System Modeling in Cellular Biology: From Concepts to Nuts and Bolts (Hardcover)

Description

Research in systems biology requires the collaboration of researchers from diverse backgrounds, including biology, computer science, mathematics, statistics, physics, and biochemistry. These collaborations, necessary because of the enormous breadth of background needed for research in this field, can be hindered by differing understandings of the limitations and applicability of techniques and concerns from different disciplines. This comprehensive introduction and overview of system modeling in biology makes the relevant background material from all pertinent fields accessible to researchers with different backgrounds.

The emerging area of systems level modeling in cellular biology has lacked a critical and thorough overview. This book fills that gap. It is the first to provide the necessary critical comparison of concepts and approaches, with an emphasis on their possible applications. It presents key concepts and their theoretical background, including the concepts of robustness and modularity and their exploitation to study biological systems; the best-known modeling approaches, and their advantages and disadvantages; lessons from the application of mathematical models to the study of cellular biology; and available modeling tools and datasets, along with their computational limitations.

 

Table of Contents

 Preface vii
 
I GENERAL CONCEPTS  1
 
1 The Role of Modeling in Systems Biology
Douglas B. Kell and Joshua D. Knowles  3
 
2 Complexity and Robustness of Cellular Systems
Jörg Stelling, Uwe Sauer, Francis J. Doyle III and John Doyle 19
 
3 On Modules and Modularity
Zoltan Szallasi, Vipul Periwal and Jörg Stelling 41
 
II MODELING APPROACHES 51
 
4 Bayesian Inference of Biological Systems: The Logic of Biology
Vipul Periwal 53
 
5 Stoichiometric and Constraint-based Modeling
Steffen Klamt and Jörg Stelling 73
 
6 Modeling Molecular Interaction Networks with Nonlinear Ordinary Differential Equations
Emery D. Conrad and John J. Tyson 97
 
7 Qualitative Approaches to the Analysis of Genetic Regulatory Networks
Hidde de Jong and Delphine Ropers 125
 
8 Stochastic Modeling of Intracellular Kinetics
Johan Paulsson and Johan Elf 149
 
9 Kinetics in Spatially Extended Systems
Karsten Kruse and Johan Elf 177
 
III MODELS AND REALITY 199
 
10 Biological Data Acquisition for System Level Modeling—An Exercise in the Art of Compromise
Zoltan Szallasi 201
 
11 Methods to Identify Cellular Architecture and Dynamics from Experimental Data
Rudiyanto Gunawan, Kapil G. Gadker and Francis J. Doyle III 221
 
12 Using Control Theory to Study Biology
Brian P. Ingalls, Tau-Mi Yi and Pablo A. Iglesias 243
 
13 Synthetic Gene Regulatory Systems
Mads Kærn and Ron Weiss 269
 
14 Multilevel Modeling in Systems Biology: From Cells to Whole Organs
Denis Noble 297
 
IV COMPUTATIONAL MODELING 313
 
15 Computational Constraints on Modeling in Systems Biology
Vipul Periwal 315
 
16 Numerical Simulation for Biochemical Kinetics
Daniel T. Gillespie and Linda R. Petzold 331
 
17 Software Infrastructure for Effective Communication and Reuse of Computational Models
Andrew Finney, Michael Hucka, Benjamin J. Bornstein, Sarah M. Keating, Bruce E. Shapiro, Joanne Matthews, Ben L. Kovitz, Maria J. Schilstra, Akira Funahashi, John Doyle and Hiroaki Kitano 355
 
A Software Tools for Biological Modeling 379
 
 References 385
 
 Contributors 435
 
 Index 439