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my Grid

my Grid. Personalised extensible environments for data-intensive in silico experiments in biology http://www.mygrid.org.uk Professor Carole Goble, University of Manchester,UK carole@cs.man.ac.uk. my Grid. EPSRC funded pilot project Generic middleware within application setting

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my Grid

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  1. myGrid Personalised extensible environments for data-intensive in silico experiments in biology http://www.mygrid.org.uk Professor Carole Goble, University of Manchester,UK carole@cs.man.ac.uk

  2. myGrid • EPSRC funded pilot project • Generic middleware within application setting • 36 month http://www.mygrid.org.uk IBM

  3. In silico experimentation • Discovery, interoperation, fusion, sharing • Process is as important as outcome • Science is dynamic – change happens • Scientific discovery is personal & global • Ad-hoc solutions, people-powered

  4. myGrid resources Question: Nucleotide binding protein in mouse Answer: P12345 in Swiss-Prot is an ATPase Terri Attwood is an expert on this Jackson labs have a database but you need to register A paper has just been published in Proteins by the Stanford lab on this.

  5. Grid viewpoints What is it? Where is it? How to get it? When did it happen? Who knows it? Why does it? What are you doing? interrogation results private New Biology workflows public Governance & Control Technology Grid Access Grid

  6. myGrid e-Science objectives Active support of scientific practice in biology • Straightforward discovery, interoperation, sharing • information AND processes AND best practice • Improving quality of both experiments and data • provenance through information <-> process linkage • propagating change • Individual creativity & collaborative working • personalisation Cottage Industry to an Industrial Scale

  7. myGrid operational environment Open Source Open-Bio Foundation, Bio* Consortium Expertise View propagation, reasoning, workflow … (DeFacto) Standards OMG LSR, I3C, MGED, Gene Ontology Semantic Web RDF, RDFS, DAML+OIL Bioinformatics integration platforms DAS,OpenBSA, ISYS, OpenMMS, Kleisli, Ensembl, AppLab, SRS, BioNavigator, DiscoveryLink, GX, OPM, TAMBIS Web Services XML, SOAP, WSDL, UDDI Distributed Computing Environments CORBA, RMI, Jini, JXTA, DCOM GRID Globus/SRB/Condor

  8. Applications Toolkits Context mgt Process mgt Data mgt Communication fabric myGrid Stack Approach Metadata Personalisation Interoperation layer

  9. Context mgt Process mgt Data mgt 1. Resource management 2. Middleware technologies incl. Globus 3. Incorporating existing resources Applications Toolkits Metadata Personalisation Interoperation layer Communication fabric

  10. 1. Integration & distributed queries 2. View management3. Personal repositories Applications Toolkits Metadata Personalisation Interoperation layer Context mgt Process mgt Data mgt Communication fabric

  11. 1. Process description & storage 2. Process enactment 3. Process personalisation Applications Toolkits Metadata Personalisation Interoperation layer Context mgt Process mgt Data mgt Communication fabric

  12. Security & Confidentiality & Trust • Provenance & Attribution • Versioning Applications Toolkits Metadata Personalisation Interoperation layer Context mgt Process mgt Data mgt Communication fabric

  13. Context mgt Process mgt Data mgt 1. Ontology languages & services 2. Resource service descriptions 3. Annotation with metadata Applications Toolkits Metadata Personalisation Interoperation layer Communication fabric

  14. Context mgt Process mgt Data mgt 1. Agent based communication abstraction 2. Software engineering paradigm for extensible distributed services 3. Foundation for architectural evolution Applications Toolkits Metadata Personalisation Interoperation layer Communication fabric

  15. Context mgt Process mgt Data mgt • Personal data repositories • Personal processes • Models of sharing Applications Toolkits Metadata Personalisation Interoperation layer Communication fabric

  16. Context mgt Process mgt Data mgt 1. User interfaces & visualisation 2. Collaboration environments 3. Environment development 4. User-centred application development Applications Toolkits Metadata Personalisation Interoperation layer Communication fabric

  17. Context mgt Process mgt Data mgt 1. Specialist process: information extraction Applications Toolkits Metadata Personalisation Interoperation layer Communication fabric

  18. myGrid outcomes • e-Scientists • Environment built on toolkits for service access, personalisation & community • Gene function expression analysis using S. cerevisiae • Annotation workbench for the PRINTS pattern database • Developers • myGrid-in-a-Box developers kit • Re-purposing DAS, AppLab and OpenBSA … • Integrating ISYS & GlaxoSmithKline platforms

  19. myGrid generic technologies • Database access from the Grid • Process enactment on the Grid • Personalisation services • Metadata services • Laying the foundations for Agent Services • Ontologies, Protocols & APIs Grid+ Services+ Semantic Web

  20. Interoperability, higher level ontologies, reasoning, discovery, Reasoning services, Discovery services Fulfillment Grid Scientific Problems Knowledge Knowledge / capability Processes Information Value chain Semantics / process Jobs and Data Data Data / applications Raw Resources "Reproduced by permission of the IT Innovation Centre, University of Southampton."http://www.it-innovation.soton.ac.uk

  21. myGrid phased development 6 months • Versions of myGrid • Varying degrees of functionality Pre-prototype 12 months Architecture Simple services 24 months Early toolkit trials 33 months Extended services Application trials Developers toolkit Release

  22. myGrid Personalised extensible environments for data-intensive in silico experiments in biology http://www.mygrid.org.uk Professor Carole Goble, University of Manchester,UK

  23. Presented at the BiGUM1: Biological Grid Users Meeting 1 • NeSC, Glasgow, Scotland • October 30th 2001 • http://www.nesc.ac.uk/esi/progs/bigum1.html

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