Biological Petri Nets (Technology and Informatics, Vol. 162)

Description

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.

This unique compilation of articles is the first book from the journal In Silico Biology (ISB) on Biological Petri Nets. 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.

CONTENTS

• Front Matter
• Preface

• Petri Nets and the Simulation of Metabolic Networks
  Ralf Hofestädt
• Quantitative Modeling of Biochemical Networks
  R. Hofestädt, S. Thelen
• Topological Analysis of Metabolic Networks Based on Petri Net Theory
  Ionela Zevedei-Oancea, Stefan Schuster
• Quantitative Petri Net Model of Gene Regulated Metabolic Networks in the Cell
  Ming Chen, Ralf Hofestädt
• Petri Nets for Steady State Analysis of Metabolic Systems
  Klaus Voss, Monika Heiner, Ina Koch
• Biopathways Representation and Simulation on Hybrid Functional Petri Net
  Hiroshi Matsuno, Yukiko Tanaka, Hitoshi Aoshima, Atsushi Doi, Mika Matsui, Satoru Miyano
• Constructing Biological Pathway Models with Hybrid Functional Petri Nets
  Atsushi Doi, Sachie Fujita, Hiroshi Matsuno, Masao Nagasaki, Satoru Miyano
• STEPP – Search Tool for Exploration of Petri net Paths: A New Tool for Petri Net-Based Path Analysis in Biochemical Networks
  Ina Koch, Markus Schüler, Monika Heiner
• Short Communication: Ontology Based Standardization of Petri Net Modeling for Signaling Pathways
  Takako Takai-Igarashi
• Simulation-Based Validation of the p53 Transcriptional Activity with Hybrid Functional Petri Net
  Atsushi Doi, Masao Nagasaki, Hiroshi Matsuno, Satoru Miyano
• Analyzing Stationary States of Gene Regulatory Network Using Petri Nets
  Anna Gambin, Sławomir Lasota, Michał Rutkowski
• Cell Illustrator 4.0: A Computational Platform for Systems Biology
  Masao Nagasaki, Ayumu Saito, Euna Jeong, Chen Li, Kaname Kojima, Emi Ikeda, Satoru Miyano
• Modeling of Cell-to-Cell Communication Processes with Petri Nets Using the Example of Quorum Sensing
  Sebastian Janowski, Benjamin Kormeier, Thoralf Töpel, Klaus Hippe, Ralf Hofestädt, Nils Willassen, Rafael Friesen, Sebastian Rubert, Daniela Borck, Peik Haugen, Ming Chen
• On Determining Firing Delay Time of Transitions for Petri Net Based Signaling Pathways by Introducing Stochastic Decision Rules
  Yoshimasa Miwa, Chen Li, Qi-Wei Ge, Hiroshi Matsuno, Satoru Miyano
• Impact of Delays and Noise on Dopamine Signal Transduction
  Jialiang Wu, Zhen Qi, Eberhard O. Voit
• Role of mRNA Gestation and Senescence in Noise Reduction during the Cell Cycle
  Attila Csikász-Nagy, Ivan Mura
• Exhaustive Analysis of the Modular Structure of the Spliceosomal Assembly Network: A Petri Net Approach
  Ralf H. Bortfeldt, Stefan Schuster, Ina Koch
• Modelling the Molecular Interactions in the Flower Developmental Network of Arabidopsis thaliana
  Kerstin Kaufmann, Masao Nagasaki, Ruy Jáuregui

• Subject Index
• Author Index