Article

Natural Computing

, Volume 9, Issue 4, pp 955-989

First online:

Petri nets for modelling metabolic pathways: a survey

  • Paolo BaldanAffiliated withDipartimento di Matematica Pura e Applicata, Università di Padova
  • , Nicoletta CoccoAffiliated withDipartimento di Informatica, Università Ca’ Foscari di Venezia
  • , Andrea MarinAffiliated withDipartimento di Informatica, Università Ca’ Foscari di Venezia
  • , Marta SimeoniAffiliated withDipartimento di Informatica, Università Ca’ Foscari di Venezia Email author 

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Abstract

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.

Keywords

Petri nets Metabolic pathways Qualitative and quantitative analysis Tools