OCR – Online Collaborative Resources

Author
Affiliation

Marie-Pierre Etienne

https://github.com/MarieEtienne/reproductibilite

Published

Last Updated on Sep 4, 2026

Welcome

The course OCR (Online Collaborative Resources) introduces tools and practices for reproducible and collaborative science.
It is designed for students who want to learn how to:

  • Organize their work for transparency and reproducibility
  • Use version control systems such as Git
  • Collaborate effectively on shared projects
  • Document analyses and results in a reproducible way

Course content

During this course, you will explore:

  1. Introduction
    Why reproducibility and collaboration matter in science, and the main challenges researchers face.

  2. Setting up your framework
    Installing and configuring the software environment (Git, Quarto, etc.).

  3. Git basics (working alone)
    Understanding repositories, commits, and tracking changes in your own projects.

  4. Working collaboratively
    Using branches, pull requests, and collaborative workflows on shared repositories.

  5. Final assignment
    Applying what you learned in a collaborative project.

Final Assignment

The final project of this course is to collaboratively produce a set of well documented dataset.

  • Each student will produce a basic description of a dataset and provide ideas of what statistical method could be used to explore this dataset.
  • Notes will be written in Quarto (.qmd) files inside a shared repository.
  • You will practice quarto to produce generated figures, and cite bibliography.
  • You will practice Git collaboration by creating branches, making commits, and opening pull requests.
  • You will have to be careful as your production should not impact the work produced by others
  • At the end, all contributions will be merged into a collective resource: a mini-encyclopedia of nice ecological datasets to illustrate statistical concept .

This project will allow you to experience real-world collaborative workflows.

How to use this website

Use the top menu to navigate through the course:

  • Introduction – motivations and context
  • Quarto – a brief presentation of quarto to mix up codes and text
  • Set up your Git framework – installing Git tools
  • Basics in Git, working alone – first steps with Git
  • Working collaboratively – branches, merges, pull requests
  • Final assignment – description of the project and instructions
  • Stats Reminders – where all student contributions will appear