1. What Python Can Do for You

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

2. Organizing and Storing Data

  1. Lists, Dictionaries, Tuples, and Sets (Mel)
  2. Tests, Loops, and Escapes (James)

3. Making the Computer Make Decisions

  1. Fancy Data Structures: Nested Loops (James)
  2. Reading and Writing from Files (Fernando)

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

  1. Functions, Modules, and Code Reuse (Mel)
  2. Interactive Python, testing, and more useful modules (Fernando)

5. Interacting with the Outside World

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

6. Useful Modules for Data Analysis

  1. Numpy, Scipy, and Pylab (Aisha)
  2. Pandas, Biopython, and more parsing (Aisha)

7. Applications of High Throughput Sequencing

  1. System Calls, External Programs and Running BLAST (Courtney)
  2. Mapping Reads to a Genome (Matching, Slices, Indices) (Courtney)

8. Applications continued

  1. Statistics for Sequencing (Mel)
  2. SNP Calling (James)

9. RNA-Seq

  1. RNA-Seq Introduction: Tools and Approach (Courtney)
  2. In Depth RNA-seq analysis (Courtney)

10. Making Figures

  1. Introduction to Plotting (Aisha)
  2. More on making fancy figures (Aisha)