8 Posts with tag: BIOE504 posts

A review of probability

Questions on probability

1. Calculate the probability of four heads one after the other of a fair coin 
2. Calculate the probability of two consecutive heads in a series of four plays of a fair coin. Compare this probability with that of seeing two consecutive heads alone 
3. Consider a simple weather system with the following rules: If it rains today, it will rain tomorrow with a probability of 0.7 If it is dry today, tomorrow will be dry with a probability ...

Tags: BIOE504 posts

Data analysis with R

Many of you are sending me emails with typos and problems with the PDF text of Modeling and Simulation with R. All reviews are highly appreciated, and your comments will make the document stronger for future users. Please feel free to leave me notes about comments, suggestions and typos in the manuscript using the form below. 

Again, your critical reviews are highly appreciated. 

Tags: BIOE504 posts , publications

Installing R

Everything you want to know about installing R is available here. However, the quick instructions are as follows:

Mac OS X - instructions here

Linux - refer your distribution instructions - on ubuntu it is simply

> sudo apt-get install R

Windows - here.

Generally you don't want to install it from source - on systems other than Linux, that is a bit of a pain. 

Let me know if you have trouble with the installation. If you can get it installed successfully, look for ...

Tags: BIOE504 posts

Stochastic kinetics solution

This post is related to the problem posed in the stochastic kinetics lecture. Attached here (link missing) is the solution to the problem (the .R code). To run the code, you will need this reaction.csv input file. The file is a text description of the reaction as a graph. The format is very simple: nodes are the reaction states, and are described by the line e.g. "node, Pyruvate" or "node, Pyruvate_PDC". State transitions are described by "edge, Pyruvate ...

Tags: BIOE504 posts , courses , programming

[Update] Stochastic kinetics

Edit: Added mock NADH data at the bottom of this post

Here I am including the code used to produce the enzyme kinetic plots this morning. Feel free to use the following as a template to create your plotting program.

# Experiments in Markov Models
# E + S <---> ES ---> E + P
# Let
# Pr(E + S ---> ES) = 0.3
# Pr(E + S ---> E + S) = 0.7
# Pr(E + S ---> E + P) = 0
# Pr(ES --> E + P) = 0.1
# Pr(ES --> ES) = 0.4 ...

Tags: BIOE504 posts

Nonlinear regression

Lecture notes available here

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HW1: Linear Regression

Lecture notes for lectures on linear regression

Available here.

Try your hand at analyzing large data set using multiple regression and other advanced techniques

Take a look at the data set provided here. This is a data set of a number of physical dimensions. Can you find a regression model that will provide a good prediction of body weight as a function of other parameters?

Please prepare your report using your favorite statistical computing language. I like R, but you ...

Tags: BIOE504 posts

Day 1 Quiz

Please feel free to post your comments and questions about the Day 1 quiz here. Thanks K

Tags: BIOE504 posts