Implementing Petri Nets for Modelling and Simulation in Biosciences

ABSTRACT: It was in 1993 that Petri nets were introduced for modelling of biochemical reactions. Since that time Petri nets are increasingly used to dive deep into the details of functioning of cumbersome biological processes. In this context, Petri nets have become anindispensable tool for modeling and simulation of biochemical reactions, biomedical systems, processes arising in molecular biology and genetics. This thesis intends to present a comprehensive overview of bibliography on application of Petri nets in biosciences. Based on analysis of bibliographical information covering the period of from January 1993 to July 2010, we provide statistical data on subject areas investigated with Petri nets, use of Petri net types, analysis methods as well as dedicated software tools. We detail HFPN – a Petri net with extension that combines both discrete and continuous components in it – and Cell Illustrator 5.0 – a licensed powerful software tool for modeling and simulation of biological systems. In order to show effectiveness of both HFPN and Cell Illustrator in modelling and simulation of biopathways, we introduce three case studies: (i) validation of the p53 transcriptional activity through modelling with HFPN and performing simulation in Cell Illustrator software; (ii) modelling of gene regulatory mechanism of the lac operon and glycolytic pathway; (iii) circadian rhythms in Drosophila. Keywords:Petri Nets,metabolic pathways, signal transduction networks, gene regulatory pathways. ……………………………………………………………………………………………………………………………………………………………………………………………………………………