Natural Computing

, Volume 9, Issue 4, pp 955–989

Petri nets for modelling metabolic pathways: a survey

  • Paolo Baldan
  • Nicoletta Cocco
  • Andrea Marin
  • Marta Simeoni
Article

DOI: 10.1007/s11047-010-9180-6

Cite this article as:
Baldan, P., Cocco, N., Marin, A. et al. Nat Comput (2010) 9: 955. doi:10.1007/s11047-010-9180-6

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 netsMetabolic pathwaysQualitative and quantitative analysisTools

Copyright information

© Springer Science+Business Media B.V. 2010

Authors and Affiliations

  • Paolo Baldan
    • 1
  • Nicoletta Cocco
    • 2
  • Andrea Marin
    • 2
  • Marta Simeoni
    • 2
  1. 1.Dipartimento di Matematica Pura e ApplicataUniversità di PadovaPadovaItaly
  2. 2.Dipartimento di InformaticaUniversità Ca’ Foscari di VeneziaVenezia MestreItaly