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.