Taverna Workbench – tools for designing and executing workflow

The Taverna workbench is an open source software tool for designing and executing bioinformatics workflows created by the myGrid project.

Taverna allows users to integrate many different software components, including SOAP or REST Web services, such as those provided by the National Center for Biotechnology Information, the European Bioinformatics Institute, the DNA Databank of Japan (DDBJ), SoapLab, BioMOBY and EMBOSS. The set of available services is not finite and users can import new service descriptions into the Taverna Workbench.

The Taverna suite is written in Java and includes the Taverna Engine (used for enacting workflows) that powers both the Taverna Workbench (the desktop client application) and the Taverna Server (which allows remote execution of workflows). Taverna is also available as a Command Line Tool for a quick execution of workflows from a terminal.

Taverna is used by users in many domains, such as bioinformatics, cheminformatics, medicine, astronomy, social science and music.

Features include:

  • Fully featured, extensible and scalable scientific Workflow Management System:
    • Tabs for finding, designing and executing workflows.
    • Fully graphical workflow design.
    • Drag and drop workflow components.
    • Comprehensive undo/redo.
    • Built-in help facility.
    • Annotations for describing workflows, services, inputs, outputs.
    • Workflow validation and debugging.
  • Execute and debug workflows:
    • Execute workflows.
    • Remember previously used workflow inputs.
    • Save workflow input values used to a file.
    • Load workflow input values from a file.
    • Pipelining and streaming of data.
    • Implicit iteration of service calls.
    • Conditional and repeated calling of services.
    • Customizable looping over a service.
    • Failover and retry of service calling.
    • Parallel execution and configurable number of concurrent threads.
    • Improved error handling and reporting for debugging during run time.
    • Monitor workflow execution.
    • Pause/resume or cancel workflow execution.
    • Manage previous runs and workflow results.
    • View intermediate results and debug workflows at run time.
    • Filter and save intermediate and final workflow results.
  • Available as a desktop Workbench, from a command line or remotely as a Server.
  • Access to local and remote resources and analysis tools, Web and grid services; 3500+
 service
s 
available
 on 
start
up.
  • Not restricted to predetermined services – rapid 
incorporation of 
new 
services
 without
 coding.
  • Extensible service plug-in architecture for adding new service type.
  • Excel and csv spreadsheet support.
  • Invoke general SOAP/WSDL or REST Web services, and more specific SADI, BioMart, BioMoby and SoapLab Web services.
  • Invoke R statistical services.
  • Invoke local Java code.
  • Invoke external tools on remote machines (via ssh), D.
  • Do XPath and other text manipulation.
  • Import a spreadsheet and include sub-workflows.
  • Search for services described in BioCatalogue to include within workflows.
  • Search for workflows on myExperiment. You can download, modify and run the workflows discovered on myExperiment from within the Taverna Workbench.
  • Plugins to extend functionality.

Website: taverna.incubator.apache.org
Support: Documentation
Developer: myGrid
License: GNU LGPL 2.1

Taverna

Taverna is written in Java. Learn Java with our recommended free books and free tutorials.

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