technical report Modeling Biological Systems with Stochastic Petri Nets


This report introduces the basics concepts underlying the stochastic modeling of biological systems with Petri Nets. It introduces a timed interpretation of the occurrence of transitions in a net that suites the randomness observed in biochemical reactions occurring in living matter. Thanks to the foundational work of Gillespie in the 70’s, this randomness can be easily accounted for by the representative power of Stochastic Petri Nets. The document illustrates the Stochastic Petri Net model specification process, the possibilities of analytical and numerical evaluation of model dynamics as well as the basic concepts underlying the simulative approaches, through the application to simple instances of biological systems to help the reader familiarizing with this discrete stochastic modeling formalism.

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I. Mura