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Instructor notes

Total time: 1 - 1.5 hours

Lecture - File Organization

See File organization slides.

Lecture - File Naming

See File naming slides.

Activity 01 - Setting up a new project

Time required: 30 minutes

Now that they have seen the best practices slides, the students will apply these lessons to set up a new project. This activity should reinforce the idea that it is much easier to set things up right from the start, rather than cleaning up messes at a future date. It is meant to get the learners thinking about file names, file organization, and file content and what these can tell us about a project.

Point the students to the slides for reference, as well as the two example projects, in the Resources section. Have them work in pairs to set up a new project in a way that facilitates reproducibility. Let the students come up with the project themselves, rather than providing sample ecology / genomics / social science / etc projects.

Potential examples for the resources section (feel free to highlight ones relevant for your workshop):

  • Jackman et al. "UniqTag: Content-Derived Unique and Stable Identifiers for Gene Annotation": publication and repo
  • Finnegan et al. "Paleontological baselines for evaluating extinction risk in the modern
  • FitzJohn et al. "How much of the world is woody?" publication and repo

oceans": publication and repo

Put the Exercise and Questions on the screen.

Give them about 20 minutes.

Discussion:

  • how did your structure differ from the resources?
  • why did you make changes?
  • what did you and your partner agree / disagree on?
  • were there aspects of the best practices that were difficult to apply to your project?
  • can you imagine this structure evolving over the life of the project? how would you make this structure extensible?