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In Silico Biology 10, 0003 (2010); ©2009, Bioinformation Systems e.V.  



Modeling of cell-cell communication processes with Petri nets using the example of quorum sensing

Sebastian Janowski1*, Benjamin Kormeier1, Thoralf Töpel1, Klaus Hippe1, Ralf Hofestädt1, Nils Willassen2, Rafael Friesen1, Sebastian Rubert1, Daniela Borck1, Peik Haugen2 and Ming Chen3

1 Department of Bioinformatics, Bielefeld University, Faculty of Technology, D-33501 Bielefeld, Germany
2 Department of Molecular Biotechnology, Faculty of Medicine, University of Tromsø, N-9037 Tromsø, Norway
3 Department of Bioinformatics, College of Life Science, Zhejiang University, Zijingang Campus, Hangzhou 310058, P.R. China

* Corresponding author
   Email: sjanowski1@uni-bielefeld.de


Edited by E. Wingender; received October 02, 2009; revised December 23, 2009; accepted December 28, 2009; published February 01, 2010


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