Skip Navigation


Bioinformatics Advance Access originally published online on December 1, 2007
Bioinformatics 2008 24(2):287-289; doi:10.1093/bioinformatics/btm578
This Article
Right arrow Full Text
Right arrow Full Text (Print PDF)
Right arrow All Versions of this Article:
24/2/287    most recent
btm578v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (1)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Li, P.
Right arrow Articles by Kell, D. B.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Li, P.
Right arrow Articles by Kell, D. B.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© 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, 2EMBL European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD and 3School of Computing Science, University of Manchester, M13 9PL, UK

*To whom correspondence should be addressed.


  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. This selection is stored as an XML file which enables Taverna to present the subset of the API for use in the composition of 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 a 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 data and documentation are available from http://www.mcisb.org/software/taverna/libsbml/index.html

Associate Editor: Chris Stoeckert

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

Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?




Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.