Expa: a program for calculating extreme pathways in biochemical reaction networks.

TitleExpa: a program for calculating extreme pathways in biochemical reaction networks.
Publication TypeJournal Article
Year of Publication2005
AuthorsBell SL, Palsson BØ
JournalBioinformatics (Oxford, England)
Volume21
Issue8
Pagination1739-40
PubMed Date2005 Apr 15
ISSN1367-4803
KeywordsAnimals, Biochemistry, Cell Physiological Phenomena, Energy Metabolism, Gene Expression Regulation, Humans, Proteome, Signal Transduction, Software
Abstract

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@ucsd.edu.

Alternate JournalBioinformatics
PubMed ID15613397

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