Organize Lab Protocols with GitHub: A Step-by-Step Guide

🧭 Why bother

Creating a GitHub repository for lab protocols helps make your research more organized, transparent, and reproducible. Instead of protocols being buried in notebooks or scattered across emails, GitHub keeps everything versioned, searchable, and shareable. You can track updates. Collaborate with labmates in real time. Make sure everyone is always using the latest, most accurate procedures. It’s a simple step that saves time, reduces errors, and strengthens your lab’s collective knowledge. Chen et al. (2025) recently published a very interesting article on that matter.

⚙️ What Is Git?

Git is a version control system — a tool that helps you track and manage changes to files over time. Linus Torvalds (the creator of Linux) originally created it to handle large, collaborative coding projects. Yet, it’s just as useful for any work that evolves through edits and versions, like lab protocols.

With Git, you can:

• See what changed in each file and who made the change
• Revert to earlier versions if something goes wrong
• Work on new ideas safely in separate “branches”
• Merge updates from different people without losing work

In short, Git keeps your files organized, traceable, and safe, no matter how many revisions or collaborators you have. If you want to know more, look here. But it’s not necessary to continue with this little guide.

🤔 Why Isn’t Everyone Using It Then?

Despite its advantages, Git and GitHub can seem intimidating at first — especially for people without a programming background. The terminology can feel overly technical for researchers. Terms like “commits,” “branches,” or “pull requests” can be confusing. Additionally, command-line tools can be complex for those who just want to record their protocols. Many labs also rely on familiar tools like Word or shared drives, which feel simpler for quick edits. But once the basics are learned, Git and GitHub offer far more control. They allow better collaboration and give long-term reliability than traditional methods. This makes the initial learning curve well worth it.

Here I want to take your hand and walk you through the process. Step by step. It’s not as hard as it sounds!

Step by step guide

1. Create a GitHub Account

• Go to https://github.com
• Click Sign up (if you don’t already have an account)
• Follow the prompts to create your username, password, and verify your email

2. Start a New Repository

1. After logging in, click the “+” icon in the top-right corner
2. Select “New repository”
3. Give your repository a clear name — for example: lab-protocols
4. Add a short description, e.g.: A collection of standardized lab protocols for molecular biology experiments.
5. Choose whether to make the repo Public (recommended for sharing) or Private (if you are unsure, use private, later you can still make it public)
6. Check the box “Add a README file” — this will help describe your project
7. Click Create repository

3. Organize Your Protocols

Structuring your protocols is important. You already have some sort of system going on, even if you don’t use git. Here is how an example structure looks like:

lab-protocols/
│
├── README.md
├── molecular_biology/
│   ├── DNA_extraction.md
│   ├── PCR_protocol.md
│
├── cell_culture/
│   ├── cell_passaging.md
│   ├── transfection_protocol.md
│
└── safety/
    └── waste_disposal.md

4. Write Your Protocols in Markdown

Now that everything is set up, its time to write/transfer your first protocol in GitHub! When writing protocols use Markdown.

✍️ Why Markdown?

Markdown is a simple, text-based format that’s perfect for writing and sharing lab protocols. It uses plain text with lightweight formatting (like # for headings or **bold** for emphasis), which makes it easy to read even without special software.

Markdown files (.md) are:

• Human-readable — look clean in any text editor
• Version-friendly — changes are easy to track with Git
• Flexible — can be viewed beautifully on GitHub or converted into PDFs, Word docs, or web pages
• Future-proof — since it’s plain text, it won’t become obsolete or tied to a single program

In short, Markdown keeps your protocols clear, portable, and easy to maintain.

This is how a small example protocol could look like:

# DNA Extraction Protocol
**Objective:** Extract genomic DNA from cultured cells.
## Materials
- Lysis buffer
- Ethanol (70%)
- Nuclease-free water
## Steps
1. Harvest 1×10⁶ cells.
2. Add 200 µL of lysis buffer.
3. Incubate at 56°C for 10 min.
4. Add ethanol, mix, and proceed with spin column purification.
## Notes
- Store extracted DNA at -20°C.

Find more information on how to write in markdown here.

5. Commit and Push Changes

If you’re editing files directly on GitHub, each change is automatically saved as a commit. If you are new to coding and git, I recommend doing this all of the time. Once you get more familiar with git and GitHub, you can start having your repository locally and push/pull from there. If you feel like you want to give it a try, look here.

6. Keep It Updated

• Add new protocols as separate Markdown files in the correct subfolders
• Update existing ones when procedures change
• Use clear commit messages (e.g., “Updated PCR cycle conditions because Hannah told me XYZ which helps with ABC”)
• Using clear commit messages is crucial to later understand why you change a part of the protocol. This is very powerful!
• If you document your changes like that it will be easy to change something back once you get another information/insight

7. Share and (Optional) Collaborate

Now that you have all your protocols online you can easily share them! The easiest why is to make your repository public. I have printed some QR codes linking to specific protocols and have them glued in the lab.

Now that they are online, you might motivate your co-workers. They can help build up more protocols. They can also help you keep them updated. But this is getting quite advanced already, so maybe just an outlook for now:

• Add collaborators under Settings → Collaborators
• Use Issues to track suggestions or improvements
• Use Branches for testing new versions of protocols

Read more

Many people are already doing the exact thing. Now that you have the basics down, try to get inspired by other people’s work! Here are some protocol repositories I found:

• https://github.com/mjmlab/protocols
• https://gallowaylabmit.github.io/protocols/en/latest/ (they went the extra mile and turned it into a web page, but its the same principle)
• https://github.com/boehmax/protocols (my protocols hehe)

Don’t stress yourself if your layouts are not perfect, or your protocols are not fully finished. It’s already great of you that you try it out! Let it grow naturally. Revise older layouts and protocols once you are more experienced. Do this when you have the time for it.

Thank you!