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Bioinformatics Advance Access originally published online on December 21, 2004
Bioinformatics 2005 21(8):1739-1740; doi:10.1093/bioinformatics/bti228
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© The Author 2004. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

expa: a program for calculating extreme pathways in biochemical reaction networks

Steven L. Bell and Bernhard Ø. Palsson *

Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA

*To whom correspondence should be addressed.

Summary: The set of extreme pathways, a generating set for all possible steady-state flux maps in a biochemical reaction network, can be computed from the stoichiometric matrix, an incidence-like matrix reflecting the network topology. Here, we describe the implementation of a well-known algorithm to compute these pathways and give a summary of the features of the available software.

Availability: The C-code, along with a Windows executable and sample network reaction files, are available at http://systemsbiology.ucsd.edu

Contact: palsson{at}ucsd.edu


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