myGrid: Personalised Bioinformatics on the Information Grid

1
myGrid Personalised Bioinformatics on the
Information Grid            

• Robert Stevens, Alan Robinson
• Carole Goble
• University of Manchester EBI, UK
• myGrid project
• http//www.mygrid.org.uk

2
The Biology
Autoimmune Antibodies attach to TSH receptors,
competing with TSH

• Graves Disease caused by the stimulation of the
  thyrotrophin receptor by thyroid-stimulating
  autoantibodies secreted by lymphocytes of the
  immune system.
• What is the molecular basis for this autoimmune
  response?

3
Bioinformatics
Peter Li1, Claire Jennings2, Simon Pearce2 and
Anil Wipat1, (2003) 1School of Computing Science
and 2Institute of Human Genetics, University of
Newcastle-upon-Tyne.
Candidate gene pool
Annotation Pipeline
Genotype Assay Design System
3D Protein Structure
What is known about my candidate gene?
What is the structure of the protein product
encoded by my candidate gene?
Select a SNP from candidate gene. Is this SNP
associated with Disease?
Medline
Gene ID
Primer Design
GO
EMBL
Emboss Eprimer application in SoapLab
Use primers designed by myGrid to amplify region
flanking SNP on the gene
SNP
Query
Restriction Fragment Length Polymorphism
experiment
OMIM
BLAST
Selection of restriction enzyme
Talisman
Emboss Restrict in SoapLab
DQP
SN
SNP
P
SN
P
4
Workflows are in silico experiments
http//cvs.mygrid.org.uk/scufl/NucleotideSeqAnnota
tionPipelineWithGoTerms/
5
myGrid

• EPSRC UK e-Science pilot project
• Open Source Upper Middleware for Bioinformatics
• (Web) Service-based architecture -gt Grid services
• 42 months, 20 months in.
• Prototype V0 technical and user requirements
• Prototype V1 Release Sept 2004, some services
  available now.

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myGrid Services
Work bench
Taverna workflow environment
Talisman application
Portal
Bioinformaticians
Gateway
Personalisation
Service and Workflow Discovery
myGrid Information Repository
Registries
Provenance mgt
Ontology Mgt
Ontologies
Event Notification
Metadata Mgt
Tool Providers
Workflow enactment engine
Distributed Query Processor
Soaplab
Web Service Grid communication fabric
Service Providers
Bio Services
Text Extraction Service AMBIT
Bio Services
Bio Services
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A work bench for demonstrating services
myView on the mIR
Workflow
Metadata about workflow
note about workflow
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The annotation pipeline to identify Genes of
Interest

• Look at contents of work bench
• User notified of new Affy data
• Run a workflow over new Affy data
• Launch workflow wizard
• Discover appropriate workflow
• Enact workflow
• Monitor workflow
• Look at provenance
• Select and view results

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Summary

• myGrid offers service based middleware components
• Open source and free
• Open Grid Service Architecture-compliant
• Allows the scientist to be at the centre of the
  Grid -- Personalisation
• Generic middleware that suits the creation of
  bioinformatics applications
• Inclusion of rich semantics to facilitate the
  scientific process
• Available from http//www.mygrid.org.uk

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Our Biology colleagues
Claire Jennings

• Institute of Human Genetics School of Clinical
  Medical Sciences
• University of Newcastle
• UK

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The rest of the team

• Matthew Addis, Nedim Alpdemir, Rich Cawley, Vijay
  Dialani,
• Alvaro Fernandes, Justin Ferris, Rob Gaizauskas,
• Kevin Glover, Carole Goble (director), Chris
  Greenhalgh,
• Mark Greenwood, Ananth Krishna, Xiaojian Liu,
  Darren Marvin,
• Karon Mee, Simon Miles, Luc Moreau, Juri Papay,
  Norman Paton,
• Steve Pettifer, Milena Radenkovic, Peter Rice,
  Angus Roberts,
• Alan Robinson, Martin Senger, Nick Sharman, Paul
  Watson,
• Anil Wipat Chris Wroe.