Computational Biology (BIOL F692)
Introduction to Computational Biology (BIOL F492)
-- Fall 2011

Instructor: Naoki Takebayashi
Class meetings: Irving I 303, 9:45-11:15AM on Tuesday and Thursday

Syllabus: BIOL F692, BIOL F492

2008 Syllabus: BIOL F694, BIOL F493

Setting up Desktop computers

Introduction to unix

Introduction to C programming 1: Variable, conditional, loop, printf()
Reading: Philosophy of modeling from Introduction to Mathematical modeling and applications by D. Maki and M. Thompson.

Introduction to C programming 2: Function and array

Probability theory and Pseudo-random number generators
Answers to probability exercises
Example of polyploid simulation analysis

Pointer, Passing function arguments by memory address

Debugger tutorial


Introduction to Perl 1: Basic opertors, Variable types and scopes, Flow control, File I/O, Functions

Introduction to Perl 2: Regular Expressions, diamond operator

Introduction to Perl 3: Data manipulation functions

Perl: driving other programs, Coalescent simulation, Simple example of Approximate Bayesian Computation.

Naoki's useful perl scripts for sequence analysis

Very Quick Tour of Bioperl