Creating BioMoby Workflows In Taverna

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Creating BioMoby WorkflowsIn Taverna

• Mark Wilkinson
• Edward (Eddie) Kawas
• iCAPTURE Centre, St. Pauls Hospital
• Vancouver, BC

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Downloading Taverna
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• Taverna can be obtained fromhttp//taverna.sourc
  eforge.net

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• Once at the site, click on Download

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• Download the version appropriate for your
  operating system.

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• Between releases, the Moby functionality may be
  updated and you can find instructions on how to
  acquire those updates fromhttp//biomoby.open-bi
  o.org/index.php/moby-clients/taverna_plugin

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Running

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

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• 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)

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• Tavernas splash screen

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

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• The Advanced model explorer is Tavernas primary
  editor and allows you to load, save and edit any
  property of a workflow.

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

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

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• Under the node Biomoby _at_ 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

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• 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

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• Enter the registrys location and click okay.

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Creating Workflows

• I have the workflow saved and would like to offer
  it for download.

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

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• 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

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• We can discover services that consume our data
  type, context click on Object and choose Moby
  Object Details

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

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• 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

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• We will choose to add the service called
  MOBYSHoundGetGenBankFasta to our workflow.

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• A look at the state of our current workflow.

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

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• 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.

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• 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

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• 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

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• 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

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

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• We will add the service getDragonBlastText to our
  workflow by choosing Add service - from the
  context menu

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• The current state of our workflow shown
  graphically.

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• A more complex view of our workflow

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• Finding services that consume NCBI_BLAST_Text
  starts by viewing the details of the service
  getDragonBlastText

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• Conduct a brief search

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• Add the service parseBlastText to our workflow

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• Our current workflow

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• Workflow inputs are added by context clicking on
  Workflow inputs in the Advanced model explorer
  and choosing Create New Input

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• The result from adding 2 inputs
• Id
• namespace

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• The workflow input id will be connected to
  Objects input port id

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• Workflow after connecting the workflow input id

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• The workflow input namespace will connect to
  Objects input port namespace

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• Workflow after connection the workflow inputs.

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• Workflow outputs are added by context clicking on
  Workflow outputs in the Advanced model explorer
  and choosing Create New Output

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• The result from adding 2 workflow outputs
• moby_blast_ids
• fasta_out

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• The output moby_blast_ids will be connected to
  parseBlastTexts output port Object(Collection
  hit_ids)

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• The output fasta_out will be connected to
  Parse_Moby_Data_FASTAs output port
  fasta_content

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• To run the workflow, click on Tools and Workflow
  Invocation
• Choose Run workflow

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• A prompt to add values to our 2 workflow inputs

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• To add a value to the input id click on id from
  the left pane and choose New Input

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• Enter 656461 as the id

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• Choose namespace from the left and click on New
  Input

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• Enter NCBI_gi as the value for namespace
• Once you are done, click on Run Workflow

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• Our workflow in action

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

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

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

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

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• Intermediate inputs allow us to examine what a
  service has accepted as input

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

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• 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

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

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• Moby services can interact with the other
  services in Taverna.
• Lets add a Soaplab service.

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• We will choose a nucleic_restriction soaplab
  service called restrict

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• Choose the restrict service and add it to the
  workflow.

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• We will connect the output port fasta_content
  from the service Parse_Moby_Data_FASTA to the
  input port sequence_direct_data from the
  service restrict

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

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• Create an output called restrict_out

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• Connect the output port outfile from the
  service restrict to the workflow output
  restrict_out

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

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• 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

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• 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

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• 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.

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

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• Lets run the workflow

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

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• 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

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

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

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• 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

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• 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.

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• 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

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• Go ahead an enter any FASTA sequence as the input
  to the workflow input sequence
• Run the workflow

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• 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.