myGrid: Personalised Bioinformatics on the Information Grid
Robert Stevens, Alan Robinson & Carole GobleUniversity of Manchester & EBI, UKmyGrid project http://www.mygrid.org.uk
The Biology
• Grave’s 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?
PituitaryGland
Thyroid Hormones Released
ThyroidCell
TSH Receptor
TSH
-ve feedbackeffect
Autoimmune Antibodies attach to TSH receptors, competing with TSH
Bioinformatics
Annotation PipelineWhat is known about my
candidate gene?
Medline
OMIM
GO
BLAST
EMBL
DQP
Query
Genotype Assay Design System 3D Protein Structure
Select a SNP from candidate gene. Is this SNP associated with
Disease?
What is the structure of the proteinproduct encoded by my candidate gene?
Primer Design
Gene ID
Restriction FragmentLength Polymorphism experiment
SNPSN
PSN
P
Use primers designed by myGrid to amplify region flanking SNP on the gene
PDB
Query PDB & display proteinstructure using Rasmol
Obtain information about protein& extract information about active site
Swiss-Prot AMBITInterpro
Emboss Eprimer applicationin SoapLab
Selection of restriction enzyme
Talisman
SNP
Emboss Restrictin SoapLab
AMBIT
Determine whether coding SNPsaffects the active site of the protein
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 genepool
Workflows are in silico experiments
Annotation PipelineWhat is known about my
candidate gene?
Medline
OMIM
GO
BLAST
EMBL
DQP
Query
http://cvs.mygrid.org.uk/scufl/NucleotideSeqAnnotationPipelineWithGoTerms/
myGrid
• EPSRC UK e-Science pilot project• Open Source Upper Middleware for Bioinformatics• (Web) Service-based architecture -> Grid services• 42 months, 20 months in.• Prototype V0 technical and user requirements• Prototype V1 Release Sept 2004, some services
available now.
myGrid Services
Web Service & Grid communication fabric
Text Extraction ServiceAMBIT
Workflow enactment engine
Distributed Query Processor
Provenance mgt
Personalisation
Event Notification
Gateway
Service and WorkflowDiscovery myGrid
Information Repository
Ontology Mgt
Metadata Mgt
Work bench Taverna workflow environment Talisman application
Bio Services
Soaplab
Portal
Bio Services
Bio
info
rmat
icia
nsTo
ol P
rovi
ders
Ser
vice
Pro
vide
rs
Registries
Ontologies
Bio Services
A work bench for demonstrating services
myView on the mIR
Workflow
Metadata about
workflow
note aboutworkflow
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
Annotation PipelineWhat is known about my
candidate gene?
Medline
OMIM
GO
BLAST
EMBL
DQP
Query
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
Our Biology colleagues
Institute of Human Genetics School of Clinical Medical Sciences
University of NewcastleUK
Simon Pearce Claire Jennings
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.