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Volume 3

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In Silico Biology 3, 0032 (2003); ©2003, Bioinformation Systems e.V.  

Biopathways representation and simulation on hybrid functional Petri net

Hiroshi Matsuno1,*, Yukiko Tanaka1, Hitoshi Aoshima1, Atsushi Doi1, Mika Matsui2 and Satoru Miyano3

1Faculty of Science, Yamaguchi University
2 Oshima National College of Maritime Technology
3 Human Genome Center, Institute of Medical Science, University of Tokyo

* corresponding author

Edited by E. Wingender; received April 28, 2003; revised and accepted May 28, 2003; published June 23, 2003


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/.

Key words: Petri net, modeling, simulation, circadian rhythms, apoptosis, Genomic Object Net