Genomic Object Net 1.5: A Platform for Biopathway Modeling and Simulation

In the post-genome era, biopathway information processing is one of the most important issues in bioinformatics. Development of Genomic Object Net [6] is our approach to this issue. This software aims at describing and simulating structurally complex dynamic causal interactions and processes such as metabolic pathways, signal transduction cascades, gene regulations. In Dec/2002, we have released Java based software Genomic Object Net 1.0 [1, 3]. The software was based on Hybrid Functional Petri net (HFPN) [2]. With HFPN, we can model rule based biological processes in biopathways, e.g. gene regulation and also ODEs-based kinetics, e.g. chemical processes in biopathways. In fact, with HFPN, we have modeled and simulated: the glycolytic pathway of Escherichia coli, gene regulation of circadian rhythms in Drosophila, boundary formation by notch signaling in Drosophila, and apoptosis induced by Fas ligand [5].