title: Exploiting stoichiometric redundancies for computational efficiency and network reduction.
abstract: Analysis of metabolic networks typically begins with construction of the stoichiometry matrix, which characterizes the network topology. This matrix provides, via the balance equation, a description of the potential steady-state flow distribution. This paper begins with the observation that the balance equation depends only on the structure of linear redundancies in the network, and so can be stated in a succinct manner, leading to computational efficiencies in steady-state analysis. This alternative description of steady-state behaviour is then used to provide a novel method for network reduction, which complements existing algorithms for describing intracellular networks in terms of input-output macro-reactions (to facilitate bioprocess optimization and control). Finally, it is demonstrated that this novel reduction method can be used to address elementary mode analysis of large networks: the modes supported by a reduced network can capture the input-output modes of a metabolic module with significantly reduced computational effort.
authors.forename: Brian P
authors.initials: BP
authors.lastname: Ingalls
authors.forename: Eric
authors.initials: E
authors.lastname: Bembenek
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods / Q000592:standards; D003198:Computer Simulation; D053858:Metabolic Networks and Pathways; D008954:Models, Biological
keywords: Metabolic network; elementary flux modes; metabolic control analysis; metabolic flux analysis; metabolic module; network reduction