MyGrid: Personalised e-Biology on the Grid Professor Carole Goble Contact e-Science.

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Presentation transcript:

myGrid: Personalised e-Biology on the Grid Professor Carole Goble Contact e-Science

myGrid: Personalised e-Science on the Grid Personalised extensible environments for data-intensive in silico experiments in biology

e-Science & Biology Biology is a multi-faceted & increasingly multi-disciplinary science. Bioinformatics is an “e-Science”. –Discovery is done in silico on results obtained from experiments using a number of analysis & data resources. Molecular biology & genomics are our particular focus.

Circadian Rhythms Has anyone studied the effect of neurotransmitters on the circadian rhythms in Drosophila? How do the functions of the clusters of proteins from my experiment interrelate? What are the proteins with a particular function? Is a structure known for this protein and what other proteins have a similar structure? Can I build a homology 3D model? What is known about the homologous protein?

Information Weaving Large amounts of data & many applications. Highly heterogeneous. –Different types, algorithms, forms, implementations, communities, service providers Highly complex and inter-related. Highly volatile. Obstacles Everywhere

Descriptive knowledge

Circadian Rhythms 1.Has anyone else studied the effect of neurotransmitters on the circadian rhythms in Drosophila? 2.How do the functions of the clusters of proteins from my experiment interrelate? And what are the proteins with a particular function? 3.Is a structure known for this protein and what other proteins have a similar structure? 4.Can I build a homology 3D model? 5.What is known about the homologous protein?

E-Science Q & A Who else has asked this question & can I use/adapt their approach? –Workflow. What were the results at each stage? –Dynamic Data Repositories. When was P12345 last updated? Which BLAST did I use? –Provenance. Has PDB changed since I last ran this? –Notification Personalisation. 3 54

myGrid Objectives Straightforward discovery, interoperation, fusion, sharing of data, knowledge and workflows. Explicit management of workflows. –information & processes & best practice. Improving quality of experiments & data. –provenance & propagating change. Scientific discovery is personal & global. –personalisation & collaborative working. Security, ownership -> valuable assets.

Who is myGrid for? –Users, developers, maintainers. –Biologists. –Bioinformaticians, resource providers. –Tool builders, system administrators. myGrid users biologists IS specialists infrequent problem specific bioinformaticians tool builders service provider systems administrators bioinformatics tool builders

myGrid Outcomes 1.e-Scientists –Environment built on toolkits for service access, personalisation & community. –Gene function expression analysis (fly & yeast). –Annotation workbench for the PRINTS pattern database. 2.Developers –Protocols and service descriptions. – my Grid-in-a-Box developers kit of core services. –Reference implementation services & applications. –Bio services – already delivered.

myGrid Stack Metadata Services Coordination Services DataWorkflowDirectory Networked Services Applications Client Framework Governance DirectoryProvenancePersonalisation Semantic Services Info. ExtractionWorkflowOntology PortalUser AgentCollaboration Data Admin

myGrid Pre-Prototype Portal Bioinformatic Services Personal Repository Metadata: Ontology Workflow Enactment Metadata: Service Directory Workflow Repository Bioinformatic Services

Portal Personal Repository Meta Data: Ontology Workflow Repository Meta Data: Service Type Directory Repository Client Ontology Client Workflow Client How do the functions of the clusters of proteins from my experiment interrelate? Locating a workflow

Portal Personal Repository Meta Data: Ontology Workflow Repository Meta Data: Service Type Directory Repository Client Ontology Client Workflow Client Locating a workflow

Portal Personal Repository Meta Data: Ontology Workflow Repository Meta Data: Service Type Directory Repository Client Ontology Client Workflow Client Locating a workflow

Portal Personal Repository Meta Data: Ontology Workflow Repository Meta Data: Service Type Directory Repository Client Ontology Client Workflow Client Locating a workflow

Repos. Client Bioinformatic Services Personal Repository Workflow Enactment Service Directory 4 2 2? Provenance Data 3 Workflow Client Service Selection Client 1 Running a workflow

Repos. Client Bioinformatic Services Personal Repository Workflow Enactment Service Directory 4 2 2? Provenance Data 3 Workflow Client Service Selection Client 1 Running a workflow

myGrid generic technologies 1.Ontologies, Protocols & APIs. 2.Database access from the Grid. Reference implementation for UK DBTF. 3.Process enactment on the Grid. 4.Provenance services. 5.Metadata services. –From Semantic Web: DAML+OIL, RDF(S). 6.Personalisation services. 7.Reference implementation of OGSA.

Converging Technologies Agents Grid Computing Web Technologies Globus, Sun Grid Engine, Condor, DS (Jini, Corba) SOAP, WSDL, UDDI, WSFL DAML+OIL, OWL, RDF(S) ACL, methodology An early adopter for OGSA

The myGrid Team Carole Goble Norman Paton Brian Warboys Stephen Pettifer Luc Moreau Dave De Roure Chris Greenhalgh Tom Rodden John Brooke Paul Watson Alan Robinson Rob Gaizauskas Robert Stevens Ian Horrocks Neil Wipat Matthew Addis Nick Sharman Rich Cawley Simon Harper Karon Mee Simon Miles Vijay Dailani Xiaojian Liu Tom Oinn Martin Senger Milena Radenkovic Kevin Glover Angus Roberts Chris Wroe Mark Greenwood Phil Lord Neil Davis Darren Marvin Justin Ferris Peter Li Nedim Alpdemir Luca Toldo Robin McEntire Anne Westcott Tony Storey Bernard Horan Paul Smart Robert Haynes

myGrid Partners m

myGrid Summary myGrid aims to develop infrastructure middleware for an e-Biologist’s workbench. The setting is bioinformatics but the results are intended to be generally applicable to e-Science. A mix of standard, vanguard and bleeding edge technologies, advanced development and (some) research. Academic & commercial partnership. myGrid project is timely & reflects a community desire to “collaborate, or die”.

myGrid: Personalised e-Science on the Grid. Professor Carole Goble Contact