Recreating Biopathway Databases towards Simulation

Abstract

Genomic Object Net (GON) is a biopathwaymodeling and simulation platform that employs the originally developed notion, hybrid functional Petri Net with extension (HFPNe)that extends the hybrid functional Petri Net (HFPN) [2],[3], and is developedwith JAVA [1]. With this platform, we have succeeded in modelingand simulating glycolytic pathway of E. coli, boundary formationby notch signaling in Drosophila, and apoptosis induced by Fas ligand,etc [1]. For the modeling and simulation of a biopathway, suitable informationselection from public biopathway databases, such as Kyoto Encyclopedia of Genes and Genomes(KEGG) and BioCyc, would be useful. Although the first aim for these pathway databases is to reorganize biochemical information for usage on computers and is not for modeling and simulation of biopathways. Thus, we have developed a way to transform these pathway databases so that the converted biopathways can run on GON. The transformation of the static biopathway models in KEGG and BioCyc leads users (biologists) to modify and refine the resulting dynamic biopathway models for their own interests on GON. This will be a first step for recreating biopathway databases towards simulation.