| Date Assigned |
Type |
Assignment |
Date Due |
| 8/25 |
Reading |
- Read NCM Chapter 1 (skip 1.5), from course packet. See
NCMChap1guide.txt. Bring questions about Matlab to class.
- Read for discussion:
Statistical Fluctuations in Autocatalytic Reactions
M. Delbruck
Journal of Chemical Physics 1940 Volume 8 pp 120-124 (search for volume 8, page 120)
Or try this link.
- Start Ecoli world contest in matlab -- see matlab file ecoliworld2b.m. Simulations due 9/1 but please bring questions about writing your matlab code to class on 8/27.
The challenge is to write an improved "rule" for survival. The contest is to see who lives the longest, on average, over 50 trials.
- For those without a prior course in probability, please begin reading
Stochastic Modeling for Systems Biology (SMSB) Chapter 3. We'll go over basic probability in detail in the third
week.
|
8/27 |
| 8/27 |
Reading |
- Stochastic Modelling for Systems Biology Chapter 1
(Introduction) & Chapter 2 (Petri net formalism).
- Review article: Modeling and Simulating Chemical Reactions,
Desmond J. Higham, SIAM Review 2008 (Society for Industrial and Applied
Mathematics Vol. 50, No. 2, pp. 347Ð368)
- As an example of a signal transduction system, please read:
Spiro PA, Parkinson JS, Othmer HG. A model of excitation and adaptation
in bacterial chemotaxis. Proc Natl Acad Sci U S A. 1997 Jul
8;94(14):7263-8.
|
9/3 |
| 9/3 |
Reading |
- Spiro et al (above)
- Higham review article (above)
- Keep working on Wilkinson chapter 3.
|
9/8 |
| 9/3 |
Exercises |
Problem set 1 |
9/10 due in class |
| 9/8-9/15 |
Reading |
Finish Wilkinson Chapter 3 (probability review) |
9/8-9/15 |
| 9/11 |
Exercises |
Problem set 2 |
9/17 due in class |
| 9/15 |
Reading |
- Background, not required reading: Neher E, Sakmann B.
Single-channel currents recorded from membrane of denervated frog muscle fibres.
Nature. 1976 Apr 29;260(5554):799-802. Unfortunately, this is not available except by paying heavy roylaties to Nature Magazine.
- Single-Channel Recording, Chapter 9.1-9.3 (course packet)
|
9/17 |
| 9/17 |
First Project Proposal |
Project proposal (one page) due. As a guide to what I expect for the projects, here is a rubric I will use for grading the projects.
|
9/24 |
| 9/17 |
Reading |
- Moler, Numerical Computing with Matlab Chapter 1.7, Floating Point Arithmetic (course packet).
- Moler, Numerical Computing with Matlab Chapter 9, Random Numbers (course packet).
|
9/22 |
| 9/17 |
Reading |
- Wilkinson, Chapter 4, Stochastic Simulation. Read sections 4.1-4.7 on numerical generation
of pseudorandom samples from different distributions. Also read section 4.8 (optional) if you would like
an introduction to the R programming language.
|
9/24 |
| 9/25 |
Exercises |
Problem set 3 |
FRIDAY 10/3 |
| 9/29-10/8 |
Readings on Markov Chains and Time Series Analysis |
- Wilkinson Chapter 5 "Markov Processes" (required)
- Colquhoun & Hawkes (Stochastic Interpretation of Ion-Channel Mechanisms, course packet) sections 4-10 (required)
- Taylor & Karlin, An Introduction to Stochastic Modeling, Chapters III-IV (optional: supplementary material on Markov Chains).
- Chatfield, The analysis of time series: an introduction, Chapters 3 & 6 (spectral analysis of stochastic time series) (required)
- Chatfield, The analysis of time series: an introduction, Chapters 7 & 8 (more on spectral analysis of stochastic time series) (optional)
- Austin et al, Nature 2006 Vol 439 No 2, Gene network shaping of inherent noise spectra. (for discussion)
- Pedraza et al, Science 2005 Vol 307, Noise Propagation in Gene Networks. (for discussion)
|
|
| 10/6 |
Exercises |
Problem set 4 |
10/20 |
| 10/8 |
Reading |
Wilkinson Chapter 6 "Chemical and Biochemical Kinetics"
Review Higham article |
10/13 |
| 10/27 |
Readings on Diffusion & Brownian Motion |
- Berg, Random Walks in Biology, Chapters 1-5. This is a treatment of random walks and diffusion
from a biologist's point of view.
- Taylor & Karlin Chapter VIII (Brownian Motion) -- on reserve at KSL. This is an introductory treatment of diffusion processes
from a mathematical point of view. Read after finishing the chapters in Berg's book.
|
11/3 |
| 11/2 |
Readings on diffusion models |
- Berg & Purcell, Biophysical Journal 1977, Physics of Chemoreception
- Gerstein & Mandelbrot, Biophysical Journal 1964, RANDOM WALK MODELS FOR THE
SPIKE ACTIVITY OF A SINGLE NEURON
|
optional for 11/2-4 |
| |
Reading |
- Terman & Ermentrout draft chapter
|
|
| 11/19 |
Exercises |
Problem set 5 |
12/3 |
| 11/19 |
Reading |
- Wilkinson Chapter 7, "Case Studies"
- Finish/review Higham review article.
- optional: further case studies in C. Fall et al, Computational Cell Biology Chapters 12-13. See in particular 13.1 on the bacterial flagellar motor.
|
11/24 |
| 11/19 |
Reading |
Wilkinson Chapter 8, "Beyond the Gillespie Algorithm" |
11/26 |
| 11/19 |
Reading |
- Vellela & Qian (2007). A Quasistationary Analysis of a Stochastic Chemical Reaction:
Keizer's Paradox, Bull Math Biol. 2007 Jul;69(5):1727-46. Epub 2007 Feb 23
- Kurtz, T.G. (1972). The relationship between stochastic and deterministic models for chemical
reactions. J. Chem. Phys. 57, 2976–2978.
|
12/1 |
| Assigned |
|
|
Due |
