTES Data Federation Portal Beta Prototype

  21. VOTES Data Federation Portal Beta Prototype

  22. Generation Scotland Scottish Family Health Study • Five (2+3) year proposal (£4.6M) started January 2006 • 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, … • Recruitment process has started already!

  23. Security Related Projects • GLASS • JISC funded started January 2006 • Exploring early adoption of Shibboleth • Working with Computer Services directly • Scenarios based upon teaching and access to NHS resources/data • Builds upon university wide unified account management system being rolled out (based on Novell nSure technology) • ESP-Grid • JISC/Oxford University funded • Developing demonstrator to show how Grid resources can be accessed and used via Shibboleth technology • Initial prototypes already available • Grid Security Report • JISC/JCSR funded • Focus on Grid security practices, middleware and outlook • Contact me if want a copy!

  24. Glasgow SoA using Edinburgh DIS DyVOSE Project Glasgow Edinburgh Condor pool Create new ACs for Glasgow users/roles LDAP LDAP Glasgow Education VO policies Edinburgh Education VO policies PERMIS based Authorisation checks/decisions Job scheduling/ data management Grid BLAST Service Grid BLAST Data Service Nucleotide + Protein Sequence DB Implemented by Students data input Protein/nucleotide sequence data returned based on student team and Edinburgh policy Grid-data Client

  25. Future • The Grid is not a magic wand • Your data quality issues won’t go away • We can however identify what these are • SCIStore schema incompatibilities • Ethics and legal aspects essential • Working closely with NHS • Consent crucial • Scenarios now implemented looking at patient consent via GPASS

  26. The Future… Hypothesis driven systems biology + Personalised e-Health + ... Tissues Cell Organs Protein functions Protein Structures Organisms Physiology Gene expressions GRID + Security Populations Nucleotide structures Cell signalling Nucleotide sequences Protein-protein interaction (pathways) Needs research pull not Grid middleware push...

  27. Questions?

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