It was suggested some years ago that Petri nets might be well suited to modeling metabolic networks, overcoming some of the limitations encountered by the use of systems employing ODEs (ordinary differential equations). Much work has been done since then which confirms this and demonstrates the usefulness of this concept for systems biology. Petri net technology is not only intuitively understood by scientists trained in the life sciences, it also has a robust mathematical foundation and provides the required degree of flexibility. As a result it appears to be a very promising approach to modeling biological systems. Subjects covered include a summary of essential topics, basic requirements and constraints; quantitative modeling of metabolic networks, gene regulatory and cell-cell communication processes; the concept of hybrid Petri nets; modeling signal transduction pathways; net models of metabolic steady states as well as a number of further applications of Petri net based modeling. The book helps to illustrate the value of Petri net approach to modern life sciences. It is dedicated to the memory of Prof. Dr. Carl Adam Petri.IOS Press is an international science, technical and medical publisher of high-quality books for academics, scientists, and professionals in all fields. Some of the areas we publish in: -Biomedicine -Oncology -Artificial intelligence -Databases and information systems -Maritime engineering -Nanotechnology -Geoengineering -All aspects of physics -E-governance -E-commerce -The knowledge economy -Urban studies -Arms control -Understanding and responding to terrorism -Medical informatics -Computer Sciences
Author(s): E. Wingender
Series: Studies in Health Technology and Informatics 162
Edition: 1
Publisher: IOS Press
Year: 2011
Language: English
Pages: 314
Tags: Биологические дисциплины;Матметоды и моделирование в биологии;
Preface......Page 8
Contents......Page 12
Petri Nets and the Simulation of Metabolic Networks......Page 14
Quantitative Modeling of Biochemical Networks......Page 16
Topological Analysis of Metabolic Networks Based on Petri Net Theory......Page 30
Quantitative Petri Net Model of Gene Regulated Metabolic Networks in the Cell......Page 51
Petri Nets for Steady State Analysis of Metabolic Systems......Page 69
Biopathways Representation and Simulation on Hybrid Functional Petri Net......Page 90
Constructing Biological Pathway Models with Hybrid Functional Petri Nets......Page 105
STEPP - Search Tool for Exploration of Petri Net Paths: A New Tool for Petri Net-Based Path Analysis in Biochemical Networks......Page 126
Ontology Based Standardization of Petri Net Modeling for Signaling Pathways......Page 135
Simulation-Based Validation of the p53 Transcriptional Activity with Hybrid Functional Petri Net......Page 143
Analyzing Stationary States of Gene Regulatory Network Using Petri Nets......Page 156
Cell Illustrator 4.0: A Computational Platform for Systems Biology......Page 173
Modeling of Cell-to-Cell Communication Processes with Petri Nets Using the Example of Quorum Sensing......Page 195
On Determining Firing Delay Time of Transitions for Petri Net Based Signaling Pathways by Introducing Stochastic Decision Rules......Page 217
Impact of Delays and Noise on Dopamine Signal Transduction......Page 235
Role of mRNA Gestation and Senescence in Noise Reduction During the Cell Cycle......Page 249
Exhaustive Analysis of the Modular Structure of the Spliceosomal Assembly Network: A Petri Net Approach......Page 257
Modelling the Molecular Interactions in the Flower Developmental Network of Arabidopsis Thaliana......Page 292
Subject Index......Page 312
Author Index......Page 314
