Colored Petri nets to Model and Simulate Biological Systems
نویسندگان
چکیده
Petri nets have become an effective formalism to model biological systems. However, attempts to simulate biological systems by low-level Petri nets are restricted to relatively small models, and they tend to grow quickly for modeling complex systems, which makes it more difficult to manage and understand the nets. Motivated by this, we propose a colored Petri net-based framework for modeling, simulating, and analyzing complex biological systems. We give the definitions of biochemically interpreted colored qualitative Petri nets (QPN) and colored stochastic Petri nets (SPN) and describe their functionalities and features implemented in the Petri net tool Snoopy. We use two examples, the cooperative ligand binding and the repressilator, to demonstrate how to construct and simulate QPN and SPN models, respectively.
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