Indiana University Department of Physics - James A. Glazier

Spring 2006 - P548/M548 Mathematical Biology

Instructor: James A. Glazier
Classes: Tu. Thu. 8:00AM–9:30AM
Office Hours: By appointment


  1. Murray – Mathematical Biology, volumes 1 & 2
  2. Fall, Marland, Wagner and Tyson – Computational Cell Biology
  3. Keener and Sneyd – Mathematical Physiology


Weekly Homework (40% of Grade)
Written Project Report (40% of Grade)
Oral Presentation (20% of Grade)
  No Final Exam – Late Assignments Will Be Marked Down.
Software: CompuCell 3D


If you are new to using UNIX, Linux or Mac OS X, please read the first few sections of this excellent tutorial on getting started with Unix related operating systems.

Note Regarding Assignments

The purpose of the homeworks is to help you think through the meaning of what we do in class and laboratory. The homeworks certainly are not meant to be a form of torture. Especially when an assignment is new (like the computer exercises), I may have some trouble estimating the amount of time it will take.


  • 1) If you find that a simulation takes too long, try running it with a smaller lattice or for fewer time steps, for fewer different cases or display the data less frequently.
  • 2) If the methods in item 1) don't speed things up enough, just write me a note that it took too long and I will modify the homework for the future. It would be especially helpful if you:
    • a) Indicate how long you think the problem will take (using current methods).
    • b) Suggest improvements to CompuCell that would overcome these problems.

Many of you have already made such suggestions, which we really appreciate.


Lecture Powerpoints Assignments
Lecture 1 [112 KB]
Lecture 2 [459 KB]
Lecture 3 [12.7 MB]
Lecture 4 [327 KB]
Lecture 5 [244 KB]
Lecture 6 [456 KB]
Assignment 1 [12 KB]
Assignments 2 & 3 [21.5 KB]
Project Assignment [22 KB]
CompuCell3D Program Files [10.40 MB]*
Installing CompuCell on Linux [PDF, 40.5 KB]
*Updated 15 February 2006.
CompuCell3D Quick Start Guide, Version 0.5 [PDF, 1.4 MB, updated 10 March 2006]
CompuCell3D Quick Start Guide, MacOS, Version 0.5 [PDF, 296 KB]
Introduction to Excel, Version 0.5 [PDF, 629 KB]
Other Files
Ecculture - Susan C Chapman - London College [AVI, 7.89 MB]
Chemotaxis Demo [MOV, 2.24 MB]
Neutrophil [MOV, 1.74 MB]