Genomic Engineering Group / InteLAB
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Thursday, 22 February 2018
Petri Nets PDF Print

Genetic Regulatory Networks
Metabolic pathways can be described by a set of biochemical reactions coupled by a common intermediate metabolite. Each one of these reactions is facilitated by the presence of an enzyme. Biochemical reactions modeling always assume a constant enzyme concentration, and its effect on the system is abstracted by its corresponding kinetic parameter. Enzymes are the result of a complex biomolecular interactive network, ruled by a set of signals, which can activate or deactivate the process of enzyme production. Molecular biology recent discoveries and its accompanying technological innovations produce an enormous set of molecular level information, which permits to consider the inclusion of genetic regulatory networks to the analyses of biochemical networks. Genetic regulatory networks have a strongly combinatorial behavior, while biochemical networks exhibits a fluid and continuous character. Therefore, regulated biochemical networks are naturally under hybrid system domain of modeling and analysis. However, discrete mathematical methods can be used to model regulated metabolic pathways as a first method to validate or refuse biological hypothesis. Our work is concerned with genetic regulatory networks that can be modeled and analyzed under the regulatory graph formalism, and biochemical networks as Petri nets. In the sequel, the logic regulatory graph is translated to an equivalent Petri net model. Finally, the model resulted from the integration of biochemical networks with the genetic regulatory network, both in terms of Petri nets, is analyzed. The regulatory mechanisms of tryptophan production by Escherichia coli has been successfully used as a biological model.

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