Petri Nets and GRN Models

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Author(s): Ina Koch (Beuth University for Technology Berlin, Germany)
Copyright: 2010
Pages: 34
Source title: Handbook of Research on Computational Methodologies in Gene Regulatory Networks
Source Author(s)/Editor(s): Sanjoy Das (Kansas State University, USA), Doina Caragea (Kansas State University, USA), Stephen Welch (Kansas State University, USA)and William H. Hsu (Kansas State University, USA)
DOI: 10.4018/978-1-60566-685-3.ch025

Keywords: Biologically-Inspired Computing / Medical Information Science Reference / Medical Technologies / Medicine & Healthcare

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Abstract

In this chapter, modeling of GRNs using Petri net theory is considered. It aims at providing a conceptual understanding of Petri nets to enable the reader to explore GRNs applying Petri net modeling and analysis techniques. Starting with an overview on modeling biochemical networks using Petri nets, the state-of-the-art with focus on GRNs is described. Other modeling techniques, for example, hybrid Petri nets are discussed. Basic concepts of Petri net theory are introduced involving special analysis techniques for modeling biochemical systems, for example, MCT-sets, T-clusters, and Mauritius maps. To illustrate these Petri net concepts, a more complex case study–the gene regulation in Duchenne Muscular Dystrophy–is explained in detail, considering the biological background and the interpretation of analysis results. Considering both, advantages and disadvantages, the chapter demonstrates the usefulness of Petri net modeling, in particular for GRNs.

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