Course Overview

This is the first open-access online course from the Center for Reproducible Biomedical Modeling which provides an overview of the biomodeling process and the theory behind core concepts of cellular pathway modeling. This course will discuss the elements necessary for model construction and the mathematical representations of these elements at an introductory level. A review of basic differential equations will be provided, and subsequent lessons will apply fundamental concepts of differential equations to biomodeling through mass-action and enzyme kinetics. Steady state and stability will be addressed from conceptual and mathematical perspectives.


Veronica Porubsky 
PhD Student, University of Washington

Recommended Textbooks

A textbook is not required for this course. However, we recommend the following textbooks as supplementary resources:

  • Herbert Sauro, Systems Biology: Introduction to Pathway Modeling
  • Brian Ingalls, Mathematical Modeling in Systems Biology: An Introduction
  • Fall et al, Computational Cell Biology, Springer
  • Uri Alon, An Introduction to Systems Biology: Design Principles of Biological Circuits

Lesson 0: Introduction to the Course

Lesson 1: Introduction to Modeling

Lesson 2: Model Elements

Lesson 3: Cellular Networks

Lesson 4: Differential Equations

Lesson 5: Mass-action Kinetics

Lesson 6: Differential Equations Modeling

Lesson 7: Steady State 1

Lesson 8: Steady State 2

Lesson 9: Stability 1

Lesson 10: Stability 2

Lesson 11: Enzyme Kinetics 1

Lesson 12: Enzyme Kinetics 2