Class
meets: Tuesdays and Thursdays 1:40-3:00,
at: SEC-211 (Busch Campus)
Text:
No textbook is required; the instructor's Lecture Notes are available from the
"Syllabus, Notes, and Homework Assignments" link below.
(For additional reading, a recommended reference is the book
L. Edelstein-Keshet, Mathematical Models in Biology, McGraw-Hill, 1988.
Some of the lecture note materials are based on that book.
It may be purchased directly from
Amazon
or from
SIAM.)
Instructor:
Eduardo Sontag,
email:
sontag@math (add .rutgers.edu if
mailing from outside Rutgers)
Office Hours: Tuesdays and Thursdays 12:30-1:30,
273 Hill
Center - but you should let me know in advance, by email or talking to me after
class, if you will be coming in - also any other mutually convenient times, by appointment, and
"24/7" communication by email.
Please add the following word: ALLOW336 (no spaces) to the subject line of any email sent to the instructor
Final
Exam: Monday, 12/18, 8-11AM, usual classroom (tentative, to be confirmed)
Important notices will be sent to you by email, to the address which the registrar provides for you (typically in the "eden" machine). You should set "forwarding" from that address if you wish to receive your emails in some other service (yahoo, gmail, etc).
Syllabus, Notes, and Homework Assignments
An introduction to molecular systems biology (optional but strongly recommended reading)
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.
In addition, 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 this, and cut and paste in to 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.
| Class attendance is mandatory. There will be no make-ups for quizzes or exams. |
Noteworthy quotes:
"Complex assemblies of interacting proteins carry out most of the interesting jobs in a cell, such as metabolism, DNA synthesis, movement and information processing. These physiological properties play out as a subtle molecular dance, choreographed by underlying regulatory networks. To understand this dance, a new breed of theoretical molecular biologists reproduces these networks in computers and in the mathematical language of dynamical systems." (From "Network dynamics and cell physiology", by Tyson, Chen, and Novak, Nature Reviews in Molecular Cell Biology, 2001.)
"The slippery gooiness of biology is a consequence of its incredible complexity, consisting as it does of complex systems based upon chemistry. And chemistry obeys the rules of physics, which exists because of, and is consequently best described by, mathematics." (From the Mathematics in Biology page at Brandeis.)
The important thing in science is not so much to obtain new facts as to discover new ways of thinking about them. (By Sir William Bragg, Physics Nobel Prize for X-ray crystallography.)
... mathematics ... was repugnant to me ... from my not being able to see any meaning in the early steps in algebra... This impatience was very foolish ... I have deeply regretted that I did not proceed far enough at least to understand something of the great leading principles of mathematics, for men thus endowed seem to have an extra sense. (From Charles Darwin's Autobiography, 1876.)
biomath major
at Rutgers
Mathematical
Biology web sites
back to Eduardo Sontag's Web page