Dynamic Systems Biology Modeling and Simulation

1. Biosystem Modeling and Simulation: Nomenclature and Philosophy2. Math Models of Systems: Biomodeling 1013. Computer Simulation Methods4. Structural Biomodeling from Theory & Data: Compartmentalizations5. Structural Biomodeling from Theory & Data: Sizing, Distinguishing & Simplifying Multicompartmental Models6. Nonlinear Mass Action & Biochemical Kinetic Interaction Modeling7. Cellular Systems Biology Modeling: Deterministic & Stochastic8. Physiologically Based, Whole-Organism Kinetics & Noncompartmental Modeling9. Biosystem Stability & Oscillations10. Structural Identifiability11. Parameter Sensitivity Methods12. Parameter Estimation & Numerical Identifiability13. Parameter Estimation Methods II: Facilitating, Simplifying & Working With Data14. Biocontrol System Modeling, Simulation, and Analysis15. Data-Driven Modeling and Alternative Hypothesis Testing16. Experiment Design and Optimization17. Model Reduction and Network Inference in Dynamic Systems Biology1. Biosystem Modeling and Simulation: Nomenclature and Philosophy 2. Math Models of Systems: Biomodeling 101 3. Computer Simulation Methods 4. Structural Biomodeling from Theory & Data: Compartmentalizations 5. Structural Biomodeling from Theory & Data: Sizing, Distinguishing & Simplifying Multicompartmental Models 6. Nonlinear Mass Action & Biochemical Kinetic Interaction Modeling 7. Cellular Systems Biology Modeling: Deterministic & Stochastic 8. Physiologically Based, Whole-Organism Kinetics & Noncompartmental Modeling 9. Biosystem Stability & Oscillations 10. Structural Identifiability 11. Parameter Sensitivity Methods 12. Parameter Estimation & Numerical Identifiability 13. Parameter Estimation Methods II: Facilitating, Simplifying & Working With Data 14. Biocontrol System Modeling, Simulation, and Analysis 15. Data-Driven Modeling and Alternative Hypothesis Testing 16. Experiment Design and Optimization 17. Model Reduction and Network Inference in Dynamic Systems Biology

"I am just in awe of your ability to start with simple ideas and use them to explain sophisticated concepts and methodologies in modeling biochemical and cellular systems (Chapters 6 and 7). This is a great new contribution to the textbook offerings in systems biology." Alex Hoffmann, Director of the San Diego Center for Systems Biology and the UCSD Graduate Program in Bioinformatics and Systems Biology "I found Chapter 1 to be a marvel of heavy-lifting, done so smoothly there was no detectable sweat. Heavy-lifting because you laid out the big load of essential vocabulary and concepts a reader has to have to enter the world of biomodeling confidently. In that chapter you generously acknowledge some us who tried to accomplish this earlier but, compared to your Chapter 1, we were clumsy and boring. For me, now, Chapter 1 was a "page-turner" to be enjoyed straight through. You have the gift of a master athlete who does impossible performances and makes them seem easy. "Your Chapter 9 - on oscillations and stability - is a true jewel. I have a shelf full of books etc on nonlinear mechanics and system analyses and modeling, but nothing to match the clarity and deep understanding you offer the reader. You are a great explainer and teacher." F. Eugene Yates, Emeritus Professor of Medicine, Chemical Engineering and Ralph and Marjorie Crump Professor of Biomedical Engineering, UCLA "Chapter 4 covers many aspects of the notion of compartmentalization in the structural modeling of biomedical and biological models - both linear and nonlinear. Developments are biophysically motivated throughout; and compartments are taken to represent entities with the same dynamic characteristics (dynamic signatures). A very positive feature of this text is the numerous worked examples in the text, which greatly help readers follow the material. At the end of the chapter, there are further well thought out analytical and simulation exercises that will help readers check that they have