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Bioinformatics Advance Access published online on December 21, 2004
Bioinformatics, doi:10.1093/bioinformatics/bti228
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Bioinformatics © Oxford University Press 2004; all rights reserved.
Received September 10, 2004
Revised October 20, 2004
Accepted December 13, 2004

Applications note

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

Steven L. Bell 1 and Bernhard Ø. Palsson 1*

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

* To whom correspondence should be addressed.
Bernhard Ø. Palsson, E-mail: palsson{at}ucsd.edu


  Abstract

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.


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