Systems Biology: Introduction to Pathway Modeling

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Pathway Modeling Book

Pathway Modeling Book

This is an introductory book on biochemical modeling available as of April 2nd, 2014. Page content: 424 pages, 169 Illustrations, 86 Exercises.



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 the 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 Jarnac

Teaching Material 

Free Power Point Slides (public domain):

  1. Introduction to Reaction Kinetics (7 downloads)
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