Affiliations: Faculty of Science, Yamaguchi University, Japan | Oshima National College of Maritime Technology,
Japan | Human Genome Center, Institute of Medical Science,
University of Tokyo, Japan E-mail: [email protected]
Note: [] Corresponding author
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/.
Keywords: Petri net, modeling, simulation, circadian rhythms, apoptosis, Genomic Object Net
