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Petri nets for modelling metabolic pathways: a survey. (English) Zbl 1206.68209
Summary: In the last 15 years, several research efforts have been directed towards the representation and the analysis of metabolic pathways by using Petri nets. The goal of this paper is twofold. First, we discuss how the knowledge about metabolic pathways can be represented with Petri nets. We point out the main problems that arise in the construction of a Petri net model of a metabolic pathway and we outline some solutions proposed in the literature. Second, we present a comprehensive review of recent research on this topic, in order to assess the maturity of the field and the availability of a methodology for modelling a metabolic pathway by a corresponding Petri net.

MSC:
68Q85 Models and methods for concurrent and distributed computing (process algebras, bisimulation, transition nets, etc.)
92C40 Biochemistry, molecular biology
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