BioPACS: BioPathway Automatic Convert System for Genomic Object Net

Masao Nagasaki 1, Atsushi Doi2, Hiroshi Matsuno, Satoru Miyano, Human Genome Center, University of Tokyo;, Faculty of Science, Yamaguchi University

Genomic Object Net (GON) is a biopathway modeling and simulation platform that employs the originally developed notion, hybrid functional Petri Net with extension (HFPNe) that extends the hybrid functional Petri Net (HFPN) [1,2]. With this platform, we have succeeded in modeling and simulating glycolytic pathway of E. coli, boundary formation by notch signaling in Drosophila, and apoptosis induced by Fas ligand, etc. [1]. For the modeling and simulation of a biopathway, suitable information selection 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, it is not for modeling and simulation of biopathways. Thus, we have developed a method 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.

[1] http://www.GenomicObject.Net/ [2] Matsuno, H., Doi, A., Nagasaki, M. and Miyano, S.: Hybrid Petri net representation of gene regulatory network. Proc. Pacific Symposium on Biocomputing 2000 (2000) 338-349. [3] Matsuno, H., Doi, A., Hirata, H. and Miyano, S.: XML documentation of biopathways and their simulations in Genomic Object Net, Genome Informatics 12 (2001) 54-62.