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Taverna and myExperiment. SCAPE presentation at a Hack-a-thon


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Presentation by Alexandra Nenadic, University of Manchest, of how to create workflows in Taverna and how the SCAPE project shares its workflows via myExperiment.
Presented at 'Practical Tools for Digital Preservation: A Hack-a-thon' in York, September 28, 2011.

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Taverna and myExperiment. SCAPE presentation at a Hack-a-thon

  1. 1. SCAPE TavernaTaverna and myExperimentTools for creating and sharing workflowsAlexandra Nenadic, David WithersUniversity of ManchesterPractical Tools for Digital Preservation: A Hack-a-thonYork, 28th September 2011
  2. 2. SCAPE What is a workflow?• Connecting a set of tools/services to create automated and repeatable processing/analysis
  3. 3. SCAPEDesign and run workflows Taverna
  4. 4. SCAPE Taverna Features - Overview• Access to remote, distributed or local services and resources• Enables service interoperability and integration• Automates data flow between services• Implicit iteration over data sets, list handling and control links to determine order of service invocation• Extensible • Large external developer base • Various third party plugins available• Data and provenance collection
  5. 5. SCAPE Taverna Workbench• Graphical desktop tool• Drag-and-drop services into diagram• Connect services, run, reconnect, rerun• Integrates diverse set of tools
  6. 6. SCAPE Workflow Design Available Workflow services diagram Tree view ofthe workflow structure
  7. 7. SCAPETaverna Workflows – Features in Detail • A set of (local and remote) services to analyze or manage data • Data-links connects services • i.e. output from service A is input to service B and C • Describes the desired dataflow instead of process coordination • Nested workflows are also services • Automatic iterations • Parallelization • Can customize list handling and control links • Fault tolerance • Retry (with delay and back off) • Failover (alternate services)
  8. 8. SCAPE Supported Services• SOAP/WSDL Web services• REST Web services• SoapLab Web services• R statistical services• Inline Beanshell scripts• External tools and scripts (via ssh or localhost)• Spreadsheet import• XPath and text manipulation services• SADI semantic Web services• Nested workflows (workflow within workflow)• BioMoby• BioMart• … your tool (write your own Taverna plugin)
  9. 9. SCAPE Workflow Results Progress reportPrevious runs Input data and results per port
  10. 10. SCAPE Workflow Provenance• Information about a workflow run • What happened? • And when?• Lineage tracing • Which input produced which output• Intermediate data • Inputs and outputs for each workflow step • Useful for debugging• Saved in standard format (such as OPM)
  11. 11. SCAPE Taverna is Domain-Independent• Bioinformatics• Biomedicine• Chemistry Pharmacogenomics HIV and TB research in Association study of Systems Biology for South Africa Nevirapine-induced skin Crop research, Sleeping Sickness in rash in Thai Population BioDiversity African Cattle
  12. 12. SCAPE Taverna is Domain-Independent• Astronomy• Data and text mining• Digital content preservation (IMPACT)• Social simulations Observing Systems Simulation Library Document Astronomy & Experiments Preservation HelioPhysics JPL, NASA British Library
  13. 13. SCAPEShare, discover and reuse workflows
  14. 14. SCAPE myExperiment•• Social networking for people to share workflows and collaborate• Makes it easy for people to contribute to a pool of workflows, build communities and form relationships• Enables people to share, describe, reuse and repurpose workflows, reduce time-to-production, share expertise and avoid reinvention
  15. 15. SCAPEmyExperiment
  16. 16. SCAPE Workflow Sharing, Ownership and Attribution• myExperiment can provide a central location for workflows from one community/group• myExperiment allows you to say – Who can look at your workflow – Who can download your workflow – Who can modify your workflow – Who can run your workflow• Workflow ownership and attribution • Users do not need to start from scratch – reuse or modify existing workflows • Attribute/credit original author
  17. 17. SCAPEUse myExperiment from Taverna
  18. 18. SCAPE Training• Tutorials and Training • 58+ tutorials to >900 people • >20 Universities, institutes and networks • Major conferences • Summer schools• Developer and User Days • Annotation Jamborees• Undergraduate and Postgraduate Bioinformatics in > 30 Universities
  19. 19. SCAPE Taverna and SCAPE• SCAPE preservation components/actions as services in Taverna workflows• Use Taverna Workbench to create and test SCAPE preservation workflows on local data• Then scale-up and run the workflows on a parallelized platform using Hadoop MapReduce• Share Taverna SCAPE workflows on myExperiment