This course introduces students to computer modeling and simulation in biology. Biological research involves the formulation and testing of conceptual models. One important means of testing conceptual models is to convert them to mathematical models that can be simulated on the computer. The course begins by giving the student the necessary tools to do models with MATLAB. An exam at the end of the fourth week tests these skills. The rest of the course involves developing models, doing simulations and analyzing results in a number of different areas of biology.
The university has a site license for MATLAB, so MATLAB should be available on the Dorm computers and on computers in computer labs across campus.
Grading Basis: In a typical year, the grading basis is : 50% from assigned computer exercises, 20% from the 5 special lab exercises, 20% from the exam in week 4, and 10% from an in depth exploration of one particular exercise (to be submitted at the final exam time). Since students are allowed to redo the computer exercises until they get them right (within limits), most students put in the work to get full credit for this portion of the grade. The lab exercises and the exam are graded strictly and tend to separate the A grades from the B grades for those who put in the time and effort to do all of the computer exercises correctly.
Attendance at the OPEN LAB sessions is not required, but students
tend to use this time to get help with the computer exercises. Since
the computer exercises are numerous, getting behind in the work can have
dire consequences for the grade.
| DATE | CLASS TOPIC | LAB TOPIC |
| First 4 weeks | GETTING STARTED WITH MODELS | Learning MATLAB |
| Week 1 Monday | Modeling, course mechanics, lab schedule | MATLAB Introduction |
| Wednesday | Analytical Models, Math review | MATLAB topics |
| Friday | More analtical models | more on MATLAB |
| Week 2 Monday | Simulations of stable states | Curve fitting |
| Wednesday | Simulations of stable states | Michaelis-Menten exercise |
| Friday | Fitting equations to data | OPEN LAB |
| Week 3 Monday | Numerical Integration | MATLAB help |
| Wednesday | Numerical integration in MATLAB | Curve-fitting exercise |
| Friday | MATLAB programming suggestions | OPEN LAB |
| Week 4 Monday | Biochemical Kinetics | OPEN LAB |
| Wednesday | Population Models--logistic equation | OPEN LAB--Exam review |
| Friday | EXAM | |
| Last 6 weeks | MODELS IN VARIOUS AREAS OF BIOLOGY | |
| Week 5 Monday | Logistic equation and chaos | OPEN LAB |
| Wednesday | Lotka-Volterra Predator-Prey | Chaos exercise |
| Friday | Phase Plane analysis of predator-prey | Chaos exercise (cont) |
| Week 6 Monday | Microbial growth | OPEN LAB |
| Wednesday | Age-specific models of populations | OPEN LAB |
| Friday | Population genetics | OPEN LAB |
| Week 7 Monday | Compartmental models of biogeochemistry | Age specific models exercise |
| Wednesday | Diffusion models | OPEN LAB |
| Friday | Calcium oscillations | OPEN LAB |
| Week 8 Monday | Compartmental models of physiology | OPEN LAB |
| Wednesday | Matrix methods in simulations | OPEN LAB |
| Friday | Models of Physiological Control | OPEN LAB |
| Week 9 Monday | Monte Carlo methods | Bilirubin exercise |
| Wednesday | Random walks in biology | OPEN LAB |
| Friday | Epidemics | OPEN LAB |
| Week 10 Monday | MEMORIAL DAY HOLIDAY | |
| Wednesday | Epidemics (cont) | OPEN LAB |
| Friday | AIDS model | AIDS model simulation |