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A true understanding of genetic and metabolic function and design is facilitated by mathematical and computational methods for analyzing biochemical systems. This hands-on reference teaches biochemists and molecular biologists the use of modern computational methods for the analysis of complex biomedical systems requiring a modest mathematical background. The book begins with representations of biochemical systems, provides guidelines for setting up models, details mathematical and computational methods of parameter estimation and model analysis, and connects to the modern literature with four detailed case studies. Every step is illustrated with examples and explored with accompanying PLAS software. The volume also features over 250 exercises with about one quarter fully or partially solved.
Preface; Introduction; 1. Graphical representation of biochemical systems; 2. Models of biochemical systems; 3. From maps to equations; 4. Computer simulation; 5. Parameter estimation; 6. Analytical steady-state evaluation; 7. Sensitivity analysis; 8. Case study 1 - Anaerobic fermentation pathway in Saccharomyces cerevisiae; 9. Case study 2 - diagnosis and refinement of a model of the tricarboxylic acid cycle in Dictyostelium discoideum; 10. Case study 3 - A sequence of models describing purine metabolism; 11. Case study 4 - Algebraic analysis of the initial steps of the Glycolytic-Glycogenolytic pathway in perfused rat liver; 12. Epilogue-Canonical modeling beyond biochemistry; Appendix; Hints and solutions; References; Author index; Subject index.