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The Queen’s University of Belfastwww.qub.ac.uk/escience The Queen’s University of Belfast
GeneGrid :Using OgsaDai in
Bioinformatics
Noel Kelly
Belfast e-Science Centre
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
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 3rd Party Use
• Institute of Bioinformatics R&D
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 GAM Database Factory
Database Factory
www.qub.ac.uk/escience The Queen’s University of Belfast
GeneGrid Architecture
GeneGrid Enviroment
GeneGrid Data Manager Registry
Database Factory
Database Factory
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
www.qub.ac.uk/escience The Queen’s University of Belfast
Databases in GeneGrid
GeneGridDatabases
Public Databases
ProprietaryDatabases
OGSA-DAI
Grid Environment
www.qub.ac.uk/escience The Queen’s University of Belfast
Databases in GeneGrid
GeneGridDatabases
Public Databases
ProprietaryDatabases
OGSA-DAI
Grid Environment
www.qub.ac.uk/escience The Queen’s University of Belfast
Proprietary Databases
Oracle Database T.B.C.
www.qub.ac.uk/escience The Queen’s University of Belfast
GeneGrid Databases
Results(Xindice/ Exist)
Workflow Status
(Xindice)
WorkflowDefinition(Xindice)
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)
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
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
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.
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
www.qub.ac.uk/escience The Queen’s University of Belfast
Misc. Contacts
• Dr. Paul Donachy – Project Supervisor– [email protected]
• Noel Kelly – Software Engineer– [email protected]
• GeneGrid web site – www.qub.ac.uk/escience/projects.php
• Encyclopaedia of Life– eol.sdsc.edu
