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The models in these pages are examples of dynamic biological processes such as glycolysis, cell cycle progression and calcium signalling.

Dynamics refers to the changes in the biological system relative to time, a version of kinetics. The pages provide the information needed to go through the process of creating mathematical models of biological behaviors.

The features of the biological models discussed in these pages:

  1. Biological/conceptual model: depicts the components and their relationships.
  2. Dynamic behaviors: Each model is of a system that changes over time.
  3. Parameter values: rate constants and concentrations to use in initial models.
  4. Rate equations: Mass action, Michaelis-Menten rate equations are suggested for beginning to model.
  5. Suggested software: The models described are biochemical reactions that can be modeled in many freely available simulation tools. Many of the exerices assume the use of Stella. However, they can be used in a tool of your choice (short list of Tools).

Biological processes: Examples of conceptual maps/models using Stella representations.

Contexts for modeling

Modeling process


These pages are dedicated to assisting biologists and biology educators to develop skills needed to make use of computer models in their biological research and teaching.


Created by Dr. Raquell M. Holmes