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.
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By definition, a mole of any substance contains the same number of elementary particles as there are atoms in exactly 12 g of the 12C isotope of carbon.
We denote by \({\mathbb{N}}\) the set of natural numbers, \( {\mathbb{N}} = \{ 0, 1, 2, \ldots\}.\)
Some papers do not mention explicitly the use of any specific tool, even if the complexity of the considered case studies clearly suggests that calculations have not been performed manually. Still, in this case the tool entry will be empty.
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Acknowledgements
The authors are grateful to Marcantonio Bragadin of the Dipartimento di Scienze Ambientali—Università Ca’ Foscari di Venezia, for enlightening discussions on metabolic pathways and biochemical issues. They are also greatly indebted to the anonymous referees for their extensive and valuable comments and suggestions on preliminary versions of the paper.
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Baldan, P., Cocco, N., Marin, A. et al. Petri nets for modelling metabolic pathways: a survey. Nat Comput 9, 955–989 (2010). https://doi.org/10.1007/s11047-010-9180-6
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DOI: https://doi.org/10.1007/s11047-010-9180-6