Taverna is a workflow management system that allows users to design and execute workflows by connecting different services. It provides features like access to remote services, automated data flow between services, workflow provenance tracking, and the ability to share workflows on myExperiment. The document discusses Taverna's workflow design interface, supported service types, workflow execution features, and its use in domains like bioinformatics and with tools like SCAPE for digital preservation.

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

3. SCAPE
Design and run workflows
Taverna

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

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

7. SCAPE
Taverna 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. 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. SCAPE
Workflow Results
Progress report
Previous runs
Input data and
results per port

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. 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. 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. SCAPE
Share, discover and reuse workflows

14. SCAPE
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. SCAPE
myExperiment

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. SCAPE
Use myExperiment from Taverna

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. 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