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myGrid: Personalised e-Biology on the Grid

myGrid: Personalised e-Biology on the Grid. Professor Carole Goble http://www.mygrid.org.uk Contact mygrid@cs.man.ac.uk. myGrid: Personalised e-Science on the Grid. Personalised extensible environments for data-intensive in silico experiments in biology. e-Science & Biology.

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myGrid: Personalised e-Biology on the Grid

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  1. myGrid: Personalised e-Biology on the Grid Professor Carole Goble http://www.mygrid.org.uk Contact mygrid@cs.man.ac.uk

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

  3. e-Science & Biology • Discovery is increasingly done in silico on results obtained from experiments using computational analysis & data repositories. • A new era of collection based and simulation based science. integration mining analysis hypothesis prediction integration mining analysis experiment results

  4. curation e-Science & Biology • Discovery is increasingly done in silico on results obtained from experiments using computational analysis & data repositories. • A new era of collection based and simulation based science. integration mining analysis hypothesis prediction integration mining analysis experiment results

  5. 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.

  6. 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

  7. Descriptive knowledge

  8. Circadian Rhythms • Has anyone else studied the effect of neurotransmitters on the circadian rhythms in Drosophila? • How do the functions of the clusters of proteins from my experiment interrelate? And 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? 1 2 3 4 5

  9. 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. 1 2 3 4 5 Personalisation.

  10. 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. 1 2 3 4 5 Personalisation.

  11. 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. 1 2 3 4 5 Personalisation.

  12. 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. 1 2 3 4 5 Personalisation.

  13. 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. 1 2 3 4 5 Personalisation.

  14. 3 4 5 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. 1 2 3 4 5 Personalisation.

  15. 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.

  16. myGrid Middlewareremoving the obstacles myGrid Middleware

  17. Who is myGrid for? myGrid users IS specialists biologists systems administrators tool builders infrequent problem specific service provider bioinformaticians bioinformatics tool builders

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

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

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

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

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

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

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

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

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

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

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

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

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

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

  32. Two videos • Experimental pre-prototype for requirements capture. • How do the functions of a cluster of proteins interrelate? • The other one, with provenance and temporary parking in repository.

  33. Applications Client Framework Admin Portal User Agent Collaboration Semantic Services Info. Extraction Data Workflow Ontology Metadata Services Personalisation Provenance Directory Coordination Services Governance Workflow Data Directory Networked Services myGrid Stack

  34. myGrid generic technologies • Ontologies, Protocols & APIs. • Database access from the Grid. Reference implementation for UK DBTF. • Process enactment on the Grid. • Provenance services. • Metadata services. • From Semantic Web: DAML+OIL, RDF(S). • Personalisation services. • Reference implementation of OGSA.

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

  36. 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

  37. m myGrid Partners

  38. myGridSummary • 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 ofstandard, vanguard and bleeding edgetechnologies, advanced development and (some) research. • Academic & commercial partnership. • myGrid project is timely & reflects a community desire to “collaborate, or die”.

  39. myGrid: Personalised e-Scienceon the Grid. Professor Carole Goble http://www.mygrid.org.uk Contact mygrid@cs.man.ac.uk

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