Modeling in Systems Biology

1. Front Matter

   Pages I-XXIII

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2. Foundations

   1. Front Matter

      Pages 1-1

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   2. Introduction

      • Ina Koch, Falk Schreiber

      Pages 3-18

   3. Biochemical Fundamentals

      • Tiina Liiving, Syed M. Baker, Björn H. Junker

      Pages 19-36

   4. Petri Nets

      • Wolfgang Reisig

      Pages 37-56

3. Modeling Techniques

   1. Front Matter

      Pages 57-57

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   2. Discrete Modeling

      • Andrea Sackmann

      Pages 59-72

   3. Modeling Genetic Regulatory Networks

      • Richard Banks, Victor Khomenko, L. Jason Steggles

      Pages 73-100

   4. Hybrid Functional Petri Net with Extension for Dynamic Pathway Modeling

      • Ayumu Saito, Masao Nagasaki, Hiroshi Matsuno, Satoru Miyano

      Pages 101-120

   5. Stochastic Modeling

      • Ivan Mura

      Pages 121-151

   6. Quantitative Analysis

      • Jörg Ackermann, Ina Koch

      Pages 153-178

   7. Fuzzy Modeling

      • Lukas Windhager, Florian Erhard, Ralf Zimmer

      Pages 179-205

4. Biochemical Applications

   1. Front Matter

      Pages 207-207

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   2. Topological Analysis of Metabolic and Regulatory Networks

      • Stefan Schuster, Björn H. Junker

      Pages 209-224

   3. Analysis of Dynamical Models of Signaling Networks with Petri Nets and Dynamic Graphs

      • Simon Hardy, Ravi Iyengar

      Pages 225-251

   4. A Modular, Qualitative Modeling of Regulatory Networks Using Petri Nets

      • Claudine Chaouiya, Hanna Klaudel, Franck Pommereau

      Pages 253-279

   5. A Case Study of HFPN Simulation: Finding Essential Roles of Ror Gene in the Interaction of Feedback Loops in Mammalian Circadian Clock

      • Natsumi Mitou, Hiroshi Matsuno, Satoru Miyano, Shin-Ichi T. Inouye

      Pages 281-306

   6. Prediction of Network Structure

      • Annegret Wagler

      Pages 307-336

5. Back Matter

   Pages 337-364

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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.

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

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)

• Institute for Computer Science, J.W. Goethe University Frankfurt, Frankfurt am Main, Germany

  Ina Koch

• Department of Computer Science, Humboldt-Universität zu Berlin, Berlin, Germany

  Wolfgang Reisig

• Institute of Computer Science, Martin Luther Univ. Halle-Wittenberg, Halle, Germany

  Falk Schreiber

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