Modeling in Systems Biology: The Petri Net Approach

ISBN-13: 9781849964739 / Angielski / Twarda / 2010 / 364 str.

Ina Koch; Wolfgang Reisig; Falk Schreiber

Opis

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 Delbruck 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.

Recenzje

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)

Spis treści

Part I: Foundations

Introduction
Ina Koch and Falk Schreiber

Biochemical Fundamentals
Tiina Liiving, Syed M. Baker, and Björn H. Junker

Petri Nets
Wolfgang Reisig

Part II: Modeling Techniques

Discrete Modeling
Andrea Sackmann

Modeling Genetic Regulatory Networks
Richard Banks, Victor Khomenko, and L. Jason Steggles

Hybrid Functional Petri Net with Extension for Dynamic Pathway Modeling
Ayumu Saito, Masao Nagasaki, Hiroshi Matsuno, and Satoru Miyano

Stochastic Modeling
Ivan Mura

Quantitative Analysis
Jörg Ackermann and Ina Koch

Fuzzy Modeling
Florian Erhard, Lukas Windhager, and Ralf Zimmer

Part III: Biochemical Applications

Topological Analysis of Metabolic and Regulatory Networks
Stefan Schuster and Björn H. Junker

Analysis of Dynamical Models of Signaling Networks with Petri Nets and Dynamic Graphs
Simon Hardy and Ravi Iyengar

A Modular, Qualitative Modeling of Regulatory Networks Using Petri Nets
Claudine Chaouiya, Hanna Klaudel, and Franck Pommereau

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

Prediction of Network Structure
Annegret Wagler

O autorze

Prof. Dr. Wolfgang Reisig is a professor at Humboldt Universität zu Berlin, Germany. He has over 30 years experience in the theory, applications, and teaching of Petri nets and related techniques; and he has been closely involved in the key community initiatives such as related conferences. Among his books are titles in the areas of Petri nets, distributed algorithmsm, and computational systems biology.

Blurb

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.