Biology Reference
In-Depth Information
Table 1
Comparison of Petri net-based simulation tools
Feature
Tool
GEPASI/
Jarnac
Dbsolve
E-
Virtual
Cell
Cell
COPASI
CELL
Cell
Designer
Illustrator
Pathway DB retrievability
w
w
w
s
w
w
s
Pathways graphic editor
n
s
s
w
m
s
s
Kinetic types
s
s
s
m
w
w
s
Virtual cell model
w
w
w
m
m
w
m
Simulation graphic display
m
s
s
m
w
w
s
Mathematical model modification
s
s
s
s
w
w
m
2D and 3D plots
s
w
w
w
w
w
m
3D spatial model
n
n
n
n
m
n
n
SBML compatibility
m
s
s
s
s
m
m
User interface
m
m
m
m
m
s
s
Listed are the major features of the compared Petri net simulation tools [Chen
et al.
, 2009].
Notation: s
=
strong, m
=
moderate, w
=
weak, n
=
none.
In view of the quorum sensing network, still many biological questions are not yet answered. The
quorum sensing system and its topology and dynamics is very complex and difficult to represent with
sophisticated mathematical equations. Much improvement is needed before applying mathematical
equations, such as stochastic differential equations for whole cell simulations [Meng
et al.
, 2004].
Another problem is the lack of actual laboratory data. In many cases it is not possible to formulate a
mathematical system.
Finally, we made use of the Petri net language to model and simulate cell-to-cell-communication
processes to construct a sophisticated base for further experiments, analysis and simulation techniques.
Petri net simulation tools
Presently, several biological simulators exist that use the Petri net language as modeling and sim-
ulation technique. A list of well-known simulation software packages that provide biological net-
work modeling and simulation is given at the System Biology Markup Language website (
http://sbml.
org/SBML Software Guide/SBML Software Summary
)
. In view of the amount of available tools, spe-
cial respect was given to the quality of the architectural design and system. Requirements such as
performance, security, reliability were examined in the first term to select the most suiting software
applications. For our research aims worth mentioning are software packages such as GEPASI [Mendes,
1993] and COPASI [Hoops
et al.
2003], E-CELL [Tomita
et al.
, 1999] and Cell Illustrator [Nagasaki
et
al.
, 2003] for qualitative and quantitative simulation of biological networks. Table 1 shows a comparison
of the best suiting systems.
From Table 1, the Petri net tool Cell Illustrator obtains very good remarks. The software application
allows users to model, visualize and simulate various biological systems using the Cell System Markup
Language (CSML). The software application is powerful, intuitive and easy to use. The most important
advantages are the strong pathway database retrievability, the various kinetic types for modeling and
the mathematical model modification. It also provides the CSML3.0 exchange format for visualizing,
modeling and simulating biological pathways. Additionally, it supports the System Biology Markup
Language (SBML) for dynamic simulations. For further details, see the contribution of Nagasaki
et al.
to this Special [Nagasaki
et al.
, 2010].
The only disadvantage of the software solutions presented in Table 1 is their lack of access to external
databases. For our research project, however, databases such as KEGG, BRENDA, ENZYME among
