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3 Why build good workflows? Introduction Good workflow design = good science!
30
The 10 Best Practices for Workflow Design BioVeL M6 Workshop Göteborg, 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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Page 1: The 10 Best Practices for Workflow Design BioVeL M6 Workshop Gteborg, May 10-11, 2012 Kristina Hettne, Marco Roos (LUMC), Katy Wolstencroft, Carole Goble.

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)

Page 2: The 10 Best Practices for Workflow Design BioVeL M6 Workshop Gteborg, May 10-11, 2012 Kristina Hettne, Marco Roos (LUMC), Katy Wolstencroft, Carole Goble.

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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

Page 3: The 10 Best Practices for Workflow Design BioVeL M6 Workshop Gteborg, May 10-11, 2012 Kristina Hettne, Marco Roos (LUMC), Katy Wolstencroft, Carole Goble.

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Why build good workflows?Introduction

Good workflow design = good science!

Page 4: The 10 Best Practices for Workflow Design BioVeL M6 Workshop Gteborg, May 10-11, 2012 Kristina Hettne, Marco Roos (LUMC), Katy Wolstencroft, Carole Goble.

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Best Practices for workflow design=

Best Practices experimental science+

Best Practices software engineering

Introduction

Best practices for workflow design

Page 5: The 10 Best Practices for Workflow Design BioVeL M6 Workshop Gteborg, May 10-11, 2012 Kristina Hettne, Marco Roos (LUMC), Katy Wolstencroft, Carole Goble.

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1Make a sketch workflow

Page 6: The 10 Best Practices for Workflow Design BioVeL M6 Workshop Gteborg, May 10-11, 2012 Kristina Hettne, Marco Roos (LUMC), Katy Wolstencroft, Carole Goble.

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Powerpoint courtersy of Eleni Mina

Sketch an Abstract Workflow

Best practice 1

Page 7: The 10 Best Practices for Workflow Design BioVeL M6 Workshop Gteborg, May 10-11, 2012 Kristina Hettne, Marco Roos (LUMC), Katy Wolstencroft, Carole Goble.

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2Use modules

Page 8: The 10 Best Practices for Workflow Design BioVeL M6 Workshop Gteborg, May 10-11, 2012 Kristina Hettne, Marco Roos (LUMC), Katy Wolstencroft, Carole Goble.

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http://www.myexperiment.org/workflows/74.html

Page 9: The 10 Best Practices for Workflow Design BioVeL M6 Workshop Gteborg, May 10-11, 2012 Kristina Hettne, Marco Roos (LUMC), Katy Wolstencroft, Carole Goble.

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3Think about the output

(and the data in your workflow in general)

Page 10: The 10 Best Practices for Workflow Design BioVeL M6 Workshop Gteborg, May 10-11, 2012 Kristina Hettne, Marco Roos (LUMC), Katy Wolstencroft, Carole Goble.

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http://...

Think about the output

Best practice 3

?

Page 11: The 10 Best Practices for Workflow Design BioVeL M6 Workshop Gteborg, May 10-11, 2012 Kristina Hettne, Marco Roos (LUMC), Katy Wolstencroft, Carole Goble.

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4Provide example inputs and

outputs

Page 12: The 10 Best Practices for Workflow Design BioVeL M6 Workshop Gteborg, May 10-11, 2012 Kristina Hettne, Marco Roos (LUMC), Katy Wolstencroft, Carole Goble.

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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

Page 13: The 10 Best Practices for Workflow Design BioVeL M6 Workshop Gteborg, May 10-11, 2012 Kristina Hettne, Marco Roos (LUMC), Katy Wolstencroft, Carole Goble.

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5Annotate

Page 14: The 10 Best Practices for Workflow Design BioVeL M6 Workshop Gteborg, May 10-11, 2012 Kristina Hettne, Marco Roos (LUMC), Katy Wolstencroft, Carole Goble.

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Annotate

Best practice 5

Each component in Taverna can be

annotated

Page 15: The 10 Best Practices for Workflow Design BioVeL M6 Workshop Gteborg, May 10-11, 2012 Kristina Hettne, Marco Roos (LUMC), Katy Wolstencroft, Carole Goble.

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Annotate and help your users

Best practice 5

Page 16: The 10 Best Practices for Workflow Design BioVeL M6 Workshop Gteborg, May 10-11, 2012 Kristina Hettne, Marco Roos (LUMC), Katy Wolstencroft, Carole Goble.

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6Make workflow executable from outside the local environment

Page 17: The 10 Best Practices for Workflow Design BioVeL M6 Workshop Gteborg, May 10-11, 2012 Kristina Hettne, Marco Roos (LUMC), Katy Wolstencroft, Carole Goble.

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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

Page 18: The 10 Best Practices for Workflow Design BioVeL M6 Workshop Gteborg, May 10-11, 2012 Kristina Hettne, Marco Roos (LUMC), Katy Wolstencroft, Carole Goble.

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7Choose services carefully

Page 19: The 10 Best Practices for Workflow Design BioVeL M6 Workshop Gteborg, May 10-11, 2012 Kristina Hettne, Marco Roos (LUMC), Katy Wolstencroft, Carole Goble.

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Choose services carefully

Best practice 7

Page 20: The 10 Best Practices for Workflow Design BioVeL M6 Workshop Gteborg, May 10-11, 2012 Kristina Hettne, Marco Roos (LUMC), Katy Wolstencroft, Carole Goble.

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Choose services carefully

Best practice 7

Page 21: The 10 Best Practices for Workflow Design BioVeL M6 Workshop Gteborg, May 10-11, 2012 Kristina Hettne, Marco Roos (LUMC), Katy Wolstencroft, Carole Goble.

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8Reuse existing workflows

Page 22: The 10 Best Practices for Workflow Design BioVeL M6 Workshop Gteborg, May 10-11, 2012 Kristina Hettne, Marco Roos (LUMC), Katy Wolstencroft, Carole Goble.

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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.

Page 23: The 10 Best Practices for Workflow Design BioVeL M6 Workshop Gteborg, May 10-11, 2012 Kristina Hettne, Marco Roos (LUMC), Katy Wolstencroft, Carole Goble.

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9Advertise

Page 24: The 10 Best Practices for Workflow Design BioVeL M6 Workshop Gteborg, May 10-11, 2012 Kristina Hettne, Marco Roos (LUMC), Katy Wolstencroft, Carole Goble.

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Advertise

Unique reference for in your papers and for others to cite

Page 25: The 10 Best Practices for Workflow Design BioVeL M6 Workshop Gteborg, May 10-11, 2012 Kristina Hettne, Marco Roos (LUMC), Katy Wolstencroft, Carole Goble.

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10Maintain

Page 26: The 10 Best Practices for Workflow Design BioVeL M6 Workshop Gteborg, May 10-11, 2012 Kristina Hettne, Marco Roos (LUMC), Katy Wolstencroft, Carole Goble.

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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

Page 27: The 10 Best Practices for Workflow Design BioVeL M6 Workshop Gteborg, May 10-11, 2012 Kristina Hettne, Marco Roos (LUMC), Katy Wolstencroft, Carole Goble.

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Bonus tipUse common sense as scientist

Page 28: The 10 Best Practices for Workflow Design BioVeL M6 Workshop Gteborg, May 10-11, 2012 Kristina Hettne, Marco Roos (LUMC), Katy Wolstencroft, Carole Goble.

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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

Page 29: The 10 Best Practices for Workflow Design BioVeL M6 Workshop Gteborg, May 10-11, 2012 Kristina Hettne, Marco Roos (LUMC), Katy Wolstencroft, Carole Goble.

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myExperiment 2.0BioCatalogueTaverna

Research ObjectsLinked Data

MethodsProtocols for

Preservation and Conservation

Wf4EverOutcomes for BioVeL

Page 30: The 10 Best Practices for Workflow Design BioVeL M6 Workshop Gteborg, May 10-11, 2012 Kristina Hettne, Marco Roos (LUMC), Katy Wolstencroft, Carole Goble.

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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


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