This page is the home for supplementary materials that accompany our textbook Dynamic Models in Biology (Princeton University Press, 2006: you can order it here). This page is maintained by the authors and hosted by the Center for Applied Mathematics at Cornell University. Its main purpose now is to distribute materials for computer lab sessions using either Matlab or R. We will also post errata for the book as they are found, and suggest some supplementary readings from the primary literature.

We also provide below, for use in teaching, a set of all Figures and selected Tables from the book. Some of the figures are our 'draft' versions, rather than the final versions that PUP re-drew for the book, but they should serve for teaching.

We would be delighted to include or link to contributions from others: more or better computer labs, “translations” into other computing languages, homework exercises, readings lists, etc. Please contact us if you have any materials of this sort that you would be willing to have us post here.

The lab materials here are put out as “open source”: you can modify them to suit your needs, so long as you retain credits to us, the book, and Princeton University Press. When you catch errors, please let us know so we can fix them. The lab manuals include a from-the-beginning introduction to the language and the rudiments of programming suitable for students with no prior programming experience.


Figures Part 1 (PDF File)

Figures Part 2 (PDF File)

Computer labs in Matlab

Lab Manual: PDF file

Matlab m-files (zip archive)

Lab Manual: LaTeX source file

Lab Manual: figures

Computer labs in R

Lab Manual: PDF file

R script files (zip archive)

Lab Manual: LaTeX source file

Lab Manual: figures

Other stuff

The data for exercises 9.7 and 9.8

For phase plane analysis in Matlab, we suggest the pplane package developed by John Polking. You can get it here. The R script files include DMBpplane.R (based on an earlier version by Danny Kaplan) which has much of the functionality of pplane, but not the nice GUI.

If you're not using Matlab or R, phase plane analysis can be done with Bard Ermentrout's XPP program. The main page for XPP is here and a precompiled version for MS Windows called WinPP is here.

The program ez-spiral by Dwight Barkley is useful for demonstrating spiral waves in 2-dimensional PDEs for excitable media. You can get it here.