Biology Reference
In-Depth Information
Biological Petri Nets
Modeling of Cell-to-Cell Communication
Processes with Petri Nets Using the Example
of Quorum Sensing
Sebastian Janowski
a
,∗
, Benjamin Kormeier
a
, Thoralf T opel
a
, Klaus Hippe
a
, Ralf Hofestadt
a
,
Nils Willassen
b
, Rafael Friesen
a
, Sebastian Rubert
a
, Daniela Borck
a
, Peik Haugen
b
and
Ming Chen
c
a
Department of Bioinformatics, Faculty of Technology, Bielefeld University, Bielefeld, Germany
b
Department of Molecular Biotechnology, Faculty of Medicine, University of Tromsø, Tromsø, Norway
c
Department of Bioinformatics, College of Life Science, Zhejiang University, Hangzhou, P.R. China
ABSTRACT:
The understanding of the molecular mechanism of cell-to-cell communication is fundamental for system biology.
Up to now, the main objectives of bioinformatics have been reconstruction, modeling and analysis of metabolic, regulatory
and signaling processes, based on data generated from high-throughput technologies. Cell-to-cell communication or quorum
sensing (QS), the use of small molecule signals to coordinate complex patterns of behavior in bacteria, has been the focus of
many reports over the past decade. Based on the quorum sensing process of the organism
Aliivibrio salmonicida
, we aim at
developing a functional Petri net, which will allow modeling and simulating cell-to-cell communication processes. Using a
new editor-controlled information system called VANESA (
http://vanesa.sf.net
)
, we present how to combine different fields of
studies such as life-science, database consulting, modeling, visualization and simulation for a semi-automatic reconstruction
of the complex signaling quorum sensing network. We show how cell-to-cell communication processes and information-flow
within a cell and across cell colonies can be modeled using VANESA and how those models can be simulated with Petri net
network structures in a sophisticated way.
KEYWORDS:
Quorum sensing, cell-to-cell communication, cellular rhythm, dynamic modeling, Petri nets, database integra-
tion, VANESA, biological network editor, simulation
INTRODUCTION
Every living cell is governed by a vast network of interacting proteins, RNA, DNA, metabolites and
other molecules. There are many biochemical processes involved in a cell. Naturally, those processes
with their elements and interactions can be captured by network representations. During research
enormous amounts of biological data are produced daily. Information from different fields of studies is
brought together in order to examine and analyze quantities and relationships. The approach of extracting,
analyzing and modeling meaningful biological data of heterogeneous data sets as a biomedical network
∗
Corresponding author. E-mail:
sjanowski1@uni-bielefeld.de
.
