myGrid: Personalised Bioinformatics on the Information Grid Robert Stevens, Alan Robinson & Carole Goble University of Manchester & EBI, UK myGrid project

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? Pituitary Gland Thyroid Hormones Released Thyroid Cell TSH Receptor TSH -ve feedback effect Autoimmune Antibodies attach to TSH receptors, competing with TSH

Bioinformatics Annotation Pipeline What is known about my candidate gene? Medline OMIM GO BLAST EMBL DQP Query Genotype Assay Design System3D Protein Structure Select a SNP from candidate gene. Is this SNP associated with Disease? What is the structure of the protein product encoded by my candidate gene? Primer Design Gene ID Restriction Fragment Length Polymorphism experiment SNP SN P P Use primers designed by my Grid to amplify region flanking SNP on the gene PDB Query PDB & display protein structure using Rasmol Obtain information about protein & extract information about active site Swiss-Prot AMBITInterpro Emboss Eprimer application in SoapLab Selection of restriction enzyme Talisman SNP Emboss Restrict in SoapLab AMBIT Determine whether coding SNPs affects the active site of the protein Peter Li 1, Claire Jennings 2, Simon Pearce 2 and Anil Wipat 1, (2003) 1 School of Computing Science and 2 Institute of Human Genetics, University of Newcastle-upon-Tyne. Candidate gene pool

Workflows are in silico experiments Annotation Pipeline What is known about my candidate gene? Medline OMIM GO BLAST EMBL DQP Query

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 Service AMBIT Workflow enactment engine Distributed Query Processor Provenance mgt Personalisation Event Notification Gateway Service and Workflow Discovery myGrid Information Repository Ontology Mgt Metadata Mgt Work bench Taverna workflow environment Talisman application Bio Services Soaplab Portal Bio Services Bioinformaticians Tool Providers Service Providers Registries Ontologies Bio Services

A work bench for demonstrating services myView on the mIR Workflow Metadata about workflow note about workflow

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 Pipeline What 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

Our Biology colleagues Institute of Human Genetics School of Clinical Medical Sciences University of Newcastle UK 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.