1. BioMoby and Taverna Tutorial

2. Downloading Taverna ► Taverna can be obtained from: http://taverna.sourceforge.net 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 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 $ 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’

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

48. ► A prompt to add values to our 2 workflow inputs

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

50. ► Enter 656461 as the id

51. ► Choose namespace from the left and click on ‘New Input’

52. ► Enter NCBI_gi as the value for namespace ► Once you are done, click on ‘Run Workflow’

53. ► Our workflow in action

54. ► Once the workflow is complete, we can examine the results of our workflow.

55. ► A detailed report is available outlining what happened when and in what order.

56. ► We can examine the intermediate inputs and output, as well as visualize our workflow.

57. ► If we choose the Graph tab, our workflow is illustrated.

58. ► Intermediate inputs allow us to examine what a service has accepted as input

59. ► Similarly, Intermediate outputs allows us to examine the output from any particular service.

60. ► Without the parser, FASTA is represented as a Moby message, fully enclosed in its wrapper. ► Non-moby services do not expect this kind of message

61. ► Non-moby services expect the just the sequence and using the Parse_Moby_Data processor, we can extract just that

62. ► Moby services can interact with the other services in Taverna. ► Let’s add a Soaplab service.

63. ► We will choose a nucleic_restriction soaplab service called ‘restrict’

64. ► Choose the restrict service and add it to the workflow.

65. ► We will connect the output port fasta_’content’ from the service Parse_Moby_Dat a_FASTA to the input port ‘sequence_direct _data’ from the service restrict

66. ► The result of our actions so far. ► We will need to add another workflow output to capture the output of restrict.

67. ► Create an output called restrict_out

68. ► Connect the output port ‘outfile’ from the service restrict to the workflow output restrict_out

69. ► Once the connections have been made, run the workflow again using the same inputs.

70. ► The workflow on the left has some extra services added to it.  FASTA2HighestGenericSequenceObject from the authority bioinfo.icapture.ubc.ca  runRepeatMasker from the authority genome.imim.es  A Moby parser for the output DNASequence from runRepeatMasker.  A workflow output Masked_Sequence ► Add them to your workflow

71. ► The service runRepeatMasker is configurable, i.e. it consumes Secondary parameters. ► To edit these parameters, context click on the service and choose ‘Configure Moby Service’

72. ► The name of the parameter is on the left and the value is on the right. ► Clicking on the Value will bring up a drop down menu, an input text field, or any other appropriate field depending on the parameter.

73. ► The parameter species contains an enumerated list of possibilities. ► Select human. ► When you have made your selection, you may close the window.

74. ► Let’s run the workflow

75. ► We will run our workflow with a list  Click on id in the left pane and then click on New Input twice

76. ► Enter 656461 and 654321 as the ids ► Enter NCBI_gi as the value for namespace ► Our workflow will now run using each id with the single namespace

77. ► Notice how the workflow is running with iterations. This is happening because the Enacter is performing a cross- product on the input

78. ► You can still view intermediate inputs and outputs. ► Using the queryIDs, you can track each invocation of a moby service through the whole workflow

79. ► Imagine now that you want to run the workflow using a FASTA sequence that you input yourself (without the gi identifier) ► To do this, context click on getDragonBlastText and choose Moby Service Details  Expand the Inputs node and context click on FASTA(‘sequence’)  Choose Add Datatype – FASTA(‘sequence’) to the workflow ► A FASTA datatype will be added to the workflow and the appropriate links created

80. ► Notice the datatype FASTA on the left of the workflow  Since the datatype FASTA hasa String, a String was also added to our workflow and the appropriate connection was made ► We will now have to add another workflow input and connect it to the String component of FASTA.

81. ► A workflow input ‘sequence’ was added to the workflow and a connection was made from the workflow input to the input port ‘value’ of String. ► We also removed the link between MOBYSHoundGetGenBankFasta and getDragonBlastText by context clicking on the link in the Advanced model explorers’ Data links and choosing to remove the link ► Now when we choose to run our workflow, we will also have the chance to enter a FASTA sequence

82. ► Go ahead an enter any FASTA sequence as the input to the workflow input ‘sequence’ ► Run the workflow

83. ► Any results can be saved by simply choosing to Save to disk  You will be prompted to enter a directory to save the results.  Each workflow output will be saved in a folder with the same name as a workflow output and the contents of the folder will be the results ► You can also choose Excel, which produces an Excel worksheet with columns representing the workflow outputs and with rows that represent the actual data.