PRELIMINARY ABSTRACT:
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Petri Nets for Integrated Models of Metabolic and Gene Regulatory Networks 
Aljoscha Palinkas and Alexander Bockmayr 
Keywords: 
Modeling, Metabolic network, Gene regulatory network, Petri Net
Abstract: 
In integrated models, metabolism and gene regulation are modeled together. 
Metabolites may regulate genes, and gene expression may activate or inhibit
metabolic reactions.  Both metabolic and gene regulatory networks can be
described by Petri nets. Although an integrated Petri net model for tryptophan
synthesis has already been proposed in the literature, a systematic and general
method is not available so far. The goal of this paper is to present such a method.
Assuming that the stoichiometry of the metabolic reactions is known, the gene
regulatory network is described in the Thomas formalism, and the interactions
with the metabolism are given by logical conditions.  For the gene regulatory
network, the resulting Petri net shows exactly the asynchronous unitary dynamics
given by the Thomas framework.