12 August 2015

Bioinformatics "Purity Test": Need more questions!

I'm prepping for the new class I'm teaching this semester, Bioinformatics for Research, and I need help! It's a graduate level class that I'm designing to introduce our Master's students to the basic computational skills they will require to perform common research tasks.

Here are the general skills we'll be covering:

  • data/metadata organization and management
  • automation of tasks with the Unix shell
  • introductory R scripting (data parsing, simple statistics, visualizations)
  • executing command-line programs on remote HPC resources
  • version control with Git
  • small projects in genome assembly/annotation and phylogenetics (common questions for which previous grad students have asked for help)
As a part of motivating students to learn these skills, I'm developing a Bioinformatics "Purity Test," similar to the ones I remember being all the rage when I was in high-school and college. Students will be presented with circumstances and they will calculate the percentage of scenarios they've encountered. Here are the survey questions so far:
Have you ever:

  1. Tried to open a file and found it corrupted
  2. Had to recreate a file because it wasn't backed up
  3. Couldn't find a file because you forgot what it was called or where you put it 
  4. Had a computer crash lose your unsaved work
  5. Had to redo work because you (or someone else) decided it needed to be done differently
  6. Couldn't redo your work because you forgot how you did it
  7. Spent hours performing the same task over and over
  8. Read a scientific paper and wondered, “How did they make those number things happen?”
  9. Created a graph/diagram in Microsoft Excel (or Powerpoint)
Calculate your score: 1 point for every "yes" answer, divide by total number of questions.
My question for you, dear blog readers: what other questions should I include?

Permanently deleted your work on accident (from @thatdnaguy)
Frequently copy/paste to reformat documents (from @PaulBlischak)
Found two versions of the same file, but didn't know how they differ (from @nmatasci)
Forgotten your abbreviations for samples, dates, etc in an analysis (from @nmatasci)
Been unable to use software because you can't find a computer that can run it (from @nmatasci)
Been unable to determine the required input format for a program (from @dwbapst)
Been unable to install software dependencies (from @BrownJosephW)
Had errors related to Windows vs Unix line endings (from @BrownJosephW)