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 (Sara)

2. Organizing and Storing Data

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

3. Making the Computer Make Decisions

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

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 (James)

5. Interacting with the Outside World

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

6. Intro to the Project: Structure and Sequencing

  1. Numpy, Scipy, and Pylab (Aisha)
  2. System Calls, External Programs and Running BLAST (Courtney)

7. Applications of High Throughput Sequencing

  1. Mapping Reads to a Genome (Matching, Slices, Indices (Courtney)
  2. SNP Calling (James)

8. Dealing with High Throughput Data

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

9. The actual project! Rho-dependent termination

  1. Statistics for Sequencing (Mel)
  2. Introduction to Plotting (Aisha)

10. Polishing things up

  1. More on making fancy figures (Aisha)
  2. Structure Gazing with Chimera (Mike)

Summary PDF

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