Simple guide for lab members to update docs.cnclab.io
🚀 Adding Research Notebooks (Most Common)¶
From Google Colab (Recommended)¶
Create or open your notebook in Google Colab
Name your file using our convention:
Category-##-Title.ipynb Examples: Analysis-01-Reproducible_fMRI.ipynb Methods-01-Data_Quality_Checks.ipynb Tutorials-01-Python_Setup.ipynb Resources-01-Lab_Onboarding.ipynbSave to GitHub:
File → Save a copy in GitHubRepository:
CNClaboratory/cnclab_websiteFile path:
docs-book/notebooks/Category-##-Title.ipynb
Auto-deploy: Your notebook appears on docs.cnclab.io in 2-3 minutes
Categories¶
Analysis-XX- - Research analysis, data processing, statistical workflows
Methods-XX- - Lab techniques, experimental procedures, data collection
Tutorials-XX- - How-to guides, training materials, step-by-step instructions
Resources-XX- - Lab policies, protocols, administrative information
✏️ Editing Text Content¶
Quick Edits (GitHub Web Editor)¶
Navigate to any page on docs.cnclab.io
Click “Edit this page” (GitHub icon) at the top
Make changes in GitHub’s web editor
Commit with a clear message:
feat: Update [page name] - [what changed]Changes go live in 2-3 minutes
Directory-based Organization (No manual TOC edits)¶
You can now organize pages using folders and numeric prefixes. The site auto-generates the table of contents from the directory tree.
Rules¶
Create folders as sections (nested subfolders allowed)
Order pages with numeric prefixes:
01-Intro.md,02-Setup.ipynb,10-Advanced.mdNames are prettified (numbers and dashes are removed in the sidebar)
Supported files:
.md,.mdx,.ipynb
Examples¶
docs-book/
├── index.md # Always pinned first
├── editing-guide.md # Pinned
├── ACCESS_CONTROL.md # Pinned
├── Tutorials/
│ ├── 01-Getting-Started.md
│ ├── 02-Python-Setup.ipynb
│ └── Advanced/
│ ├── 01-Vectorization.md
│ └── 02-Numba.md
└── Methods/
├── 01-Data-Quality.md
└── 02-Preprocessing.mdNo need to edit myst.yml for ordering or nesting—it’s generated at build time.
Files You Can Edit¶
docs-book/
├── index.md # Homepage
├── editing-guide.md # This guide
├── notebooks/ # Research notebooks
│ ├── Analysis-XX-*.ipynb
│ ├── Methods-XX-*.ipynb
│ ├── Tutorials-XX-*.ipynb
│ └── Resources-XX-*.ipynb
└── myst.yml # Auto-updated TOC (advanced; no edits needed)🔧 Advanced: Table of Contents¶
To add new sections or reorder content, edit docs-book/myst.yml:
toc:
- title: Home
file: index.md
- title: 🧠 Research Analysis
children:
- title: Your New Analysis
file: notebooks/Analysis-02-YourStudy.ipynb📝 Writing in MyST Markdown¶
Basic Syntax¶
# Main Heading
## Subheading
**Bold text** and *italic text*
- Bulleted lists
1. Numbered lists
[Links](https://example.com)Advanced Features¶
# Cross-references
{doc}`other-page` or {doc}`notebooks/Analysis-01-Reproducible_fMRI`
# Admonitions
:::{note}
Important information here
:::
:::{warning}
Be careful with this!
:::
# Code blocks
```python
import pandas as pd
# Your code here
## 🆘 Getting Help
- **Quick questions**: Edit this page to add common issues
- **Technical problems**: [Open a GitHub issue](https://github.com/CNClaboratory/cnclab_website/issues)
- **Major changes**: Contact lab administrators
## ✅ Quality Guidelines
Before publishing content:
- [ ] **Test notebooks** - "Restart and run all" works completely
- [ ] **Clear documentation** - Every step explained
- [ ] **Proper naming** - Follows Category-##-Title convention
- [ ] **Complete outputs** - All results and figures preserved
- [ ] **Bibliography** - Citations for methods and datasets used
---
**Remember**: This documentation follows [open science principles](https://www.poldracklab.org/) - be transparent, reproducible, and helpful to others!