https://github.com/datacarpentry/rr-organization1
The Organization lesson for the Reproducible Science Curriculum
https://github.com/datacarpentry/rr-organization1
carpentries data-carpentry english lesson on-hold project-organisation r reproducibility
Last synced: 2 months ago
JSON representation
The Organization lesson for the Reproducible Science Curriculum
- Host: GitHub
- URL: https://github.com/datacarpentry/rr-organization1
- Owner: datacarpentry
- License: other
- Created: 2014-12-11T14:25:38.000Z (over 11 years ago)
- Default Branch: gh-pages
- Last Pushed: 2021-10-06T15:59:24.000Z (over 4 years ago)
- Last Synced: 2025-09-05T11:12:43.124Z (8 months ago)
- Topics: carpentries, data-carpentry, english, lesson, on-hold, project-organisation, r, reproducibility
- Language: HTML
- Homepage: http://www.datacarpentry.org/rr-organization1/
- Size: 81.4 MB
- Stars: 42
- Watchers: 16
- Forks: 22
- Open Issues: 7
-
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE.md
- Code of conduct: CODE_OF_CONDUCT.md
- Citation: CITATION
Awesome Lists containing this project
README
# 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
- [Minnesota Historical Society](http://www.mnhs.org/preserve/records/electronicrecords/erfnaming.php)
- [University of Edinburgh, Records Management](http://www.recordsmanagement.ed.ac.uk/InfoStaff/RMstaff/RMprojects/PP/FileNameRules/Rules.htm)
- 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.
[@iamciera]: http://github.com/iamciera
[List of filename extensions]: http://en.wikipedia.org/wiki/List_of_file_formats
[ISO 8601 standard for dates]: http://en.wikipedia.org/wiki/ISO_8601
[Good practice guidance on releasing statistics in spreadsheets]: https://gss.civilservice.gov.uk/wp-content/uploads/2012/12/Releasing-statistics-in-spreadsheets-Good-practice-guidance.pdf
[10.4033/iee.2013.6b.6.f]: https://doi.org/10.4033/iee.2013.6b.6.f
[10.1371/journal.pcbi.1000424]: https://doi.org/10.1371/journal.pcbi.1000424
[CC Zero]: https://creativecommons.org/publicdomain/zero/1.0/
[1. Reproducible Science Curriculum Hackathon]: https://github.com/Reproducible-Science-Curriculum/Reproducible-Science-Hackathon-Dec-08-2014