论文标题
建模分子相互作用图的框架
A framework for modelling Molecular Interaction Maps
论文作者
论文摘要
由一系列代谢途径形成的代谢网络由细胞内和细胞外反应制成，这些反应决定了细胞的生化特性，以及一组指导和调节这些反应活性的相互作用。这些途径大多数是由复杂且复杂的链反应网络形成的，可以使用描述细胞周期检查点途径的图表以人的可读形式表示。 本文提出了一种表示线性时间逻辑中分子相互作用图（复杂代谢网络的图形表示）的方法。此类网络的逻辑表示允许人们对它们进行推理，例如检查图表是否满足给定的属性$ ϕ $，并找出哪些初始conditons可以保证$ ϕ $，否则如何更新图表以满足$ ϕ $。 翻译方法和分辨率方法均已在一个能够解决此类问题的工具中实现，这要归功于命题逻辑，该命题逻辑允许利用经典的SAT求解器。
Metabolic networks, formed by a series of metabolic pathways, are made of intracellular and extracellular reactions that determine the biochemical properties of a cell, and by a set of interactions that guide and regulate the activity of these reactions. Most of these pathways are formed by an intricate and complex network of chain reactions, and can be represented in a human readable form using graphs which describe the cell cycle checkpoint pathways. This paper proposes a method to represent Molecular Interaction Maps (graphical representations of complex metabolic networks) in Linear Temporal Logic. The logical representation of such networks allows one to reason about them, in order to check, for instance, whether a graph satisfies a given property $ϕ$, as well as to find out which initial conditons would guarantee $ϕ$, or else how can the the graph be updated in order to satisfy $ϕ$. Both the translation and resolution methods have been implemented in a tool capable of addressing such questions thanks to a reduction to propositional logic which allows exploiting classical SAT solvers.
