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Biotechnol J. 2013 Sep;8(9):997-1008. doi: 10.1002/biot.201200291. Epub 2013 Jul 29.

Basic concepts and principles of stoichiometric modeling of metabolic networks.

Author information

1
Life Sciences, Center for Mathematics and Computer Science, Amsterdam, The Netherlands; Systems Bioinformatics, Amsterdam Institute for Molecules Medicines and Systems, VU University Amsterdam, Amsterdam, The Netherlands; BioSolar Cells, Wageningen, The Netherlands.

Abstract

Metabolic networks supply the energy and building blocks for cell growth and maintenance. Cells continuously rewire their metabolic networks in response to changes in environmental conditions to sustain fitness. Studies of the systemic properties of metabolic networks give insight into metabolic plasticity and robustness, and the ability of organisms to cope with different environments. Constraint-based stoichiometric modeling of metabolic networks has become an indispensable tool for such studies. Herein, we review the basic theoretical underpinnings of constraint-based stoichiometric modeling of metabolic networks. Basic concepts, such as stoichiometry, chemical moiety conservation, flux modes, flux balance analysis, and flux solution spaces, are explained with simple, illustrative examples. We emphasize the mathematical definitions and their network topological interpretations.

KEYWORDS:

Constraint-based modeling; Flux balance analysis; Flux modes; Metabolism; Optimal solution space

PMID:
23893965
PMCID:
PMC4671265
DOI:
10.1002/biot.201200291
[Indexed for MEDLINE]
Free PMC Article

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