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

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.

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

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

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

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

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”

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

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

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

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

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

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”

Exercise 2: Using REST Services Searching the service catalogue

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

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

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

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

Exercise 2: Using REST Services