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Bioinformatics Advance Access published online on June 16, 2004
Bioinformatics, doi:10.1093/bioinformatics/bth361
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received February 5, 2004
Revised May 25, 2004
Accepted May 31, 2004

Article

Taverna: a tool for the composition and enactment of bioinformatics workflows

Tom Oinn 1, Matthew Addis 2, Justin Ferris 2, Darren Marvin 2, Mark Greenwood 3, Tim Carver 4, Matthew R. Pocock 5, Anil Wipat 5, Peter Li 5*

1 EMBL European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK
2 IT Innovation Centre, University of Southampton, SO16 7NP, UK
3 Department of Computing Science, University of Manchester, M13 9PL, UK
4 MRC Rosalind Franklin Centre for Genomics Research, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
5 School of Computing Science, University of Newcastle, NE1 7RU, UK

* To whom correspondence should be addressed. E-mail: taverna-users{at}sourceforge.net.


  Abstract

Motivation: In silico experiments in bioinformatics involve the co-ordinated use of computational tools and information repositories. A growing number of these resources are being made available with programmatic access in the form of Web services. Bioinformatics scientists will need to orchestrate these Web services in workflows as part of their analyses.

Results: The Taverna project has developed a tool for the composition and enactment of bioinformatics workflows for the life sciences community. The tool includes a workbench application which provides a graphical user interface for the composition of workflows. These workflows are written in a new language called the Simple conceptual unified flow language (Scufl), where by each step within a workflow represents one atomic task. Two examples are used to illustrate the ease by with which in silico experiments can be represented as Scufl workflows using the workbench application.

Availability: The Taverna workflow system is available as open source and can be downloaded with example Scufl workflows from http://taverna.sourceforge.net.


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