Biology Reference
In-Depth Information
Biopathways Representation and Simulation
on Hybrid Functional Petri Net
Hiroshi Matsuno
a
,∗
, Yukiko Tanaka
a
, Hitoshi Aoshima
a
, Atsushi Doi
a
, Mika Matsui
b
and
Satoru Miyano
c
a
Faculty of Science, Yamaguchi University, Yamaguchi, Japan
b
Oshima National College of Maritime Technology, Oshima, Japan
c
Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
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
INTRODUCTION
Considerable attention has been paid to the biopathway representation and simulation in the literature.
The most traditional approach is to employ ordinary differential equations (ODEs) such as Michaelis-
Menten equations and to represent biochemical reactions as a systems of ODEs. This approach provides
mathematically well-founded and fine interpretations of biopathways, especially for enzyme reactions.
Gepasi [1] is a software package based on this approach for modeling biochemical systems and it aims
at assisting users in translating reaction processes to matrices and ODEs. E-Cell [2] is a system for
representation and simulation with GUI and, with this tool, a model of a hypothetical cell with only 127
genes sufficient for transcription, translation, energy production and phospholipid synthesis has been
constructed.
As is stressed in [3,4], in order for software tools to be accepted by users in biology/medicine for
biopathway modeling, we consider the following two matters should be resolved, at least: (1) Remove
issues which are biologically irrelevant; otherwise, users might be unnecessarily burdened with special
∗
Corresponding author. E-mail:
matsuno@sci.yamaguchi-u.ac.jp
.
