Computational Biology (Botany 4550/5550) -- Fall 2007

Instructor: Alex Buerkle
Class meetings: Earth Sciences Building 1004, 3:10-5:00 p.m. on Tuesday and Thursday

Course syllabus (fall 2007) (pdf)

Code and data:

• Illustration of a permutation test in R (permTest.txt).
• Illustration of a golden section search using R.
• Perl code to jump-start Project 4 (eddy4.txt).
  Sample data file with 500 lines (met_test.txt).
  Entire, compressed data file with 331,544 lines (met_measurement.txt.gz). Sample code for HRMN regular expression (hrmn.txt). Astronomical data for Julian date 261.

Text editors:

• A quick reference card for Emacs.
• The Emacs manual.
• Emacs for Windows and Mac OS.
• TextWrangler -- a nice, free editor for Mac OS.

Unix:

• A bash_profile file to modify the default behavior of bash on lab computers. Move this file to ~/.bash_profile and open a new Terminal window.
• UW IT documents for unix support: Files and directories, basic commands.

Tools for Windows:

• Perl for Windows
• GNU Utilities for Windows
• cygwin distribution of GNU Utilities for Windows
• 

• R statistical software
• Download R
• R FAQ

Perl

• Giovanni Baiocchi. 2004. Using Perl for Statistics: Data Processing and Statistical Computing. Journal of Statistical Software 11 (1). (abstract, pdf).

UC-Berkeley Stat Labs links:

• Data for Stat Labs (local copy)
• FAQ on using R

Statistics and probability

• Introduction to Statistical Thought (Michael Lavine, Duke University) -- free book with strong statistics and probability material, as well as R code.

Videos:

• Hans Rosling at TED (video of graphical analysis of public health data).
• Peter Donnelly at TED (video with illustrations of statistical thinking).
• Jeff Han at TED (video with demonstration of multi-touch interface.