Petri nets for modeling and analyzing biochemical reaction networks

Abstract

Petri nets have been widely used to model and analyze biochemical reaction networks. This chapter gives an overview of different types of Petri nets within a unifying Petri net framework that comprises the qualitative, stochastic, continuous, and hybrid paradigms at both uncolored and colored levels. The Petri net framework permits to investigate one and the same biological reaction network with different modeling abstractions in various complementary ways. We describe the use of the framework to investigate biochemical reaction networks with the help of the unifying Petri net tool, Snoopy, and its close friends Charlie and Marcie. The repressilator example serves as running case study.