Discrete Event Dynamic Systems
Petri nets for systems and synthetic biology
SFM'08 Proceedings of the Formal methods for the design of computer, communication, and software systems 8th international conference on Formal methods for computational systems biology
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We present a new Petri net simulation environment to enable graphical hierarchical modeling, hybrid simulation, and animation of processes in life sciences, and technical applications, among others. In order to model these most different processes, a new powerful and universally usable mathematical modeling concept -- extended Hybrid Petri (xHPN) -- has been established. This specification is used for the Petri Net library (PNlib) realized by the object-oriented modeling language Modelica. In contrast to other approaches, we enable users to simultaneously reconstruct, analyze, and simulate complex dynamic models in one view. Therefore, we have connected the PNlib to VANESA, an open source tool for visualization and analysis of networks. Additionally, the PNlib is connected to Matlab/Simulink to use all the Matlab power for post-processing simulation results. To demonstrate this powerful environment, we are reporting our experience by modeling a technical and a general biological application case.