A Platform for Biopathway Modeling/simulation and Recreating Biopathway Databases towards Simulation

In the post-genome era, biopathway information processing is one of the most important research topics in Bioinformatics. From a biochemical and biomedical viewpoint, research progress will be very beneficial to human beings, e.g. developments of medicine manufacture and effective medical treatment for each patient. Thus, this thesis discusses the importance of a biopathway development environment that can easily and smoothly, (i) import existing biopathway databases, (ii) model biopathways, (iii) simulate biopathways, (iv) visualize biopathways, while developing the applications; (i) BPE, BPEOS, (ii/iii) GON, GONML, (iv) Visualizer. Moreover, this thesis demonstrates the newly developed biopathway modeling/simulation architecture based on Petri nets, HFPN and HFPNe. Chapter 1 describes the outline of the thesis and gives an overview of related works of this study, especially why we select Petri nets as the core architecture of modeling and simulating biopathways. It should be noted that the last section of each Chapter 2–5 discusses the related works for each chapter in more detail. Chapter 2 describes existing Petri nets (PN, TPN, CTPN, HPN) while discussing the advantages and limitations when modeling and simulating biopathways with these Petri nets. We then demonstrate newly developed Petri nets, HFPN and HFPNe, that inherit the features of HON, HPN, HDN, in order to model and simulate biopathways that are difficult to handle with these Petri nets. In the HFPN hybrid system, continuous and discrete events can be modeled with functional enhancement for processes, which enables to model various interactions and reactions. In addition, complex objects can be modeled with the enhancement of hierarchization, which enables easy modeling for large-scale path-