The Queen’s University of Belfast The Queen’s University of Belfast GeneGrid : Using OgsaDai in Bioinformatics Noel Kelly Belfast e-Science Centre

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

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

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

The Queen’s University of Belfast GeneGrid Architecture GeneGrid Enviroment GeneGrid Data Manager Registry Database Factory

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

The Queen’s University of Belfast Databases in GeneGrid GeneGrid Databases Public Databases Proprietary Databases OGSA-DAI Grid Environment

The Queen’s University of Belfast Databases in GeneGrid GeneGrid Databases Public Databases Proprietary Databases OGSA-DAI Grid Environment

The Queen’s University of Belfast Proprietary Databases Oracle DatabaseT.B.C.

The Queen’s University of Belfast GeneGrid Databases Results (Xindice / Exist) Workflow Status (Xindice) Workflow Definition (Xindice)

The Queen’s University of Belfast Public Biological Databases trEMBL_new (File) ENSEMBL (MySQL) trEMBL (File) EMBL (File) SwissProt (File)

The Queen’s University of Belfast What OGSA-DAI done for GeneGrid… “Ready to Go” Solution Easy Implementation Good Documentation Helpful & Useful Support

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

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.

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

The Queen’s University of Belfast Misc. Contacts Dr. Paul Donachy – Project Supervisor Noel Kelly – Software Engineer GeneGrid web site – Encyclopaedia of Life –eol.sdsc.edu