Open Science Guide for Parkinson’s Research

Authors

Matthew J. Kmiecik

Hirotaka Iwaki

Jean-François Daneault

Published

July 22, 2025

Doi

10.5281/zenodo.14984668

Preface

Welcome to the Open Science Guide for Parkinson’s disease research!

This is an online book written with the following aims:

  • help educate on principles of open science
  • provide ideas, resources, and examples to facilitate open and reproducible science

This online book was written as a high-level, easily readable, and accessible guide for Parkinson’s disease researchers across all levels of expertise, but we hope that it’s useful for others as well.

Interested in contributing?

Feel free to contribute if you find a section with missing, incomplete, or incorrect information. For more substantive edits, such as an entire section or chapter, we recommend submitting an issue for clearance from admins (see below).

Here are three ways you can contribute:

  1. Go to our GitHub repo and file an issue.

  2. Visit our GitHub repo, modify a .qmd file directly, and submit a pull request

  3. Clone our GitHub repo, create a branch, modify documents, and submit a pull request

Step-by-step to contribute on Github

  1. Fork the repository:
    • Go to the GitHub page of the repository you want to contribute to.
    • Click the “Fork” button (this creates a copy of the repository under your GitHub account).
  2. Clone your fork:

    • Open a terminal and run the following command, replacing your-username/repo-name with your GitHub username and the name of the repository:

      git clone https://github.com/your-username/repo-name.git

    • Change into the cloned directory:

      cd repo-name
  3. Set up the original repository as a remote (optional but recommended):

    • This allows you to keep your fork updated with the latest changes from the original repository.

      git remote add upstream https://github.com/original-owner/repo-name.git
git fetch upstream
  4. Create a new branch for your changes:

    • It’s good practice to make changes on a separate branch instead of main.

      git checkout -b feature-branch-name

    • Replace feature-branch-name with a descriptive name for your changes (e.g., fix-typo-docs).

  5. Make your changes and commit them:

    • Edit the files as needed.

    • Stage your changes:

      git add .

    • Commit your changes with a descriptive message:

      git commit -m "Brief description of your changes"
  6. Keep your branch up to date (to prevent conflicts):

    • Before pushing your changes, update your branch with the latest changes from the original repository:

      git fetch upstream
git merge upstream/main

    • If there are conflicts, resolve them before continuing.

  7. Push your changes to your fork:

    • Once your branch is up to date, push it to your GitHub fork:

      git push origin feature-branch-name
  8. Create a Pull Request (PR):
    • Go to your forked repository on GitHub.
    • Click the “Compare & pull request” button.
    • Provide a clear description of your changes and submit the PR.

Notes:

  • If you are asked to make changes, update your branch, commit the changes, and push again.
  • If you’re unfamiliar with resolving merge conflicts, GitHub provides a web interface to help you.

Acknowledgements

This project is supported by the Michael J. Fox Foundation for Parkinson’s Research.