View
52
Download
0
Category
Tags:
Preview:
DESCRIPTION
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?. - PowerPoint PPT Presentation
Citation preview
SCAPE
Alexandra Nenadic, David WithersUniversity of Manchester
Practical Tools for Digital Preservation: A Hack-a-thonYork, 28th September 2011
Taverna and myExperimentTools for creating and sharing workflows
Taverna
SCAPEWhat is a workflow?
• Connecting a set of tools/services to create automated and repeatable processing/analysis
SCAPE
Design and run workflows
Taverna
SCAPETaverna 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
SCAPETaverna Workbench
• Graphical desktop tool
• Drag-and-drop services into diagram
• Connect services, run, reconnect, rerun
• Integrates diverse set of tools
SCAPEWorkflow Design
Available services
Tree view of the workflow
structure
Workflow diagram
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)
SCAPESupported 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)
SCAPEWorkflow Results
Input data and results per port
Progress report
Previous runs
SCAPEWorkflow 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)
SCAPETaverna is Domain-Independent
• Bioinformatics• Biomedicine• Chemistry
PharmacogenomicsAssociation study of Nevirapine-induced skin rash in Thai Population
HIV and TB research in South AfricaSleeping Sickness in African Cattle
Systems Biology for Crop research, BioDiversity
SCAPETaverna is Domain-Independent
• Astronomy• Data and text mining• Digital content preservation (IMPACT)• Social simulations
Astronomy & HelioPhysics
Observing Systems Simulation ExperimentsJPL, NASA
Library Document PreservationBritish Library
SCAPE
Share, discover and reuse workflows
SCAPEmyExperiment
• 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
SCAPEmyExperiment
SCAPEWorkflow 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
SCAPEUse myExperiment from Taverna
SCAPETraining
• 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
SCAPETaverna 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
Recommended