Modeling of Cell-to-Cell Communication Processes with Petri Nets Using the Example of Quorum Sensing.

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.

CELLmicrocosmos 2.2 MembraneEditor: a modular interactive shape-based software approach to solve heterogeneous membrane packing problems.

New perspectives have been developed to understand the processes of modeling heterogeneous membranes. These are crucial steps prior to applying advanced techniques like molecular dynamic simulations of whole membrane systems. Lipid, protein, and membrane packing problems are addressed based on biochemical properties in combination with computational optimization techniques. The CELLmicrocosmos 2.2 MembraneEditor (CmME) is introduced as an appropriate framework to handle such problems by offering diverse algorithmic approaches. Its algorithm plug-in-interface enables modelers to generate problem-specific algorithms. Good solutions concerning runtime and lipid density are realized by focusing on the outer shapes of the PDB-based molecules. Application cases are presented like the publication-based modeling of inner and outer mitochondrial membrane-fragments, semiautomatic incorporation of proteins, and the assembly of rafts. Concerning geometrical aspects of the lipids, the achieved results are consistent with experimental observations related to lipid densities and distributions. Finally, two membranes simulated with GROMACS are analyzed and compared: the first is generated with conventional scripting techniques, the second with the CmME Distributor algorithm. The examples prove that CmME is a valuable and versatile tool for a broad set of applications in analysis and visualization of biomembranes.

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

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.