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Bioinformatics Advance Access published online on December 1, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm578
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© The Author (2007). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Automated manipulation of systems biology models using libSBML within Taverna workflows

Peter Li 1,*, Tom Oinn 2, Stian Soiland 3 and Douglas B. Kell 1

1School of Chemistry and Manchester Centre for Integrative Systems Biology, Manchester Interdisciplinary Biocentre, University of Manchester, M1 7DN, UK, 2EMBL European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK, 3School of Computing Science, University of Manchester, M13 9PL, UK.

*To whom correspondence should be addressed. Dr. Peter Li, E-mail: peter.li{at}manchester.ac.uk


  Abstract

Summary: Many data manipulation processes involve the use of programming libraries. These processes may beneficially be automated due to their repeated use. A convenient type of automation is in the form of workflows that also allow such processes to be shared amongst the community. The Taverna workflow system has been extended to enable it to use and invoke Java classes and methods as tasks within Taverna workflows. These classes and methods are selected for use during workflow construction by a Java Doclet application called the API Consumer. The API Consumer generates an XML file that enables Taverna to select a subset of Java classes and methods for use in the composition of Taverna workflows. The ability of Taverna to invoke Java classes and methods is demonstrated by a workflow in which we use libSBML to map gene expression data onto a metabolic pathway represented as an SBML model.

Availability: Taverna and the API Consumer application can be freely downloaded from http://taverna.sourceforge.net.

Contact: peter.li{at}manchester.ac.uk

Supplementary information: Supplementary material and documentation are available from http://www.mcisb.org/software/taverna/libsbml/index.html.

Associate Editor: Dr. Chris Stoeckert

Received on October 11, 2007; revised on November 13, 2007; accepted on November 18, 2007

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