Computation of elementary modes: a unifying framework and the new binary approach.
Computation of elementary modes: a unifying framework and the new binary approach.
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DOI：
10.1186/1471-2105-5-175
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发表时间：
2004-11-04
影响因子：
3
通讯作者：
Klamt S
中科院分区：
文献类型：
--
作者：
Gagneur J;Klamt S
代谢途径分析已被公认为代谢网络结构分析的核心方法。基本（通量）模式的概念提供了一个严格的形式主义来描述和评估路径，并已被证明是有价值的许多应用。然而，计算基本模式是一项艰巨的计算任务。近年来，我们协助乘法算法专用于它。我们需要一个总结的观点和不断改进的当前方法。我们表明，计算的基本模式的集合是等价于计算的凸锥的极端射线的集合。这个标准的数学表示提供了一个统一的框架，包含了计算基本模式的最突出的算法方法，并允许它们之间进行清晰的比较。从这个基准的教训，我们在这里介绍了一种新的方法，二进制的方法，它计算的基本模式作为二元模式的参与反应，从各自的化学计量系数可以计算在后处理步骤。我们在FluxAnalyzer 5.1中实现了二进制方法，这是一个免费的学术软件。二进制方法减少了高达96%的内存需求，而不损失速度，从而提供了迄今为止最有效的计算基本模式的方法。基本模式和极端射线计算之间的等效性为采用多面体计算工具进行代谢途径分析提供了机会。本文介绍的新的二进制方法是从这个一般的理论框架，并有利于在相当大的网络中的基本模式的计算。
Metabolic pathway analysis has been recognized as a central approach to the structural analysis of metabolic networks. The concept of elementary (flux) modes provides a rigorous formalism to describe and assess pathways and has proven to be valuable for many applications. However, computing elementary modes is a hard computational task. In recent years we assisted in a multiplication of algorithms dedicated to it. We require a summarizing point of view and a continued improvement of the current methods. We show that computing the set of elementary modes is equivalent to computing the set of extreme rays of a convex cone. This standard mathematical representation provides a unified framework that encompasses the most prominent algorithmic methods that compute elementary modes and allows a clear comparison between them. Taking lessons from this benchmark, we here introduce a new method, the binary approach, which computes the elementary modes as binary patterns of participating reactions from which the respective stoichiometric coefficients can be computed in a post-processing step. We implemented the binary approach in FluxAnalyzer 5.1, a software that is free for academics. The binary approach decreases the memory demand up to 96% without loss of speed giving the most efficient method available for computing elementary modes to date. The equivalence between elementary modes and extreme ray computations offers opportunities for employing tools from polyhedral computation for metabolic pathway analysis. The new binary approach introduced herein was derived from this general theoretical framework and facilitates the computation of elementary modes in considerably larger networks.