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

描述

系統生物學的研究需要來自不同背景的研究人員的合作，包括生物學、計算機科學、數學、統計學、物理學和生物化學等。由於這個領域的研究需要廣泛的背景知識，這些合作可能會受到不同學科對技術限制和應用的理解不同而受阻。這本全面介紹和概述生物系統建模的書籍使得所有相關領域的背景材料對具有不同背景的研究人員來說都易於理解。

細胞生物學中的系統級建模領域一直缺乏批判性和全面的概述。這本書填補了這一空白。它是第一本提供必要的概念和方法比較的書籍，並強調它們的應用可能性。它介紹了關鍵概念及其理論背景，包括韌性和模塊化的概念及其在研究生物系統中的應用；最著名的建模方法及其優缺點；從數學模型應用於細胞生物學研究中獲得的經驗教訓；以及可用的建模工具和數據集，以及它們的計算限制。

目錄

前言
第一部分 概念
1. 系統生物學中的建模角色
2. 細胞系統的複雜性和韌性
3. 關於模塊和模塊化

第二部分 建模方法
4. 生物系統的貝葉斯推斷：生物學的邏輯
5. 化學計量和基於約束的建模
6. 用非線性常微分方程模擬分子相互作用網絡
7. 遺傳調控網絡分析的定性方法
8. 細胞內動力學的隨機建模
9. 空間擴展系統中的動力學

第三部分 模型與現實
10. 系統級建模的生物數據獲取-妥協的藝術
11. 從實驗數據中識別細胞結構和動力學的方法
12. 使用控制理論研究生物學
13. 合成基因調控系統
14. 系統生物學中的多層次建模：從細胞到整個器官

第四部分 計算建模
15. 系統生物學建模的計算限制
16. 生化動力學的數值模擬