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:
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Have you ever:
- Tried to open a file and found it corrupted
- Had to recreate a file because it wasn't backed up
- Couldn't find a file because you forgot what it was called or where you put it
- Had a computer crash lose your unsaved work
- Had to redo work because you (or someone else) decided it needed to be done differently
- Couldn't redo your work because you forgot how you did it
- Spent hours performing the same task over and over
- Read a scientific paper and wondered, “How did they make those number things happen?”
- Created a graph/diagram in Microsoft Excel (or Powerpoint)
Calculate your score: 1 point for every "yes" answer, divide by total number of questions.
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My question for you, dear blog readers: what other questions should I include?
UPDATES:
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)
UPDATES:
Permanently deleted your work on accident (from
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
Had errors related to Windows vs Unix line endings (from @BrownJosephW)