Javascript Menu by Deluxe-Menu.com
640:336, Fall 2008; Home Page

640:336 DYNAMICAL MODELS IN BIOLOGY
Fall, 2008




  • Class schedule: TTH4 (1:40-3:00), SEC, Room 211
  • Text: L. Edelstein-Keshet, Mathematical Models in Biology, Classics in Applied Mathematics, 46, SIAM (2005): ISBN 0-89871-554-7.
  • Instructor: Daniel Ocone; ocone-at-math-dot-rutgers-dot-edu.
  • Office Hours: Hill 518: T3, TH5, or by appointment.
  • SYLLABUS, NOTES, and PROBLEM SETS
  • Tests, homework, grades: There will be weekly, graded problem sets, two midterms, and a final.
    The final grade will be computed from an average of the final grade (200 points), the midterm grades (100 points each), and the homework grades (100 points). The midterms are tentatively scheduled for October 9 and November 22.
  • Background reading (strongly recommended): An introduction to molecular systems biology
  • Prerequisites: This course assumes familiarity with differential equations; its prerequisites are Calc4 (640:252) and Linear Algebra (640:250).
    The first set of readings (syllabus link above) includes review notes on differential equations which may help refresh your mind, as well as a set of problems. This is review material. If you have difficulty working out the problems, perhaps you should not take this course.
    Here are also some additional notes on differential equations.


Computer Use

You should be able to use a computer for obtaining phase planes and numerical solutions of ordinary differential equations. If you have not used computers for this purpose before, it is a good time to learn.


The simplest option is to use the following Java Applet, which should run on any Java-enabled broswer:

JOde
But, if you prefer, you can use any other software which includes ODE solvers, such as Maple or Matlab (which are available on many campus computers).

For Maple, very little is needed in order to do what is needed for this course. Read the page in the next line, and cut and paste into Maple to obtain results and modify the sample equations to see what happens: one-page of instructions on solving/graphing differential equations using Maple. (Example: Maple worksheet for excitable systems (download and then input to maple)

If you want to use MATLAB instead of Maple, look at "project 2" in the projects page for self-contained instructions on how to solve ODE's using MATLAB.