Compositional colored Petri net approach to multiscale modeling for systems biology

Colored Petri nets have been demonstrated as a powerful tool for modeling multiscale systems biology. However, the construction of colored Petri nets for biological systems requires prior knowledge about colored Petri nets and is often error-prone and cumbersome for biologists, especially when the communication between components and hierarchical organization of components in a multiscale model are an issue. To address this problem, an established way is to develop small components and then compose them into bigger models. In this paper, we present a compositional colored Petri net approach to aid automatic modeling of systems biology, and demonstrate it with two case studies. We focus on the modeling of communication between components and hierarchical organization of components as they are key to build multiscale models.