AMATH 422/522: Computational Modeling of Biological Systems

SLN 10215/10231, MW 4:30-5:50, Communications Building (CMU) 228
(Prerequisites: AMATH 351/MATH 307)


Professor Hong Qian
Lewis Hall 319
tel: 543-2584
fax: 685-1440
office hours: Thursday: 10:30am-12:00pm

Course Description

Examines fundamental models that arise in biology and their analysis through modern scientific computing. Covers discrete and continuous-time dynamics, in deterministic and stochastic settings, with application from molecular biology to neuroscience to population dynamics; statistical analysis of experimental data; and R programming from scratch.

Course Textbook and Supplemental Materials

S. P. Ellner and J. Guckenheimer, "Dynamic Models in Biology" (Princeton, 2006). Available at University bookstore.

[Several chapters including Preface and Chapter 1 can be obtained free online] [Supplemental materials]

S. P. Ellner and J. Guckenheimer "Lab Manual: An Introduction to R for Dynamic Models in Biology" (Free Download 2011)

R Core Team "An Introduction to R" (Free Download 2013).

James D. Murray, "Mathematical Biology: I. An Introduction" (3rd edition, Springer, 2007).

Daniel A. Beard and Hong Qian, "Chemical Biophysics: Quantitative Analysis of Cellular Systems" (Cambridge Univ. Press, 2008).

Stormy Attaway, "Matlab: A Practical Introduction to Programming and Problem Solving" (Butterworth-Heinemann 2013). Available at University bookstore.


AMATH 422/522 Syllabus

Class Project and Presentation

Each student group will give two 6-10 mins in-class presentations of a paper that utilizes the modeling and computational methods we have learned in the class. These studies will be developed into final projects.

Two 6-10 mins presentations: Wed. February 26, 2014 in class (literature review and plan), Wed. March 12, 2014 in class (final presentation)

Final term papers are due on Wed. March 19.

Please read carefully Project and Presentation Guidelines, replacing MATLAB with R.

You can find a list of possible topics here or more advanced papers here.

Course Notes

First day of class, Monday January 6, 2014.

Jan. 6 Notes

Jan. 8 Notes, Michalis-Menten Kinetics code

Jan. 13 Notes

Jan. 15 Notes

No class on Monday January 20, Martin Luther King Day.

Jan. 22 Notes

Jan 27, Leslie Matrix Population code

Feb. 3rd Notes, Lotka-Volterra Dynamics code, Plot 2d Vector Field code

Feb. 5 Notes, Morris-Lecar Dynamics code

Feb. 10 Notes

Feb. 12 Notes

No class on Monday February 17, Presidents Day.

Wed. February 26, in class presentation on literature review and plan.

Wed. March 12, in class final presentation.

Last day of class, Wednesday March 12, 2014.

Term paper due, Wednesday March 19, 2014 .


Homework #1: Due Jan 13, Solutions

Homework #2: Due Jan 20, Solutions

Homework #3: Due Feb. 3 Solutions

Homework #4: Due Feb. 10 Solutions

Homework #5: Due ***Feb. 19*** Solutions

<> Mon Jan 6 08:16:34 PDT 2014