Colored stochastic petri nets for modeling complex biological systems

The stochastic modeling of biological systems is gaining more and more attention when stochastic fluctuations need to be described. On the other hand, the biological systems under investigation become much more complex than before. Traditional modeling methods like stochastic Petri nets do not easily scale and thus become difficult to tackle this situation. This paper aims to present a colored stochastic Petri net approach for systems biology to modeling complex biological systems. Specifically, this paper describes a type of biochemically-interpreted colored stochastic Petri nets and their extensions and analysis techniques for systems biology and illustrates their applications using Ca2+ release sites that consist of a set of coupled Ca2+ channels. © 2013 SERSC.