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BioMoby and Taverna Tutorial

BioMoby and Taverna Tutorial. Downloading Taverna. Taverna can be obtained from: http://taverna.sourceforge.net. Once at the site, click on Download. Download the version appropriate for your operating system. Running.

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BioMoby and Taverna Tutorial

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  1. BioMoby and Taverna Tutorial

  2. Downloading Taverna • Taverna can be obtained from:http://taverna.sourceforge.net

  3. Once at the site, click on Download

  4. Download the version appropriate for your operating system.

  5. Running • For a more comprehensive guide on Running and using Taverna, please refer to http://taverna.sourceforge.net/usermanual/manual.html

  6. Assuming that you have downloaded and unzipped Taverna, you can run it by double-clicking on runme.bat (windows) or executing runme.sh (Unix/Linux/OS X) • You may need to: $ chmod u+r runme.sh

  7. Taverna’s splash screen

  8. Once Taverna has loaded, you will see 3 windows: • Advanced Model Explorer • Workflow Diagram • Available Services

  9. The Advanced model explorer is Taverna’s primary editor and allows you to load, save and edit any property of a workflow.

  10. Workflow diagram contains a read only graphical representation of your workflow.

  11. The Available services window lists all of the services available to a workflow designer.

  12. Under the node ‘Biomoby @ …’ Moby services and Moby data types are represented. • The Object ontology is available as children of MOBY Objects node • Services are sorted by service provider authority

  13. If you wish to use registries other than the default one, you can add a new Moby ‘Scavenger’ by choosing to ‘Add new Biomoby scavenger…’

  14. Enter the registry’s location and click okay.

  15. Creating Workflows

  16. We will start by adding the Object ontology node Object to our workflow.

  17. The Advanced model explorer now shows that we have a processor called Object • Object has 3 input ports: id, namespace and article name • Object has 1 output port: mobyData • The Workflow diagram illustrates our processor

  18. We can discover services that consume our data type, context click on ‘Object’ and choose ‘Moby Object Details’

  19. A window will pop up that tells you what services Object feeds into and is produced by

  20. Expanding the Feeds into node results in a list of service provider authorities • Expanding an authority, for example, bioinfo.icapture.ubc.ca, reveals a list of services

  21. We will choose to add the service called ‘MOBYSHoundGetGenBankFasta’ to our workflow.

  22. A look at the state of our current workflow.

  23. And graphically. • The service consumes Object, with article name identifier, and produces FASTA, with article name fasta.

  24. To discover more services, context click on the service that outputs the data type that you would like to discover consuming services for and choose Moby Service Details.

  25. The resultant window displays the services inputs and outputs. • There are also tool tips that show up when your mouse hovers over any particular input or output that tells you what namespaces the data type is valid in

  26. Context clicking on an output reveals a menu with 3 options. • A brief search for services that consume our datatype • A semantic search for services that consume our datatype • Adding a parser to the workflow that understands our datatype

  27. The result of choosing to add a parser for FASTA to our workflow. • The parser allows us to extract: • The namespace and id from FASTA • The namespace and id from the child String • The textual content from the child String

  28. The result of choosing to conduct a brief search for services that consume FASTA

  29. We will add the service getDragonBlastText to our workflow by choosing ‘Add service -…’ from the context menu

  30. The current state of our workflow shown graphically.

  31. A more complex view of our workflow

  32. Finding services that consume NCBI_BLAST_Text starts by viewing the details of the service ‘getDragonBlastText’

  33. Conduct a brief search

  34. Add the service ‘parseBlastText’ to our workflow

  35. Our current workflow

  36. Workflow inputs are added by context clicking on Workflow inputs in the Advanced model explorer and choosing ‘Create New Input…’

  37. The result from adding 2 inputs: • Id • namespace

  38. The workflow input id will be connected to Object’s input port ‘id’

  39. Workflow after connecting the workflow input ‘id’

  40. The workflow input namespace will connect to Object’s input port ‘namespace’

  41. Workflow after connection the workflow inputs.

  42. Workflow outputs are added by context clicking on Workflow outputs in the Advanced model explorer and choosing ‘Create New Output…’

  43. The result from adding 2 workflow outputs: • moby_blast_ids • fasta_out

  44. The output moby_blast_ids will be connected to parseBlastText’s output port Object(Collection –’hit_ids’)

  45. The output fasta_out will be connected to Parse_Moby_Data_FASTA’s output port fasta_’content’

  46. To run the workflow, click on ‘Tools and Workflow Invocation’ • Choose ‘Run workflow’

  47. A prompt to add values to our 2 workflow inputs

  48. To add a value to the input ‘id’ click on id from the left pane and choose ‘New Input’

  49. Enter 656461 as the id

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