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GeneGrid : Using OgsaDai in Bioinformatics

GeneGrid : Using OgsaDai in Bioinformatics. Noel Kelly Belfast e-Science Centre. GeneGrid Background. Bioinformatics - Commercially Driven. Develop specialist tissue specific datasets. Large volumes data. Multiple sites - little collaboration. No dedicated HPC, low bandwidth.

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GeneGrid : Using OgsaDai in Bioinformatics

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  1. GeneGrid :Using OgsaDai in Bioinformatics Noel Kelly Belfast e-Science Centre

  2. GeneGrid Background • Bioinformatics - Commercially Driven • Develop specialist tissue specific datasets • Large volumes data • Multiple sites - little collaboration • No dedicated HPC, low bandwidth • Lack of in house expertise

  3. GeneGrid Objectives • Grid Based Framework for Bioinformatics • Integration of Existing Technologies & Data Sets • Gene Study in Silico • Develop Specialist Data Sets • Grid Services for Commercial or 3rd Party Use • Institute of Bioinformatics R&D

  4. GeneGrid Architecture GeneGrid Application & Resource Registry Process Manager Factory Workflow Manager Factory Database Factory Database Factory GAM GAM GeneGrid Enviroment GeneGrid Environment Interface GeneGrid Data Manager Registry

  5. GeneGrid Architecture Database Factory Database Factory GeneGrid Enviroment GeneGrid Data Manager Registry

  6. Data Access, Integration & Storage – OGSA-DAI Database Status Database SwissProt DAI Service Group Registry Grid Data Service Factory Grid Data Service Factory Grid Data Service Grid Data Service

  7. Databases in GeneGrid Grid Environment GeneGrid Databases Proprietary Databases OGSA-DAI Public Databases

  8. Databases in GeneGrid Grid Environment GeneGrid Databases Proprietary Databases OGSA-DAI Public Databases

  9. Proprietary Databases Oracle Database T.B.C.

  10. GeneGrid Databases Results (Xindice / Exist) Workflow Definition (Xindice) Workflow Status (Xindice)

  11. Public Biological Databases EMBL (File) SwissProt (File) trEMBL (File) ENSEMBL (MySQL) trEMBL_new (File)

  12. What OGSA-DAI done for GeneGrid… • “Ready to Go” Solution • Easy Implementation • Good Documentation • Helpful & Useful Support

  13. Current Issues with OGSA-DAI in GeneGrid • No Support for Flat File Databases • Service Discovery • CDATA wrappers • Perform Documents • Service Re-Registration

  14. Dealing with the Issues I • Service Discovery • Waiting for later release • Perform Documents • Upgrade to Incorporate new APIs • Service Re-Registration • T.B.D.

  15. Dealing with the Issues II • CDATA wrappers • Is this an OGSA-DAI issue? • Flat File Databases • Implemented PERL scripts in place of XML:DB / JDBC Drivers • Extensible Support requires PERL module Development

  16. Misc. Contacts • Dr. Paul Donachy – Project Supervisor • p.donachy@qub.ac.uk • Noel Kelly – Software Engineer • n.kelly@qub.ac.uk • GeneGrid web site • www.qub.ac.uk/escience/projects.php • Encyclopaedia of Life • eol.sdsc.edu

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