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Complex In-silico Experiments in Integrative Biology

Complex In-silico Experiments in Integrative Biology. Overview. Project introduction IB requirements and context Status and plans Some specific issues. Project Overview. EPSRC Best Practice project from myGrid … workflow / information model … to IB

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Complex In-silico Experiments in Integrative Biology

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  1. Complex In-silico Experiments in Integrative Biology

  2. Overview • Project introduction • IB requirements and context • Status and plans • Some specific issues

  3. Project Overview • EPSRC Best Practice project • from myGrid … • workflow / information model • … to IB – computationally demanding domain • 1 year, started Jan 2005, 2sy • CCLRC, IT Innovation, Manchester, Oxford

  4. Objectives • “Extend scientists ability to steer in-silico experiments beyond current computational steering to cover the whole experimental process” • “Provide the necessary information management to make this useful”

  5. Workflow in the IB Environment ExecutableManagement Registries Workflow Designer JobSubmission Portal WorkflowEnactment DataManagement CollaborativeWorking ComputationalSteering Security Security

  6. IB workflow characteristics • moderate workflow complexity • some tight coupling, c.f. coupled simulation models • mostly loose, linear sequences • large, long running activities • handling and monitoring HPC jobs (batch & interactive) • computational steering (of the activity) • large data flows • streaming of data between activities • separate data flows from control flows • dynamic workflows • workflow steering (ad hoc workflows)

  7. Prototype workflow

  8. Status • Initial investigations completed • issues to be addressed • initial workflows modelled • Workplan • workflow extensions for HPC (ongoing) • steering for workflows (ongoing) • provenance for steering (starting) • annotations • integration into IB • extract/capture “best practice” for reuse

  9. Steering workflows • Steering via the Taverna client • reconnection to running workflows • pause/restart facility • setting breakpoints • editing data at breakpoints • integrity in the face of concurrency • impact on provenance • invisible (to Taverna) edits • LSID versioning (see later) X A Y B C

  10. Data Management IB server NGS SRB • LSID • immutable, but not immortal => all provenance data • where, when and how to use them • intermediate results • local copies / streamed data • SRB support required • Data Marshalling • integration with SRB • pass-by-reference (using LSIDs?) • balance explicit / implicit marshalling urn:lsid:www.integrativebiology.ac.uk:CARPexpt1:1234:2 A FreeFluo B Provenance

  11. Summary • myGrid provides some quite sophisticated tools • but IB brings in a number of new wrinkles. • which myIB is addressing. • Thank you • Questions?

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