1. An Introduction to Designing and Executing Workflows with Taverna
Bioinformatics exercise
Norman Morrison
materials by:
Katy Wolstencroft
University of Manchester

2. Exercise 1: Building a Simple Workflow
We will start with something easy - retrieving a protein sequence from a remote database and identifying functional motifs
Go to the Services Panel
Type ‘Fasta’ into the ‘search’ box at the top of the panel
You will see several services in the search results
Select ‘Get Protein FASTA’ and drag-and-drop it into the workflow diagram panel.

3. Exercise 1: Building a Simple Workflow
In a blank space in the workflow diagram, right-click and select “Workflow input port” from the “Insert” section
Type in a name for this input (e.g. ID) and click “ok”
Do the same to create a new workflow output. Call this output “sequence” 3

4. Exercise 1: Building a Simple Workflow
You now have 3 boxes in the diagram and we need to connect them up
Click on the input box and drag towards “Get Protein Fasta” and let go. An arrow will connect the two boxes

5. Exercise 1: Building a Simple Workflow
Click on the output box, drag towards “Get protein fasta”, and let go. An arrow will connect the two boxes
You have now built your first workflow!
It should look something like this

6. Exercise 1: Building a Simple Workflow
Run the workflow by selecting “file -> run workflow”, or by clicking on the play button at the top of the workbench

7. Exercise 1: Building a Simple Workflow
An input window will appear. As you can see, we have not yet added a description of the workflow or of the input
Click on ‘Set Value’ in the input window and add a Uniprot protein identifier (e.g. P15409) where it says “some input data goes here”

8. Exercise 1: Building a Simple Workflow
Click “run workflow”
In the bottom left of the results window, click on the results. You will now see a protein sequence from Uniprot
Now we will find out what functional motifs the protein contains, but first we have to tell Taverna about some new services

9. Validate your Workflow
Taverna can check to see that everything is connected properly and that all the services in your workflow are available
Go to the workflow explorer and click on ‘validation report’
See if Taverna has found any problems with the workflow. Errors will be displayed in red, warnings in yellow. Workflows with warnings often still run.
If there are problems, follow the instructions to resolve them by clicking on the ‘Solution’ tab

10. Exercise 2: Adding more Services
We can connect the two services together in the same way as before
At the top of the workflow diagram panel, change the view to show all ports by clicking on the icon shown below
This view allows you to see any data input/output or parameter value options for your chosen service
Show all ports icon

11. Exercise 2: Adding more Services
Most of the time, you don’t need to connect all ports. Some are optional and some already have default values set.
Service documentation should tell you this. You can use the BioCatalogue to find documentation and user descriptions
Change the orientation of the port names to fit them on the screen more easily by clicking on the icon shown below
change orientation

12. Adding a Workflow Description
Right-click on a blank part of the workflow diagram and select “Annotate”
Add some details about the workflow e.g. who is the author, what does it do
You can also add examples and descriptions for the workflow inputs by selecting them and selecting “Annotate”
Add an example for the protein ID (e.g. P15409)
Save the workflow by going to “File -> save workflow”
Run the workflow again and look at the results

13. Exercise 2: Using REST Services
Taverna can also run WSDL and RESTful services
Go to the Service Catalogue tab of Taverna and search for dbfetch
From the REST Service results, select GET /dbfetch/{db}/{id}
Right-click on the service and select “Add to Service Panel”

14. Exercise 2: Using REST Services
Searching the service catalogue

15. Exercise 2a: Using REST Services
In the services search panel in Taverna, search for dbfetch
Right-click on the service and choose “Add to workflow with name…”
Enter a name such as “dbfetch” and click OK

16. Exercise 2a: Using REST Services
As you can see, the items from the dbfetch template become inputs in Taverna.

17. Exercise 2a: Using REST Services
You can also enter the template directly
Right-click on an empty area of the workflow and select “REST” from the “Insert” section
Enter the template and click OK

18. Exercise 2a: Using REST Services
For this service, we need to supply a database name and a protein ID.
Connect the protein ID input to the REST service ID input port
Right-click on the ‘db’ input port on the REST service and select ‘constant value’.
Add the constant value ‘uniprotkb’ and click “OK”
Add a workflow output port and connect it to the REST ‘response body’ output port
Your workflow should look something like the one on the next slide
Save and run your workflow
Now your results will include the uniprot entry for your protein

19. Exercise 2: Using REST Services