Taverna Plugin

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Taverna is an open source Workflow Management System written in Java. Interoperability between Taverna and GIMIAS can provide a lot of interesting functionalities for creating medical imaging workflows composed of several filters.

The benefits of using Taverna are:

  • Simplifies creation of workflows using the graphical interface designer
  • Facilitates reproducibility of scientific analyses and processes

Another interesting features are the possibility to connect with grid computing technologies and to discover and execute the remote services using web services technology.

A Taverna plugin has been developed that allows to discover all command line plugins. The GIMIAS plugin allows to execute Taverna workflows in GIMIAS and inspect the results.

Taverna plugin

Released the version 0.0.1 of the Taverna plugin for GIMIAS that allows to use GIMIAS command line plugins in Taverna 2.2.0.

The plugin allows discovering command line plugins, edit parameters and execute these locally or remotelly using SSH.

Taverna Workbench with GIMIAS plugin

All GIMIAS command line plugins are automatically available in Taverna. For example GaussianBlurImageFilter command line plugin applies a Gaussian blur to an input image. You can read more about command line plugins in this page: HowToAddCommandLinePlugin

When a new command line plugin is added into GIMIAS, it will be automatically available in Taverna Workbench thanks to the GIMIAS plugin provider. This provider will scan a folder and query all available command line plugins for the XML interface. The user can also configure a remote SSH plugin provider that will discover GIMIAS command line plugins in a remote computer.

Using Taverna Workbench, the user can drag and drop the available services to the workflow diagram area and connect the inputs and outputs of the used services.

GIMIAS plugin

Developed a GIMIAS plugin that allows to launch Taverna embedded in GIMIAS, read Taverna workflows, execute them and load output results. You need to install Taverna Workbench and configure the path to Taverna.

Taverna working area

Description: Launch Taverna Workbench embedded inside a Working Area

Author: Xavi Planes

Taverna plugin in GIMIAS

When the Taverna workflow is executed from GIMAS, the input data for the workflow is automatically passed from GIMIAS to Taverna. When the service being executed is located remotely, the data is transferred using SSH protocol between local and remote computers. Once the workflow is finished, the output data will be automatically loaded in GIMIAS. Taverna provides a simple command line tool that runs Taverna workflows from a terminal. From GIMIAS, this command line tool is executed directly without the need to launch Taverna Workbench. This is an interesting feature for clinicians end-users, where they just need to apply a button to execute the workflow and retrieve the results.

Notes:

  • If you receive an error message that java cannot be found, you need to set the PATH environment variable. You can read more information here
  • If you receive the error message "Could not create the Java Virtual Machine", you can try to use the executable "taverna-debug.bat". You can set this executable in the Preferences dialog. Otherwise, you need to uninstall and reinstall the Java

Tutorial videos

Limitations

Known limitations:

  • All the command line plugin parameters are stored in the workflow file. The location and the data directory are also stored. So it could be difficult to share workflows between different GIMIAS versions
  • Input image path should be set using "New value" and not "Add file location..."
  • You need to remove intermediate files manually
  • Only works in Windows due to limitations in embedding window and discovering CLP
  • Embedded Taverna window cannot be resized to a minimum size after launched. You need to minimize GIMIAS and launch Taverna.

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