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Building a simple workflow

We are going to build and run a simple workflow that retrieves data (protein sequence) from the NCBI database.

1. Search for a service

From the Service Panel:

  1. Type "fasta" into the Filter box at the top of the panel. You will see several services in the filter results.
  2. Select Get Protein FASTA service. This service returns a protein sequence in Fasta format from a database if you supply it with a sequence identifier.



2. Drag the service to the workflow diagram

3. Drag Get Protein FASTA across to the Workflow Diagram.
4. In a blank space in the Workflow Diagram, right-click and select Workflow input port.



3. Create the workflow's inputs and outputs

5. Type in a name for this input (e.g. ID) and click OK.
6. Do the same to create a new workflow output. This time select Workflow output port. Call this output Sequence.
7. You now have 3 boxes in the Workflow Diagram and need to connect them up.
8. Click on the input box (ID) and drag towards Get_Protein_FASTA and let go. An arrow will connect the two boxes.




4. Connect the service to the workflow's inputs and outputs

9. Click on the output box (Sequence), drag towards Get_protein_FASTA, and let go. An arrow will connect the two boxes.

Well done! You have built your first Taverna workflow!



Running a workflow

To run the workflow you have just built:

  1. Select Run workflow from the File menu. The Run Dialog will pop up.
  2. Click on New value from the Run Dialog and enter 1220173 where it says “some input data goes here”.




3. Click Run workflow.
4. In the bottom left of the results window, click on value. You will now see a protein sequence from NCBI.

After the worklflow run has started, the Workbench switches to the Result Perspective where you can monitor the run and view results.

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