Book Chapter Stochastic Modeling


This chapter provides an introduction to the 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 70s, this randomness can be easily accounted for by the representative power of Stochastic Petri Nets. The chapter 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. Additional examples of larger scale models are presented, and exercises suggested to consolidate the understanding of the main concepts.

Paper Details


I. Mura