Protocol Library

This repository contains the Abdullah Lab’s standardised experimental protocols, buffer recipes, and related analysis SOPs, written in Quarto.

All documents follow a common naming and identifier scheme defined in naming_guide.qmd:

• Stable protocol_id (e.g. MUS-LCMV-PROD-001)
• Versioned via YAML version: "vX.Y"

Protocols and buffers are intended to be:

• Version-controlled (git + GitHub)
• Human-readable (Markdown/Quarto)
• Rendered to PDF/HTML for internal use and GitHub Pages publication

---

Repository Structure (example)

• protocols_src/
  • _templates/
    • naming_guide.qmd – naming and ID conventions
    • buffer_template.qmd
    • protocol_template.qmd
  • general/
    • prot_gen_CTV_stain.qmd
    • prot_gen_flow_standard.qmd
  • human/
    • prot_hum_blood_PBMC_iso.qmd
    • prot_hum_NK92_culture.qmd
  • mouse/
    • prot_mus_lcmv_multi_strain_production.qmd
    • prot_mus_lcmv_plaque_assay_vero.qmd
  • buffers/
    • buf_bhk_propagation_medium.qmd
    • buf_vero_propagation_medium.qmd
• docs/ – rendered HTML/PDF for GitHub Pages

---

GitHub Pages

This README.md appears on the GitHub repository front page, but it is not automatically the homepage of your GitHub Pages site.

To enable GitHub Pages:

1. Go to Settings → Pages
2. Select:
   • Source: Deploy from a branch
   • Branch: main (or your default)
   • Folder: /docs
3. Render Quarto documents into docs/ using _quarto.yml.

Your published site will be accessible at:

https://eomesodermin.github.io/lab-protocols/

---

How to Use the Protocols

1. Edit or create a .qmd file.
2. Add YAML metadata:

title: "Descriptive title"
subtitle: "Abdullah Lab, IMMEI, University Hospital Bonn"
protocol_id: "MUS-PTPRC-GENO-001"
version: "v1.0"
date: "2025-12-01"
description: "More detailed description"

3. Write protocol content using Quarto (Markdown + callouts + code blocks).
4. Render to HTML/PDF.
5. Commit and push.

---

Quarto Formatting Cheat Sheet

Headings

# Main section
## Subsection
### Sub-subsection

Lists

- Bullet item
- Another item

1. Step one
2. Step two

Callout Blocks

::: callout-warning
This is a warning block.
:::

::: callout-tip
This is a tip block.
:::

::: callout-note
This is a note block.
:::

Tables

| Component | Amount |
|----------|--------|
| DMEM     | 500 mL |
| FBS      | 50 mL  |

Code Blocks

# Bash example
quarto render

# R example
library(dplyr)

---

Rendering Quarto Documents (Local)

Render a single file:

quarto render prot_mus_lcmv_multi_strain_production.qmd

Render all documents using _quarto.yml:

quarto render

Render directly into docs/ (recommended for GitHub Pages):

# _quarto.yml
project:
  type: website
  output-dir: docs

quarto render

---

Typical Git Workflow (render + commit + push)

git pull
quarto render
git add .
git commit -m "Update LCMV production and plaque assay protocols"
git push

---

Adding a New Protocol or Buffer

1. Copy an existing .qmd as template.
2. Update:
   • title
   • protocol_id (follow naming guide)
   • version (start at v1.0)
3. Write content.
4. Render output.
5. Commit and push.

See naming_guide.qmd for all identifier rules.