Branch	Locations	Status	Reservations	Due date	Barcode	Floor plan	Lending note
Branch: Hauptstelle	Locations: ZB-130 100	Status: available	Reservations: 0	Due date:	Barcode: 00196436	Floor plans: Floor plan	Lending note:

I GENERAL CONCEPTS 1

1 The Role of Modeling in Systems Biology

Douglas B. Kell and Joshua D. Knowles

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