© 2011

Modeling in Systems Biology

The Petri Net Approach

  • Ina Koch
  • Wolfgang Reisig
  • Falk Schreiber
  • Presents a comprehensive overview of cutting-edge research in applications of Petri nets in systems biology

  • Enables readers to apply and develop their own biochemical models using Petri net techniques

  • Contains a glossary of the concepts and notation used in the book, in addition to exercises at the end of each chapter


Part of the Computational Biology book series (COBO, volume 16)

Table of contents

  1. Front Matter
    Pages I-XXIII
  2. Foundations

    1. Front Matter
      Pages 1-1
    2. Ina Koch, Falk Schreiber
      Pages 3-18
    3. Tiina Liiving, Syed M. Baker, Björn H. Junker
      Pages 19-36
    4. Wolfgang Reisig
      Pages 37-56
  3. Modeling Techniques

    1. Front Matter
      Pages 57-57
    2. Andrea Sackmann
      Pages 59-72
    3. Richard Banks, Victor Khomenko, L. Jason Steggles
      Pages 73-100
    4. Ayumu Saito, Masao Nagasaki, Hiroshi Matsuno, Satoru Miyano
      Pages 101-120
    5. Ivan Mura
      Pages 121-151
    6. Jörg Ackermann, Ina Koch
      Pages 153-178
    7. Lukas Windhager, Florian Erhard, Ralf Zimmer
      Pages 179-205
  4. Biochemical Applications

    1. Front Matter
      Pages 207-207
    2. Stefan Schuster, Björn H. Junker
      Pages 209-224
    3. Claudine Chaouiya, Hanna Klaudel, Franck Pommereau
      Pages 253-279
    4. Annegret Wagler
      Pages 307-336
  5. Back Matter
    Pages 337-364

About this book


The emerging, multi-disciplinary field of systems biology is devoted to the study of the relationships between various parts of a biological system, and computer modeling plays a vital role in the drive to understand the processes of life from an holistic viewpoint. Advancements in experimental technologies in biology and medicine have generated an enormous amount of biological data on the dependencies and interactions of many different molecular cell processes, fueling the development of numerous computational methods for exploring this data. The mathematical formalism of Petri net theory is able to encompass many of these techniques.

This essential text/reference presents a comprehensive overview of cutting-edge research in applications of Petri nets in systems biology, with contributions from an international selection of experts. Those unfamiliar with the field are also provided with a general introduction to systems biology, the foundations of biochemistry, and the basics of Petri net theory. Further chapters address Petri net modeling techniques for building and analyzing biological models, as well as network prediction approaches, before reviewing the applications to networks of different biological classification.

Topics and features:

  • Investigates the modular, qualitative modeling of regulatory networks using Petri nets, and examines an Hybrid Functional Petri net simulation case study
  • Contains a glossary of the concepts and notation used in the book, in addition to exercises at the end of each chapter
  • Covers the topological analysis of metabolic and regulatory networks, the analysis of models of signaling networks, and the prediction of network structure
  • Provides a biological case study on the conversion of logical networks into Petri nets
  • Discusses discrete modeling, stochastic modeling, fuzzy modeling, dynamic pathway modeling, genetic regulatory network modeling, and quantitative analysis techniques
  • Includes a Foreword by Professor Jens Reich, Professor of Bioinformatics at Humboldt University and Max Delbrück Center for Molecular Medicine in Berlin

This unique guide to the modeling of biochemical systems using Petri net concepts will be of real utility to researchers and students of computational biology, systems biology, bioinformatics, computer science, and biochemistry.

Dr. Ina Koch is a Professor and holds the Chair of Bioinformatics at the Johann Wolfgang Goethe-University Frankfurt am Main, Germany.

Dr. Wolfgang Reisig is a Professor and holds the Chair in the Theory of Programming at the Humboldt University of Berlin, Germany.

Dr. Falk Schreiber is a Professor and holds the Chair of Bioinformatics at the Martin Luther University Halle-Wittenberg, Germany, and the Coordinator of Bioinformatics at the Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben, Germany.


Biochemical Systems Gene Regulatory Networks Metabolic Networks Modeling of Biological Systems Network Analysis Petri Nets Qualitative Analysis Quantitative Analysis Signal Transduction Networks Systems Biology

Editors and affiliations

  • Ina Koch
    • 1
  • Wolfgang Reisig
    • 2
  • Falk Schreiber
    • 3
  1. 1.Institute for Computer ScienceJ.W. Goethe University FrankfurtFrankfurt am MainGermany
  2. 2.Department of Computer ScienceHumboldt-Universität zu BerlinBerlinGermany
  3. 3.Institute of Computer ScienceMartin Luther Univ. Halle-WittenbergHalleGermany

Bibliographic information

  • Book Title Modeling in Systems Biology
  • Book Subtitle The Petri Net Approach
  • Editors Ina Koch
    Wolfgang Reisig
    Falk Schreiber
  • Series Title Computational Biology
  • Series Abbreviated Title Computational Biology
  • DOI
  • Copyright Information Springer-Verlag London Limited 2011
  • Publisher Name Springer, London
  • eBook Packages Computer Science Computer Science (R0)
  • Hardcover ISBN 978-1-84996-473-9
  • Softcover ISBN 978-1-4471-2598-3
  • eBook ISBN 978-1-84996-474-6
  • Series ISSN 1568-2684
  • Edition Number 1
  • Number of Pages XXIV, 364
  • Number of Illustrations 0 b/w illustrations, 0 illustrations in colour
  • Topics Computational Biology/Bioinformatics
    Systems Biology
  • Buy this book on publisher's site
Industry Sectors


From the reviews:

“This volume brings together a variety of contributions showcasing the application of modeling biological and biochemical processes using Petri nets. … it can be used as a teaching aid, and have included exercises at the end of each chapter. … the volume is best seen as a roadmap to a variety of interesting uses of a modeling technique that is particularly geared to readers who already have some experience with mathematical modeling in biology.” (Sara Kalvala, ACM Computing Reviews, August, 2011)