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Bioinformatics Advance Access originally published online on September 27, 2005
Bioinformatics 2005 21(22):4176-4180; 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{at}oxfordjournals.org

Functional stoichiometric analysis of metabolic networks

R. Urbanczik * and C. Wagner

Institute of Pharmacology, University of Bern Friedbühlstrasse 49, CH-3010 Bern, Switzerland

*To whom correspondence should be addressed.

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, owing 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 Saccharomyces cerevisiae, we demonstrate that such an analysis is computationally feasible even for genome scale networks.

Contact: robert.urbanczik{at}pki.unibe.ch

Received on May 18, 2005; revised on August 17, 2005; accepted on September 8, 2005

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