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The 10 Best Practices for Workflow Design
BioVeL M6 WorkshopGöteborg, May 10-11, 2012
Kristina Hettne, Marco Roos (LUMC), Katy Wolstencroft , Carole Goble (myGrid)Thanks: BioSemantics Group (LUMC), myGrid team (UoM), Yassene Mohamed, Harish Dharuri (LUMC)
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http://biosemantics.org
Our specialty: Knowledge Discovery
Substrates for Knowledge Discovery
Disambiguation*
Text Mining
Applications•Predict protein-protein, protein-disease associations, gene prioritization•Genotype-phenotype studies, e.g. Huntington’s Disease, Metabolic Syndrome•Yours?
* Global disambiguation initiative: http://snipurl.com/conceptweballiance
Methods for Knowledge Discovery
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Why build good workflows?Introduction
Good workflow design = good science!
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Best Practices for workflow design=
Best Practices experimental science+
Best Practices software engineering
Introduction
Best practices for workflow design
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1Make a sketch workflow
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Powerpoint courtersy of Eleni Mina
Sketch an Abstract Workflow
Best practice 1
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2Use modules
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http://www.myexperiment.org/workflows/74.html
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3Think about the output
(and the data in your workflow in general)
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http://...
Think about the output
Best practice 3
?
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4Provide example inputs and
outputs
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Taverna 2.3 RecipeSelect input/outputSelect tab ‘Details’Click ‘Annotation’
Add Example
Taverna 2.4Right-click
input/outputSelect ‘Annotation’
Add Example
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5Annotate
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Annotate
Best practice 5
Each component in Taverna can be
annotated
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Annotate and help your users
Best practice 5
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6Make workflow executable from outside the local environment
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Make workflow executable by others
Best practice 6
» Try it!› Ask a colleague› Use an external t2web runner
» Tips› Use Web Services› If you use local command line tools
• Install tools on a publicly accessible server (e.g. applies to Rserve)• Use system that your users can set up (e.g. BioLinux)
How to check that others can execute your workflow?
Proof of executability
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7Choose services carefully
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Choose services carefully
Best practice 7
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Choose services carefully
Best practice 7
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8Reuse existing workflows
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Invent a new wheel
Search the internet
The reuse workflow
Best practice 8
Check workflows on myExperiment
Contact authors
Retry
Contact authors
Retry
Use scripts from
colleagues
Not a best practice, but a tip: know-how is important for reuse
Neg.
Neg.
Neg.
Reuse, AttributeRespect licences
Check services on
BioCatalogue
Pos.
Pos.
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9Advertise
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Advertise
Unique reference for in your papers and for others to cite
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10Maintain
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Maintain
Best Practice 10
» Regularly check your workflow› Ask colleagues
» Enable support for maintenance› Register your workflow on myExperiment› Register Web Services on
» Enable peers to repair: annotate!
» Note about versioning› No need to register all edits on myExperiment: use subversion› Register important updates on myExperiment
Best practices to support maintenance
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Bonus tipUse common sense as scientist
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Workflow 74“Protein Discovery”2005
Workflow 2876“Match gene listsby literature” 2012
Preservation of good workflows for future applications
Workflow Forever
Workflow 2805“Get Pathway genes” 2012
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myExperiment 2.0BioCatalogueTaverna
Research ObjectsLinked Data
MethodsProtocols for
Preservation and Conservation
Wf4EverOutcomes for BioVeL
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1. Make a sketch workflow2. Use modules3. Think about the output4. Provide example inputs and outputs5. Annotate6. Make it executable from outside the local environment7. Choose services carefully8. Reuse existing workflows9. Advertise10. Maintain
Thank youThe 10 Best Practices of Workflow Design
Thank you for your attentionMore information:http://snipurl.com/workflowbestpractices