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System Modeling in Cell Biology From Concepts to Nuts and Bolts - Zoltan Szallasi, Jörg Stelling, Vipul Periwa

Contents


I GENERAL CONCEPTS 1
1 The Role ofModeling in Systems Biology . . . . . . . . . . . . 3
Douglas B. Kell and Joshua D. Knowles
2 Complexity and Robustness of Cellular Systems . . . . . . . . 19
Jörg Stelling, Uwe Sauer, Francis J. Doyle III,
and John Doyle
3 OnModules andModularity . . . . . . . . . . . . . . . . . . . . 41
Zoltan Szallasi, Vipul Periwal, and Jörg Stelling
II MODELING APPROACHES 51
4 Bayesian Inference of Biological Systems: The Logic of Biology 53
Vipul Periwal
5 Stoichiometric and Constraint-basedModeling . . . . . . . . . 73
Steffen Klamt and Jörg Stelling
6 Modeling Molecular Interaction Networks with Nonlinear
Ordinary Differential Equations . . . . . . . . . . . . . . . . . . 97
Emery D. Conrad and John J. Tyson

7 Qualitative Approaches to the Analysis of Genetic Regulatory
Networks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 125
Hidde de Jong and Delphine Ropers
8 Stochastic Modeling of Intracellular Kinetics . . . . . . . . . . 149
Johan Paulsson and Johan Elf
9 Kinetics in Spatially Extended Systems . . . . . . . . . . . . . 177
Karsten Kruse and Johan Elf

III MODELS AND REALITY 199
10 Biological Data Acquisition for System Level Modeling—
An Exercise in the Art of Compromise . . . . . . . . . . . . . . 201
Zoltan Szallasi
11 Methods to Identify Cellular Architecture and Dynamics from
Experimental Data . . . . . . . . . . . . . . . . . . . . . . . . . . 221
Rudiyanto Gunawan, Kapil G. Gadkar,
and Francis J. Doyle III
12 Using Control Theory to Study Biology . . . . . . . . . . . . . 243
Brian P. Ingalls, Tau-Mu Yi, and Pablo A. Iglesias
13 Synthetic Gene Regulatory Systems . . . . . . . . . . . . . . . 269
Mads Kærn and Ron Weiss
14 Multilevel Modeling in Systems Biology: From Cells to Whole
Organs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 297
Denis Noble
IV COMPUTATIONAL MODELING 313
15 Computational Constraints on Modeling in Systems Biology . 315
Vipul Periwal
16 Numerical Simulation for Biochemical Kinetics . . . . . . . . . 331
Daniel T. Gillespie and Linda R. Petzold
17 Software Infrastructure for Effective Communication and Reuse
of Computational Models . . . . . . . . . . . . . . . . . . . . . . 355
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
A Software Tools for BiologicalModeling . . . . . . . . . . . . . . 379

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