Contents -- Preface -- I GENERAL CONCEPTS -- 1 The Role of Modeling in Systems Biology -- 2 Complexity and Robustness of Cellular Systems -- 3 On Modules and Modularity -- II MODELING APPROACHES -- 4 Bayesian Inference of Biological Systems: The Logic of Biology -- 5 Stoichiometric and Constraint-based Modeling -- 6 Modeling Molecular Interaction Networks with Nonlinear Ordinary Differential Equations -- 7 Qualitative Approaches to the Analysis of Genetic Regulatory Networks -- 8 Stochastic Modeling of Intracellular Kinetics -- 9 Kinetics in Spatially Extended Systems -- III MODELS AND REALITY -- 10 Biological Data Acquisition for System Level Modeling-An Exercise in the Art of Compromise -- 11 Methods to Identify Cellular Architecture and Dynamics from Experimental Data -- 12 Using Control Theory to Study Biology* -- 13 Synthetic Gene Regulatory Systems -- 14 Multilevel Modeling in Systems Biology: From Cells to Whole Organs -- IV COMPUTATIONAL MODELING -- 15 Computational Constraints on Modeling in Systems Biology -- 16 Numerical Simulation for Biochemical Kinetics -- 17 Software Infrastructure for Effective Communication and Reuse of Computational Models -- A Software Tools for Biological Modeling -- References -- Contributors -- Index.