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Taverna and myExperiment

Taverna. Taverna and myExperiment. Tools for creating and sharing workflows. Alexandra Nenadic, David Withers University of Manchester. Practical Tools for Digital Preservation: A Hack-a-thon York, 28 th September 2011. What is a workflow?.

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Taverna and myExperiment

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  1. Taverna Taverna and myExperiment Tools for creating and sharing workflows • Alexandra Nenadic, David Withers University of Manchester Practical Tools for Digital Preservation: A Hack-a-thon York, 28th September 2011

  2. What is a workflow? • Connecting a set of tools/services to create automated and repeatable processing/analysis

  3. Design and run workflows Taverna

  4. 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. Taverna Workbench • Graphical desktop tool • Drag-and-drop services into diagram • Connect services, run, reconnect, rerun • Integrates diverse set of tools

  6. Workflow Design Available services Workflow diagram Tree view of the workflow structure

  7. 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) Taverna Workflows – Features in Detail

  8. 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 Tavernaplugin)

  9. Workflow Results Progress report Previous runs Input data and results per port

  10. 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. Taverna is Domain-Independent • Bioinformatics • Biomedicine • Chemistry Pharmacogenomics Association study of Nevirapine-induced skin rash in Thai Population HIV and TB research in South Africa Sleeping Sickness in African Cattle Systems Biology for Crop research, BioDiversity

  12. Taverna is Domain-Independent • Astronomy • Data and text mining • Digital content preservation (IMPACT) • Social simulations Observing Systems Simulation Experiments JPL, NASA Library Document Preservation British Library Astronomy & HelioPhysics

  13. Share, discover and reuse workflows

  14. myExperiment • http://www.myexperiment.org • 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. myExperiment

  16. 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. Use myExperiment from Taverna

  18. 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. 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 HadoopMapReduce • Share Taverna SCAPE workflows on myExperiment

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