Systems Biology: Introduction to Pathway Modeling

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This is an introductory book on biochemical modeling available as of April 2nd, 2014. Page content: 390 pages, 169 Illustrations, 86 Exercises. Now at revision 1.13


Computer models of biochemical systems are starting to play an increasingly important role in modern systems and synthetic biology. This monograph introduces students to some of the essential topics in biochemical modeling using differential equations and stochastic models. The book includes many hands-on modeling exercises and examples that illustrate many important concepts, including stoichiometric networks, building models, running simulations, model fitting, stability of systems and, multicompartment systems.


  1. Cellular Networks

  2. Kinetics in a Nutshell

  3. Stochiometric Networks

  4. Introduction to Modeling

  5. Differential Equation Models

  6. Stochastic Models

  7. How Systems Behave

  8. Multicompartment Models

  9. Fitting Models

  10. Parameter Estimation

  11. The Steady State

  12. Stability

  13. Modeling Feedforward Networks

  14. Behavior of Stochastic Models


Appendix A: List of Symbols and Abbreviations

Appendix B: Useful Numbers

Appendix C: Enzyme Kinetics in a Nutshell

Appendix D: Math Fundamentals

Appendix E: Statistics Reminder

Appendix F:Modeling Standards and Databases

Appendix G: Reference to Tellurium