Scripting for Scientists
Kyle Ambert & Steven Bedrick
BMI 507/607
Fall Term, 2009

Tuesdays & Friday from 1400-1500, in BICC 124.
Note: October 6th, 9th, and 30th, we will be meeting in BICC 513.

Syllabus

Required text:

Optional (but strongly recommended) texts:

Preliminaries

Miscellaneous & Helpful Readings:
---How to Think Like a Computer Scientist (Learning with Python)
---OSX command line reference
---Windows command line reference
Weeks 1 & 2:
Python & Working
with Problems Algorithmically
Reading: Week 1: Chapters 1, 2(Campbell); Week 2: 6, 7, 13, and also 4 (time permitting)
Lectures:
---Notes for Week 1, Lecture 1
---Notes for Week 1, Lecture 2
---Notes for Week 2, Lecture 1
---Notes for Week 2, Lecture 2
Resources for Week 1, Lecture 1:
---Scripting Languages: A Cross-OS Perspective
---Homework 1
---Data for Homework 1
---Revised Homework #1 Python Script.
The Python Programming Language
--> Resources for Week 1, Lecture 2:
---Scripts run in Lecture 2.
---Python Module of the Week Text
Resources for Week 2, Lecture 1:
---Homework #2
---Data for Homework #2
Resources for Week 2, Lecture 2:
--- An explanation of scope that explains some of Steve's confusion during his lecture: Python Pitfalls: Scope
--- Further discussion of Python scope stuff: Python Scopes and Name Spaces
Week 3:
Working with Files
Reading: Campbell chapter 8
Lectures: Resources for Week 3:
Weeks 4 & 5:
Working with Numbers
Reading: icebreakR (chapters 1, 3, & 6), Static Graphics (Paul Murrell)
Lectures: Resources for Week 4, Lecture 7:
---Homework 3
---Data for Homework 3
Additional Resources for Data Visualization
---Introduction to R Graphics.
Weeks 6 & 7:
Working with Strings
Lectures: Resources:
Weeks 8 & 9:
Networks
Lectures:
Week 9:
Networks
Resources:
Week 10:
Databases
Lectures: Handy Resources: