Orientation: Class Participation

Assigned reading and reading quizzes

For each unit there will be at least one assigned reading. These readings are typically review articles intended to provide the students with an introduction to a particular topic. Students will be expected to come to class prepared to take a short in-class quiz on the reading. The quiz questions will focus on relevant biological mechanism(s) and the basic computational approaches people have taken to better understand a particular characteristic of the genome. Students will be given 5-10 minutes to answer 3-4 problems. After the quiz, we will go through each question individually, select a student at random to share their answer to that question with the class, and discuss until all questions or doubts are addressed.


For each unit there will be a handful of exercises intended to teach students the mechanics of running a particular software package. Precise instructions and a detailed narration for each exercise will be posted on the class wiki, and we will attempt to complete many of these exercises during class time. The idea is that the students will look at the commands provided in the instructions, type those commands into the terminal verbatim, and get (barring any mistakes) a correct result. The data sets for these exercises will be intentionally small—often artificially small—so that we can move quickly through the exercise. Exercises do not require much critical thinking, but rather are there to help students get comfortable running software via the command line.


For each unit there will also be a handful of assignments for each student to complete once she/he is comfortable with the prerequisite exercise. The instructions for assignments are a lot more open-ended than for exercises, and require the student to do much more critical thinking on their own. Assignments often give the student the flexibility of choosing which software to use and/or which particular data set to analyze. As opposed to exercises, assignments will use full-sized data sets, which will increase the time and compute resources necessary to complete the analysis. The student will likely need to read software documentation to determine what parameters the software uses and whether the default parameter values are appropriate for their particular analysis. After running the software, the student will need to critically assess the result.

  • Does it make sense?
  • Is it believable?
  • Does it confirm what we already know?
  • Is the result robust to parameter changes?
  • If I run the analysis with a different software package, how different is the result?

Peer reviews

Students will use a class wiki as their personal lab notebook to document their work on each assignment. Frequently throughout the course, we will take 15-20 minutes at the beginning of class and randomly group students in pairs to peer review each other's lab notebook entries for the latest assignment. Each student is expected to provide their peer with some constructive criticism.

  • Is their notebook entry well organized?
  • Did they provide a clear motivation and description (in correct English!) of their analysis?
  • Are their notes sufficiently detailed so that you could replicate their analysis given enough time?
  • Do their results make sense?

At the end of peer review, one pair will be selected at random to come to the front of the class and provide a summary of their peer review session. This will give the class the benefit of learning from each others' successes and failures.

Final project

The final project will give each student the chance to explore a particular topic or data set in more depth. Students will give a short presentation right before spring break proposing a topic for their project, and then another at the end of the course describing their progress and results. A final project write-up will be due during exam week.

cgss15/orientation/participation.txt · Last modified: 2015/01/12 11:29 by standage
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