Janowski Sebastian, Kormeier Benjamin, Töpel Thoralf, Hippe Klaus, Hofestädt Ralf, Willassen Nils, Friesen Rafael, Rubert Sebastian, Borck Daniela, Haugen Peik, Chen Ming
Department of Bioinformatics, Faculty of Technology, Bielefeld University, Bielefeld, Germany.
Stud Health Technol Inform. 2011;162:182-203.
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.
理解细胞间通讯的分子机制是系统生物学的基础。到目前为止，生物信息学的主要目标一直是基于高通量技术产生的数据，对代谢、调控和信号传导过程进行重建、建模和分析。细胞间通讯或群体感应（QS），即利用小分子信号来协调细菌中复杂行为模式，在过去十年中一直是许多报道的焦点。基于嗜冷发光杆菌的群体感应过程，我们旨在开发一个功能Petri网，它将允许对细胞间通讯过程进行建模和模拟。使用一个名为VANESA（http://vanesa.sf.net）的新的编辑器控制信息系统，我们展示了如何将生命科学、数据库咨询、建模、可视化和模拟等不同研究领域结合起来，以半自动方式重建复杂的信号群体感应网络。我们展示了如何使用VANESA对细胞间通讯过程以及细胞内和跨细胞群体的信息流进行建模，以及如何用Petri网网络结构以复杂的方式模拟这些模型。
