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10 Best Practices for Workflow Design


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Presented at the 2nd BioVeL Workshop on taxonomic and phylogenetic workflows (

Published in: Technology, Business
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10 Best Practices for Workflow Design

  1. 1. 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)
  2. 2. Our specialty: Knowledge Discovery Disambiguation* Text Mining Substrates for Knowledge Discovery Methods for Knowledge Discovery Applications •Predict protein-protein, protein-disease associations, gene prioritization •Genotype-phenotype studies, e.g. Huntington’s Disease, Metabolic Syndrome •Yours?* Global disambiguation initiative: 2
  3. 3. Introduction Why build good workflows?Good workflow design = good science! 3
  4. 4. Introduction Best practices for workflow design Best Practices for workflow design =Best Practices experimental science +Best Practices software engineering 4
  5. 5. 1Make a sketch workflow 5
  6. 6. Best practice 1 Sketch an Abstract WorkflowPowerpoint courtersy of Eleni Mina 6
  7. 7. 2Use modules 7
  8. 8. 8
  9. 9. 3 Think about the output(and the data in your workflow in general) 9
  10. 10. Best practice 3Think about the output ? http://... 10
  11. 11. 4Provide example inputs and outputs 11
  12. 12. Taverna 2.3 Recipe Taverna 2.4 Select input/outputRight-click input/output Select tab ‘Details’ Select ‘Annotation’ Click ‘Annotation’ Add Example Add Example 12
  13. 13. 5Annotate 13
  14. 14. Best practice 5 AnnotateEach component in Taverna can be annotated 14
  15. 15. Best practice 5Annotate and help your users 15
  16. 16. 6Make workflow executable from outside the local environment 16
  17. 17. Best practice 6 Make workflow executable by othersHow to check that others can execute your workflow?» Try it! Proof of executability › 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) 17
  18. 18. 7Choose services carefully 18
  19. 19. Best practice 7Choose services carefully 19
  20. 20. Best practice 7Choose services carefully 20
  21. 21. 8Reuse existing workflows 21
  22. 22. Best practice 8 The reuse workflow Not a best practice, but a tip: know-how is Check important for reuse Contact authorsworkflows on Neg. RetrymyExperiment Pos. Use scripts from Neg. colleaguesCheck services Search the Contact authors on internet Neg. Retry BioCatalogue Pos. Invent a new wheel Reuse, Attribute Respect licences 22
  23. 23. 9Advertise 23
  24. 24. Advertise Unique reference forin your papers and for others to cite 24
  25. 25. 10Maintain 25
  26. 26. Best Practice 10 MaintainBest practices to support maintenance» 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 26
  27. 27. Bonus tipUse common sense as scientist 27
  28. 28. Workflow Forever Preservation of good workflows for future applications Workflow 74 “Protein Discovery” 2005Workflow 2876“Match gene listsby literature” 2012 Workflow 2805 “Get Pathway genes” 2012 28
  29. 29. Wf4Ever Outcomes for BioVeLmyExperiment 2.0BioCatalogueTavernaResearch ObjectsLinked DataMethodsProtocols for Preservation and Conservation 29
  30. 30. The 10 Best Practices of Workflow Design Thank youThank you for your attentionMore information: 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 30
  31. 31. Wf4Ever toolingSneak preview 31
  32. 32. Supporting information Workflow jargon› Scientific workflow Paradigm to describe, manage, and share complex scientific analyses› Workflow system Software to design, execute, and monitor scientific workflows› Module = nested workflow = workflow in a workflow = workflow component› Beanshell script A Java-based scripting language. Typically used for data type conversions in Taverna.› Provenance History or trace of a workflow run. Allows you to look at intermediate data, which workflows and services were run, with what data. 32