Introduction to Taverna Online and Interaction service

Aleksandra Pawlik

University of Manchester

Taverna Portal

In order to run Taverna workflows you don’t have to have the Taverna Workbench installed

Taverna Workflows can be run through the BioVel Portal which

Workflows can be run remotely No client (Workbench or Command Line Tool) is required Your workflows can be run by people who do not have

access to any of the Taverna clients Running workflows is helpful for demonstration purposes

Taverna Portal

Go to http://tavlite1.biovel.eu/

You can run Taverna Workflows as a guest user but if you want to upload your own workflows you must create an account

For the purpose of this tutorial we are using http://tavlite1.biovel.eu/ because it contains some already uploaded workflows. However, as you will see on the site the current version is http://portal.biovel.eu

Taverna Portal

Select “Workflows”

Taverna Portal

In the listed workflows find “Blast_Align_And_Tree” You can see the description, inputs, outputs and the

statistics for running the workflow

Taverna Portal

In order to run the workflow do select “Create Run”

(Please try not to run this workflow all at the same time!)

You have to provide your email address (even if you are logged in)

You can use the example values or upload a file with your own input values (which may be consistent with the input specified for the given workflow)

Click “Start run”

Sometimes it may take a few minutes to run the workflow on the Portal

Taverna Portal

The results can be browsed on the BioVel website or downloaded

You can see the past workflow runs (if you’re logged in) by selecting “Runs”

Taverna Online

Go to onlinehpc.com and register as a new user

To create a new workflow select “Workflows” -> “New Workflow” and provide its title (for example “Hello Workflow”)

Taverna Online

Taverna Online

Drag and drop “Script” and then click “Properties” We get a similar window for configuring the script, just like in

the Taverna Workbench We can specify input and output ports as well as

parallelization, the number of retries and loops

Taverna Online

We need to add output and input ports For the input select Utility components and

Constant For the output select External ports and Result

We will write a very simple script out = “Hello “ + in;

Taverna Online

To specify the input we need to click on “Properties” (enter “John” or whatever name you like)

To run the workflow click “Launch” at the top

We need to provide the title for the workflow and we can see the results

Taverna Interaction Service

Many workflows need user interaction

A workflow on a server does not need to be “press a button and wait”

Taverna Interaction Service Users interact with a workflow (wherever it is running) in

a web browser. Interaction Service Plug-in in workbench

Taverna Interaction Service

We will build a simple workflow to demonstrate how Interaction Services work

Add “ask” service from Interaction services

Taverna Interaction Service

Add a string constant to the “message” port of the ask service with value “Hello, what is your name?”

Connect the ask output with an output port and run the workflow You should see a website form where you can answer the

question

Provide the answer and click “Submit”. Then go back to Taverna

Taverna Interaction Service

You should see your answer in the output port We can now connect this output with another local service Add “Concatenate two strings” and add the string value as

an input for the port “string 1”

Taverna Interaction Service

This is a very simple example but on the BioVel Portal you can run a much more complex workflow which uses the interaction service

Go to the BioVel Portal and look for

Generic ENM workflow with interaction

(https://portal1.at.biovel.eu/workflows/21)