Ingalls Brian P, Bembenek Eric
In Silico Biol. 2015;12(1-2):55-67. doi: 10.3233/ISB-140464.
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.
代谢网络分析通常始于化学计量矩阵的构建，该矩阵表征了网络拓扑结构。通过平衡方程，此矩阵提供了对潜在稳态流分布的描述。本文首先观察到平衡方程仅取决于网络中线性冗余的结构，因此可以简洁地表述，从而在稳态分析中提高计算效率。然后，这种对稳态行为的替代描述被用于提供一种网络简化的新方法，它补充了现有的根据输入 - 输出宏观反应描述细胞内网络的算法（以促进生物过程优化和控制）。最后，证明了这种新的简化方法可用于处理大型网络的基本模式分析：简化网络支持的模式能够以显著减少的计算量捕获代谢模块的输入 - 输出模式。
