Math 4500, Spring 2025

Math 4500, Spring 2025



"Mathematics is biology's next microscope, only better; Biology is mathematics' next physics, only better." --Joel E. Cohen

"All models are wrong, but some are useful." --George E. P. Box

About the class

This class will be an introduction to mathematical modeling with a particular focus on mathematical biology. We will sample from a variety of problems and modeling techniques throughout the class. Unlike most undergraduate math classes, the scope of this class will be more about breadth than depth.

The course will be roughly divided into thirds: The first third will cover continuous models such as differential equations and difference equations, covering topics such as logistic, predator-prey, and infectious disease modeling. The second third will cover discrete models such as cellular automata, agent-based models, and Boolean models of gene networks. The last third will cover stochastic models, such as phylogentics, RNA folding, and hidden Markov models in genomics.

Resources

Software

Code

Homework

Lecture notes

These are the versions from a previous time that I taught this class, and they will likely be improved and updated as we get to them throughout the semester.

Part I. Differential and difference equations

  1. Introduction to modeling. 3 pages (handwritten). Updated Jan 23, 2022.
  2. Difference equations. 12 pages. Updated Jan 20, 2022.
  3. Analyzing nonlinear models. 4 pages (handwritten). Updated Jan 22, 2013. (will replace soon)
  4. Models of structured populations. 8 pages. Updated Jan 21, 2015.
  5. Predator-prey models. 11 pages. Updated Jan 28, 2015.
  6. Infectious disease modeling. 12 pages. Updated Feb 9, 2015.
  7. Modeling biochemical reactions. 17 pages. Updated Feb 20, 2025.
  8. Gene regulation by operons. 16 pages. Updated Feb 20, 2025.
  9. Delay differential equation models of gene regulation. 29 pages. Updated Feb 27, 2025.
Part II. Discrete and agent-based models

  1. Cellular automata and agent-based models. 18 pages. Updated February 11, 2015.
  2. Basics of Boolean modeling. 18 pages. Updated Feb 27, 2025.
  3. Boolean models of molecular networks. 14 pages. Updated Feb 27, 2025.
  4. Advanced features of Boolean models. 26 pages. Updated Mar 25, 2025.
  5. Reduction of Boolean network models. 21 pages. Updated Mar 25, 2025.
Part III. Stochastic models: genetics, nucleic acids and phylogenetics

  1. CpG islands and hidden Markov models. 12 pages. Updated October 28, 2016.
  2. Hidden Markov models and dynamic programming. 12 pages. Updated April 19, 2017.
  3. Combinatorial approaches to RNA folding. 16 pages. Updated April 15, 2016.
  4. RNA folding via energy minimization. 15 pages. Updated April 15, 2016.
  5. RNA folding via formal language theory. 14 pages. Updated April 15, 2016.