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GRAPHICAL RULE BASED MODELING OF BIOCHEMICAL NETWORKS

机译:基于图形规则的生化网络建模

摘要

Formalized graphical reaction rules and conventions accounting for chemical states and binding or reaction states are provided for modeling complex biological systems such as signal transduction pathways. A system model is derived by defining typed attributed graphs which delimit molecular entities and their possible states. Graph transformation rules defining a class of potential reactions are defined and applied to the graphs and all new graphs that subsequently arise as a result of graph transformation. In one embodiment, a model is generated through the use of graph-rewriting rules which are associated with rate laws and applied iteratively to a seed set of chemical species graphs until a termination condition occurs.
机译:提供了用于说明化学状态和结合或反应状态的形式化图形反应规则和惯例,用于对复杂的生物系统(例如信号转导途径)进行建模。通过定义界定分子实体及其可能状态的类型化属性图,可以得出系统模型。定义了定义一类潜在反应的图变换规则,并将其应用于图和随后由于图变换而出现的所有新图。在一个实施例中,通过使用与速率定律相关联的图重写规则来生成模型,并将其迭代地应用于化学物种图的种子集,直到发生终止条件为止。

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