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Bioinformatics Advance Access published online on September 27, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti674
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received May 18, 2005
Revised August 17, 2005
Accepted September 8, 2005

Article

Functional stoichiometric analysis of metabolic networks

R. Urbanczik 1* and C. Wagner 1

1 Institute of Pharmacology, University of Bern, Friedbühlstr. 49, CH-3010 Bern, Switzerland

* To whom correspondence should be addressed.
R. Urbanczik, E-mail: robert.urbanczik{at}pki.unibe.ch


  Abstract

Motivation: An important tool in Systems Biology is the stoichiometric modeling of metabolic networks, where the stationary states of the network are described by a high dimensional polyhedral cone, the so called flux cone. Exhaustive descriptions of the metabolism can be obtained by computing the elementary vectors of this cone but, due to a combinatorial explosion of the number of elementary vectors, this approach becomes computationally intractable for genome scale networks.

Result: Hence, we propose to instead focus on the conversion cone, a projection of the flux cone, which describes the interaction of the metabolism with its external chemical environment. We present a direct method for calculating the elementary vectors of this cone and, by studying the metabolism of S. cerevisiae, we demonstrate that such an analysis is computationally feasible even for genome scale networks.


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