title: Basic concepts and principles of stoichiometric modeling of metabolic networks.
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.
authors.affiliation: 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.
authors.forename: Timo R
authors.initials: TR
authors.lastname: Maarleveld
authors.forename: Ruchir A
authors.initials: RA
authors.lastname: Khandelwal
authors.forename: Brett G
authors.initials: BG
authors.lastname: Olivier
authors.forename: Bas
authors.initials: B
authors.lastname: Teusink
authors.forename: Frank J
authors.initials: FJ
authors.lastname: Bruggeman
mesh_terms: D000465:Algorithms; D002477:Cells / Q000378:metabolism; D003198:Computer Simulation; D064688:Metabolic Flux Analysis; D053858:Metabolic Networks and Pathways; D008954:Models, Biological
keywords: Constraint-based modeling; Flux balance analysis; Flux modes; Metabolism; Optimal solution space
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