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The Queen’s University of Belfast www.qub.ac.uk/escience The Queen’s University of Belfast GeneGrid : Using OgsaDai in Bioinformatics Noel Kelly Belfast.

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Presentation on theme: "The Queen’s University of Belfast www.qub.ac.uk/escience The Queen’s University of Belfast GeneGrid : Using OgsaDai in Bioinformatics Noel Kelly Belfast."— Presentation transcript:

1 The Queen’s University of Belfast www.qub.ac.uk/escience The Queen’s University of Belfast GeneGrid : Using OgsaDai in Bioinformatics Noel Kelly Belfast e-Science Centre

2 www.qub.ac.uk/escience The Queen’s University of Belfast 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 www.qub.ac.uk/escience The Queen’s University of Belfast 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 3 rd Party Use Institute of Bioinformatics R&D

4 www.qub.ac.uk/escience The Queen’s University of Belfast GeneGrid Architecture GeneGrid Enviroment GeneGrid Application & Resource Registry GeneGrid Data Manager Registry Workflow Manager Factory Process Manager Factory GeneGrid Environment Interface GAM Database Factory

5 www.qub.ac.uk/escience The Queen’s University of Belfast GeneGrid Architecture GeneGrid Enviroment GeneGrid Data Manager Registry Database Factory

6 www.qub.ac.uk/escience The Queen’s University of Belfast Data Access, Integration & Storage – OGSA-DAI Database Status Grid Data Service Factory Grid Data Service DAI Service Group Registry Grid Data Service Factory Database SwissProt Grid Data Service

7 www.qub.ac.uk/escience The Queen’s University of Belfast Databases in GeneGrid GeneGrid Databases Public Databases Proprietary Databases OGSA-DAI Grid Environment

8 www.qub.ac.uk/escience The Queen’s University of Belfast Databases in GeneGrid GeneGrid Databases Public Databases Proprietary Databases OGSA-DAI Grid Environment

9 www.qub.ac.uk/escience The Queen’s University of Belfast Proprietary Databases Oracle DatabaseT.B.C.

10 www.qub.ac.uk/escience The Queen’s University of Belfast GeneGrid Databases Results (Xindice / Exist) Workflow Status (Xindice) Workflow Definition (Xindice)

11 www.qub.ac.uk/escience The Queen’s University of Belfast Public Biological Databases trEMBL_new (File) ENSEMBL (MySQL) trEMBL (File) EMBL (File) SwissProt (File)

12 www.qub.ac.uk/escience The Queen’s University of Belfast What OGSA-DAI done for GeneGrid… “Ready to Go” Solution Easy Implementation Good Documentation Helpful & Useful Support

13 www.qub.ac.uk/escience The Queen’s University of Belfast Current Issues with OGSA- DAI in GeneGrid No Support for Flat File Databases Service Discovery CDATA wrappers Perform Documents Service Re-Registration

14 www.qub.ac.uk/escience The Queen’s University of Belfast 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 www.qub.ac.uk/escience The Queen’s University of Belfast 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 www.qub.ac.uk/escience The Queen’s University of Belfast 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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