Total time: 1 - 1.5 hours
See File naming slides.
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?