| Date
Assigned |
Date
Due |
Type |
Assignment |
| 8/24 |
9/1 |
reading |
Read Chapters
1 and 9 in Cleve
Moler's book
|
| 8/26 |
9/3
|
reading |
Read Des
Higham's article
on Modeling Chemical Reactions
|
| 8/26 |
9/3
|
programming
|
You will find
the description of a simple Matlab program simulating a random walk here.
The programs are in the same directory.
|
| 9/1 |
9/8
|
programming
|
You will find
the description of a Matlab program simulating a simple birth process here.
The two html files will give you a nice description of the progralm,
and the files are in the same directory.
|
9/3
|
9/10
|
reading
|
Here is some more information about birth
processes from the book by Taylor and Karlin. Filling in the last
character of each line on the pages on the odd pages is left as an
exercise.
|
| 9/3 |
9/10
|
programming
|
Here
is an implementation of the bin method for generating Poisson spike
trains and the perfect integrate and fire model.
|
| 9/3 |
9/10
|
programming
|
We talked last time
about the distribution of states of the birth process X(t) at a fixed
time t. Here
is a description of how to visualize this in different way - including
some cool 3d visualization tricks.
|
| 9/10 |
9/17
|
reading
|
Read Gillespie's article
on modelling chemical reactions
|
| 9/10 |
9/30
|
homework
|
First homework assignment.
To do the first problem you will need to read
this article.
|
| 9/15 |
9/22
|
reading
|
Read this article
on modeling
gene regulatory networks.
|
9/22
|
9/29
|
reading
|
Learn about the Systems Biology
Markup Language, and Systems
Biology Graphical Notation by following these links.
|
9/22
|
9/29
|
reading (optional)
|
You can learn more about the Gibson and
Bruck algorithm we discussed in class here.
|
9/24
|
10/1
|
programming
|
The following is a chapter
from Wilkinson's book. He discussed the stochastic simulation
of a number of biologically motivated models. You should at least
implement the dimerization and Michaelis-Menten reactions.
|
9/29
|
10/8
|
reading
|
The following two articles discuss the
application of generating functions to the study of network structure
and transmission of diseases in structured populations.
First read the following
introductory paper, and then read this one.
You will find both papers helpful in your next homework assignment.
|
9/29
|
10/8
|
programming
|
In this directory
you will find an example of how to compute extinction times in a Lotka
Volterra model.
|
10/6
|
10/29
|
homework
|
Second
homework assignment. For this assignment you will have to
read the papers by Gardner
et al. and Loinger
et al. You will find relevant pages from Wilkinson's
book here.
|
10/8
|
10/15
|
reading
|
Please read Gillespie's paper on the slow
scale stochastic simulation algorithm.
|
10/8
|
10/15
|
reading
|
This
article is a description of an alternative approach to the
stochastic modelling of the lac operon.
|
10/13
|
10/20
|
reading
|
Read the following
article by Scheffer, et al. about warning signs of a catastrophe.
|
11/3
|
11/10
|
programming/
reading
|
Read the following article
by Desmond Higham. Download the code that was used in the
demonstrations, and make sure you understand it.
|
11/4
|
11/29
|
homework
|
Third
homework assignment. For this assignment you will have to
read the papers by Higham, Scheffer, et al. and Renart, et al. (see
above).
|
11/3
|
11/10
|
reading
|
The following review
article by Renart, et al. describes the derivation of the
stochastic integrate and fire model.
|
11/17
|
11/24
|
reading
|
Read the following
article on bistability and stochastic switching in gene networks.
|
11/19
|
12/1
|
reading
|
I gave only an outline of stochastic
models in evolutionary theory. A good book where you can read
more is Sean Rice's Evolutionary
Theory.
|
