Logical Modeling of Biological Systems
1st Edition
Will be published approx. on 29. July 2014
Book
Hardback
410 pages
978-1-84821-680-8 (ISBN)
Description
Systems Biology is the systematic study of the interactions between the components of a biological system and studies how these interactions give rise to the function and behavior of the living system. Through this, a life process is to be understood as a whole system rather than the collection of the parts considered separately. Systems Biology is therefore more than just an emerging field: it represents a new way of thinking about biology with a dramatic impact on the way that research is performed. The logical approach provides an intuitive method to provide explanations based on an expressive relational language.
This book covers various aspects of logical modeling of biological systems, bringing together 10 recent logic-based approaches to Systems Biology by leading scientists. The chapters cover the biological fields of gene regulatory networks, signaling networks, metabolic pathways, molecular interaction and network dynamics, and show logical methods for these domains based on propositional and first-order logic, logic programming, answer set programming, temporal logic, Boolean networks, Petri nets, process hitting, and abductive and inductive logic programming.
It provides an excellent guide for all scientists, biologists, bioinformaticians, and engineers, who are interested in logic-based modeling of biological systems, and the authors hope that new scientists will be encouraged to join this exciting scientific endeavor.
This book covers various aspects of logical modeling of biological systems, bringing together 10 recent logic-based approaches to Systems Biology by leading scientists. The chapters cover the biological fields of gene regulatory networks, signaling networks, metabolic pathways, molecular interaction and network dynamics, and show logical methods for these domains based on propositional and first-order logic, logic programming, answer set programming, temporal logic, Boolean networks, Petri nets, process hitting, and abductive and inductive logic programming.
It provides an excellent guide for all scientists, biologists, bioinformaticians, and engineers, who are interested in logic-based modeling of biological systems, and the authors hope that new scientists will be encouraged to join this exciting scientific endeavor.
More details
Language
English
Place of publication
London
United Kingdom
Target group
Professional and scholarly
Product notice
sewn/stitched
Cloth over boards
Dimensions
Height: 241 mm
Width: 161 mm
Thickness: 30 mm
Weight
780 gr
ISBN-13
978-1-84821-680-8 (9781848216808)
Copyright in bibliographic data and cover images is held by Nielsen Book Services Limited or by the publishers or by their respective licensors: all rights reserved.
Schweitzer Classification
Other editions
Additional editions
Luis Fari?as del Cerro | Katsumi Inoue
Logical Modeling of Biological Systems
E-Book
08/2014
Wiley-ISTE
€168.99
Available for download
Luis Fari?as del Cerro | Katsumi Inoue
Logical Modeling of Biological Systems
E-Book
08/2014
Wiley-ISTE
€168.99
Available for download
Persons
Luis Farinas del Cerro, Professor, IRIT, Toulouse, France.
Katsumi Inoue, Professor, NII, Tokyo, Japan.
Katsumi Inoue, Professor, NII, Tokyo, Japan.
Content
Foreword xiii
Luis Farinas Del Cerro Chapter 1 Symbolic Representation and Inference or Regulatory Network Structures 1
Nataly Maimari, Krysia Broda, Antonis Kakas, Rob Krams and Alessandra Russo
Chapter 2 Reasoning on the Response of Logical Signaling Networks with ASP 49
Torsten Schaub, Anne Siegek and Santiago Videla
Chapter 3 A Logical Model for Molecular Interaction Maps 93
Robert DeMolombe, Luis Farinas Del Cerro and Naji Obeid
Chapter 4 Analyzing Large Network Dynamics with Process Hitting 125
Loic Pauleve, Courtney Chancellor, Maxime Folschette, Morgan Magnin and Olivier Roux
Chapter 5 ASP for Construction and Validation of Regulatory Biological Networks
Alexandre Rocca, Nicolas Mobilia, Eric Fanchon, Tony Ribeiro, Laurent Trilling and Katsumi Inoue
Chapter 6 Simulation-Based Reasoning about Biological Pathways Using Petri Nets and ASP 207
Saadat Anwar, Chitta Barbal and Katsumi Inoue
Chapter 7 Formal Methods Applied to Gene Networks Modeling 245
Gilles Bernot, Jean-Paul Comet and El Houssine Snaussi
Chapter 8 Temporal Logic Modeling of Dynamical Behaviors: First-Order Patterns and Solvers 291
Francois Fages and Pauline Traynard
Chapter 9 Analyzing SBGN-AF Networks Using Normal Logic Programs 325
Adrien Rougny, Christine Froidevaux, Yoshitaka Yamamoto and Katsumi Inoue
Chapter 10 Machine Learning of Biological Networks Using Abductive ILP 363
Alireza Tamassoni, Diahuan Lin, Hiroaki Watanabe, Jianzhong Chen and Stephen Muggleton
List of Authors 403
Index 407
Luis Farinas Del Cerro Chapter 1 Symbolic Representation and Inference or Regulatory Network Structures 1
Nataly Maimari, Krysia Broda, Antonis Kakas, Rob Krams and Alessandra Russo
Chapter 2 Reasoning on the Response of Logical Signaling Networks with ASP 49
Torsten Schaub, Anne Siegek and Santiago Videla
Chapter 3 A Logical Model for Molecular Interaction Maps 93
Robert DeMolombe, Luis Farinas Del Cerro and Naji Obeid
Chapter 4 Analyzing Large Network Dynamics with Process Hitting 125
Loic Pauleve, Courtney Chancellor, Maxime Folschette, Morgan Magnin and Olivier Roux
Chapter 5 ASP for Construction and Validation of Regulatory Biological Networks
Alexandre Rocca, Nicolas Mobilia, Eric Fanchon, Tony Ribeiro, Laurent Trilling and Katsumi Inoue
Chapter 6 Simulation-Based Reasoning about Biological Pathways Using Petri Nets and ASP 207
Saadat Anwar, Chitta Barbal and Katsumi Inoue
Chapter 7 Formal Methods Applied to Gene Networks Modeling 245
Gilles Bernot, Jean-Paul Comet and El Houssine Snaussi
Chapter 8 Temporal Logic Modeling of Dynamical Behaviors: First-Order Patterns and Solvers 291
Francois Fages and Pauline Traynard
Chapter 9 Analyzing SBGN-AF Networks Using Normal Logic Programs 325
Adrien Rougny, Christine Froidevaux, Yoshitaka Yamamoto and Katsumi Inoue
Chapter 10 Machine Learning of Biological Networks Using Abductive ILP 363
Alireza Tamassoni, Diahuan Lin, Hiroaki Watanabe, Jianzhong Chen and Stephen Muggleton
List of Authors 403
Index 407