Questions tagged [taverna]

Taverna is a workflow system for scientific workflows.

Taverna is a workflow system for scientific workflows. The ecosystem has several main components:

  • SCUFL2 and t2flow — languages used to define workflows. These languages are inherently parallel; data is automatically processed when it is available when the workflow is being enacted. SCUFL2 is the principal workflow language for Taverna 3, and t2flow is the principal workflow language for Taverna 2.
  • Taverna Engine — the library for executing workflows, written in Java 7. The engine has a very high degree of internal parallelism, so that it is the workflows themselves that describe the limits on what is done at once rather than the engine enforcing limits from outside.
  • Taverna Command Line Tool — a simple wrapper round the Engine to make a program that can run workflows on the command line, taking inputs from files and writing outputs to files.
  • Taverna Server — a service based on the Engine that allows running of workflows for long periods of time by multiple users at once, and which presents both REST and SOAP interfaces for working with them. Clients of Taverna Server do not need to be written in Java; all operations use data formats that are language-independent (or which work with SCUFL2 or t2flow).
  • Taverna Workbench — an IDE for Taverna Workflows that design, inspect, run, and debug those workflows.

Taverna is in the process of moving to Apache. The source code to the current development version (Taverna 3) has moved, but the current supported version (Taverna 2.5) remains a product of (principally) the University of Manchester under the LGPL. Thus, the links below are scattered between several sites.

The preferred academic citation for Taverna is:

Katherine Wolstencroft, Robert Haines, Donal Fellows, Alan Williams, David Withers, Stuart Owen, Stian Soiland-Reyes, Ian Dunlop, Aleksandra Nenadic, Paul Fisher, Jiten Bhagat, Khalid Belhajjame, Finn Bacall, Alex Hardisty, Abraham Nieva de la Hidalga, Maria P. Balcazar Vargas, Shoaib Sufi, and Carole Goble (2013): “The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud”, Nucleic Acids Research, 41(W1): W557-W561. doi:10.1093/nar/gkt328

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executing a SCUFL xml in Taverna Workbench

I am relatively new to the workflow management system and was exploring taverna. I understand Taverna workbench is a GUI for building and editing workflows, but if I have a SCUFL xml which is the underlying language that the graphical workflow…
anil keshav
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Executing Abaqus Model in Taverna

I'm pretty new to both Taverna and Abaqus but I am trying to run an Abaqus model using a "Tool" in Taverna remotely on a HPC. This works fine if I already have my model file and inputs on the HPC but I need a way of uploading the files dynamically…
Malekai
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Inserting XML data into MySQL database

I am trying to insert XML data into a MySQL database. The SAX parser I wrote works on its own when tested. However, whenever I try to insert records into the database, I get a NullPointerException even though I made sure to assign values to…
amber4478
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