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Qualitative Modelling and Analysis of Biochemical Pathways with Petri Nets.

Koch, I.; Heiner, M.

In: Germany: Tutorial Notes, 5th Int. Conference on Systems Biology - ICSB 2004, Heidelberg. October 2004.

Abstract: A crucial point in systems biology is to handle large amounts of data in a mathematically unique manner in order to built valid models, which can be used for analysis and prediction of the complex processes in living organisms. Petri net theory, in computer science a well established theory for modelling and analysis of systems of concurrent processes, provides techniques, which can be used for complex biochemical systems. Moreover, there are many reliable software tools available supporting modelling as well as automatic analysis based on implementation of essential algorithms. In this tutorial we teach the foundations in Petri net theory and its application to biological systems using several biochemical examples. The whole material will be presented in an informal way. Formal notations and proofs are omitted. The main focus is the mediation of an intuitive understanding of the basic principles. The material is presented using the following case studies as running examples: signal transduction pathway - apoptosis, metabolic pathways - carbon metabolism in potato tuber and glycolysis combined with pentosephosphate pathway.

Keywords: Petri nets, biochemical networks, metabolic networks, signal transduction networks, qualitative analysis, pathways.

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