title: Modeling of cell-to-cell communication processes with Petri nets using the example of quorum sensing.
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.
authors.affiliation: Department of Bioinformatics, Faculty of Technology, Bielefeld University, Bielefeld, Germany. sjanowski1@uni-bielefeld.de
authors.forename: Sebastian
authors.initials: S
authors.lastname: Janowski
authors.forename: Benjamin
authors.initials: B
authors.lastname: Kormeier
authors.forename: Thoralf
authors.initials: T
authors.lastname: Töpel
authors.forename: Klaus
authors.initials: K
authors.lastname: Hippe
authors.forename: Ralf
authors.initials: R
authors.lastname: Hofestädt
authors.forename: Nils
authors.initials: N
authors.lastname: Willassen
authors.forename: Rafael
authors.initials: R
authors.lastname: Friesen
authors.forename: Sebastian
authors.initials: S
authors.lastname: Rubert
authors.forename: Daniela
authors.initials: D
authors.lastname: Borck
authors.forename: Peik
authors.initials: P
authors.lastname: Haugen
authors.forename: Ming
authors.initials: M
authors.lastname: Chen
mesh_terms: D000465:Algorithms; D044165:Aliivibrio salmonicida / Q000502:physiology; D002450:Cell Communication; D003198:Computer Simulation; D025461:Feedback, Physiological; D015964:Gene Expression Regulation, Bacterial; D053263:Gene Regulatory Networks; D005798:Genes, Bacterial; D008954:Models, Biological; D053038:Quorum Sensing; D015398:Signal Transduction; D012984:Software