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Create and run Workflows across OpenTox services

Facilitated by Joerg Wicker and Fabian Buchwald

In this workshop, we will show how to access OpenTox Web Services via the Taverna workflow management system. We will create a few simple workflows. These workflows will upload a data set to an OpenTox server, modify the data or learn models. Additionally, we will present a more sophisticated workflow which demonstrates how to use Taverna for complicated workflows in OpenTox. The participants will create the demo workflows. To do this, the Taverna Workflow Management System is required. We will give the link to the required version before the workshop here. The software can also be installed in the workshop. It runs on Linux, Windows and Apple systems.

Instructions for testing the OpenTox Tavena workflows

There is a documentation at The information exists as PDF document, as well, where a few more examples are included, at . We recommend using the PDF document.

The instructions are a bit outdated in terms of downloading the latest version of Taverna. While at the time the instructions were prepared, the version needed to be the latest development version, it became the current release after 24 August 2011. So it is not necessary anymore to search for the nightly builds. Also, the instructions do not say explicitly that what is needed to be downloaded is the "Taverna Workbench".

The download link is To get the Windows installer directly, use

The installation instructions in the documentation is not accurate for Windows systems. With the Windows installer, the installation results in a link to the application in the "Start" menu of Windows, from which it can be started. Theoretically it is possible to navigate to the installation folder and start the application from there, but the file is not called "taverna.bat", but "taverna.exe".

The online documentation does not explain where to get the workflows. In fact, they can be found on the webpage of the documentation (, at the bottom under "Attachments". Also, the documentation does not explicitly state that the workflow for "List all TUM Algorithms" is list_tum_alg.t2flow, the one for "Upload and merge data" is upload_and_merge_datasets.t2flow.

The last workflow covered in the handout, to train a model using the workflow WorkflowLoMoGraph.t2flow is a bit difficult to get to run. First, one has to use the workflow getId.2.t2flow to obtain a new SSO token. This token then has to be added to all the REST services in the workflow that are protected (use advanced settings of the REST services). More specifically, the following REST services need to be reconfigured:



To do so, right-click each one of them and choose "Configure REST service...", then click "Advanced". In the table "HTTP Headers" change the value of the subjectid by clicking on the right column and paste the new token over the old. Press enter after pasting and click "Apply". Once all protected REST nodes are reconfigured, the workflow should run without any problems.

Complete the evaluation form following this link: Evaluation Form

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