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Petri net models for the semi-automatic construction of large scale biological networks. (English) Zbl 1251.92012
Summary: For the implementation of the virtual cell, the fundamental question is how to model and simulate complex biological networks. During the last 15 years, Petri nets have attracted more and more attention to help to solve this key problem. Regarding the published papers, it seems clear that hybrid functional Petri nets are the adequate method to model complex biological networks. Today, a Petri net model of biological networks is built manually by drawing places, transitions and arcs with mouse events. Therefore, based on relevant molecular data bases and information systems biological data integration is an essential step in constructing biological networks.
We motivate the application of Petri nets for modeling and simulation of biological networks. Furthermore, we present a type of access to relevant metabolic data bases such as KEGG, BRENDA, etc. Based on this integration process, the system supports semi-automatic generation of the correlated hybrid Petri net model. A case study of the cardio-disease related gene-regulated biological network is also presented. MoVisPP is available at http://agbi.techfak.uni-bielefeld.de/movispp/.

MSC:
92C42 Systems biology, networks
68Q85 Models and methods for concurrent and distributed computing (process algebras, bisimulation, transition nets, etc.)
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