Preface -- Biosystem modeling and simulation: nomenclature and philosophy -- Math models of systems: biomodeling 101 -- Computer simulation methods -- Structural biomodeling from theory and data: compartmentalizations -- Structural biomodeling from theory and data: sizing, distinguishing and simplifying multicompartmental models -- Nonlinear mass action and biochemical kinetic interaction modeling -- Cellular systems biology modeling: deterministic and stochastic -- Physiologically based, whole-organism kinetics and noncompartmental modeling -- Biosystem stability and oscillations -- Structural identifiability -- Parameter sensitivity methods -- Parameter estimation and numerical identifiability -- Parameter estimation methods II: facilitating, simplifying and working with data -- Biocontrol system modeling, simulation, and analysis -- Data-driven modeling and alternative hypothesis testing -- Experiment design and optimization -- Model reduction and network inference in dynamic systems biology -- Appendices