1. What Python Can Do for You

  1. Why We Program; What We're Learning; What We're Not (Aaron Hardin)
  2. The Very Basics: Hello, World! Variables, and Printing (Nathaniel Krefman)

2. Organizing and Storing Data

  1. Lists, Dictionaries, Tuples, and Sets (Aaron Hardin)
  2. Fancy Data Structures (Peter Combs)

3. Making the Computer Make Decisions

  1. Logical Tests and the Nature of Truth (Nathaniel Krefman)
  2. Loops and Escapes (Peter Combs)

4. Reading, Writing, Using LOTS of Data; and Using Other People's Code

  1. Files: Readin' 'Em and Writin' 'Em (Aaron Hardin)
  2. Functions, Modules, and Pickles (Nathaniel Krefman)

5. Interacting with the Outside World

  1. Common Errors, Print Debugging, and Exception Handling (Peter Combs)
  2. Best Programming Practices, and More About the Projects (Peter Combs)

6. How to Be Good: Best Practices, iPython, and the Debugger

  1. System Calls, Scripting External Programs and BLAST (Mike Lawson)
  2. Interpreter, Debugger: Things to Try When You're Stuck (Mike Lawson)

7. Numerical Computing and Data Analysis (HIV project)

  1. NumPy, SciPy, Pylab: Numerical Computing and Data Analysis (Peter)
  2. Graphing (Aaron)

8. Connecting Sequence with Structure and Function

  1. Structure Gazing with Chimera (Mike Lawson)
  2. Using Chimera and Python Together (Mike Lawson)

9. High Throughput Data

  1. All by Ourselves: Mapping Reads to the Genome (Matching, Slices, Indices) (Peter)
  2. SNP Calling (Aaron)

10. Sticking with it

  1. RNA-Seq (Peter)
  2. ChIP Seq (Aaron)