title: Biopathways representation and simulation on hybrid functional petri net.
abstract: The following two matters should be resolved in order for biosimulation tools to be accepted by users in biology/medicine: (1) remove issues which are irrelevant to biological importance, and (2) allow users to represent biopathways intuitively and understand/manage easily the details of representation and simulation mechanism. From these criteria, we firstly define a novel notion of Petri net called Hybrid Functional Petri Net (HFPN). Then, we introduce a software tool, Genomic Object Net, for representing and simulating biopathways, which we have developed by employing the architecture of HFPN. In order to show the usefulness of Genomic Object Net for representing and simulating biopathways, we show two HFPN representations of gene regulation mechanisms of Drosophila melanogaster (fruit fly) circadian rhythm and apoptosis induced by Fas ligand. The simulation results of these biopathways are also correlated with biological observations. The software is available to academic users from http://www.GenomicObject.Net/.
authors.affiliation: Faculty of Science, Yamaguchi University, Yamaguchi, Japan.
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Matsuno
authors.forename: Yukiko
authors.initials: Y
authors.lastname: Tanaka
authors.forename: Hitoshi
authors.initials: H
authors.lastname: Aoshima
authors.forename: Atsushi
authors.initials: A
authors.lastname: Doi
authors.forename: Mika
authors.initials: M
authors.lastname: Matsui
authors.forename: Satoru
authors.initials: S
authors.lastname: Miyano
mesh_terms: D000818:Animals; D003198:Computer Simulation; D004331:Drosophila melanogaster; D005786:Gene Expression Regulation; D023281:Genomics; D008954:Models, Biological; D015398:Signal Transduction; D012984:Software