Organization 1
Overview and learning objectives
Students will learn the benefits of project and folder organization, and how these enable reproducibility and reusability. They will then complete an activity where they use provided examples to set up the structure and naming conventions for a new project.
At the end of the session students will be able to
- Evaluate folder and file structure of a project.
- Recognize common problems that occur in file organization.
- Distinguish between input and output files.
- Setup up a new project with a structure that facilitates reproducibility
Materials
- organization slides:
slides/organization-slides - file naming slides:
slides/naming-slides - Lesson:
organization-01-lesson.md - Instructor notes:
organization-01-instr-notes.md
Resources and useful links
Relevant scientific papers
- EP White, E Baldridge, ZT Brym, KJ Locey, DJ McGlinn, SR Supp (2013) "Nine simple ways to make it easier to (re)use your data." Ideas in Ecology and Evolution 6(2): 1–10, 2013. doi:10.4033/iee.2013.6b.6.f (in particular the section "Use standard table formats")
- WS Noble (2009) "A Quick Guide to Organizing Computational Biology Projects." PLoS Computational Biology 5 (7): e1000424. doi:10.1371/journal.pcbi.1000424
File naming and organization
- File naming guides and suggestions from
- Wikipedia entry on list of filename extensions
- Wikipedia entry on ISO 8601 standard for dates
People and credits
This lesson was first created at the 1. Reproducible Science Curriculum Hackathon. The corresponding author is Ciera Martinez @iamciera. See the commit log for other contributors.
Please post feedback and issues with the lesson on the repository's issue tracker. For instructor questions about teaching this lesson, you can also contact the corresponding author directly.