1. What Python Can Do for You

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

2. Organizing and Storing Data

  1. Lists, Dictionaries, Tuples, and Sets (Debbie)
  2. Tests, Loops, and Escapes (Diana)

3. Making the Computer Make Decisions

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

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

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

5. Interacting with the Outside World

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

6. Intro to the Project: Structure and Sequencing

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

7. Applications of High Throughput Sequencing

  1. SNP Calling (Josh)
  2. RNA-Seq Introduction: Tools and Approach (Peter)

8. Dealing with High Throughput Data

  1. Numpy, Scipy, and Pylab (Peter)
  2. Structure Gazing with Chimera (Mike)

9. The actual project! Rho-dependent termination

  1. In Depth RNA-seq analysis (Peter)
  2. Statistics for Sequencing (Josh)

10. Polishing things up

  1. More on making fancy figures (Peter)
  2. Advanced Data Structures and Parsing Structural Data (Diana)

Summary PDF