Affiliations: Department of Bioinformatics, Faculty of Technology,
Bielefeld University, Bielefeld, Germany | Department of Molecular Biotechnology, Faculty of
Medicine, University of Tromsø, Tromsø, Norway | 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 integration, VANESA, biological network editor, simulation
