用基本通量模计算弱可逆亏损零网络平移
Computing Weakly Reversible Deficiency Zero Network Translations Using Elementary Flux Modes
摘要：
我们提出了一种计算方法进行结构翻译，这已被研究最近在分析的背景下，来自生化反应网络的质量作用系统的稳态和动力学行为。我们的程序涉及解决一个二元线性规划问题，其中的决策变量对应于原始网络的反应之间的相互作用。我们将得到的网络称为反应到反应图，并形式化了这样的构造与原始反应网络和结构转换的关系。我们通过在欧洲生物信息学研究所的BioModels数据库中的508个网络上运行该算法来证明该算法的有效性和效率。我们还总结了如何将这项工作纳入最近提出的算法建立单和多稳态生化反应系统。
英文摘要：
We present a computational method for performing structural translation, which has been studied recently in the context of analyzing the steady states and dynamical behavior of mass-action systems derived from biochemical reaction networks. Our procedure involves solving a binary linear programming problem where the decision variables correspond to interactions between the reactions of the original network. We call the resulting network a reaction-to-reaction graph and formalize how such a construction relates to the original reaction network and the structural translation. We demonstrate the efficacy and efficiency of the algorithm by running it on 508 networks from the European Bioinformatics Institutes' BioModels database. We also summarize how this work can be incorporated into recently proposed algorithms for establishing mono and multistationarity in biochemical reaction systems.
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