Ocean Recoveries Lab Manual

Lab manual for the Stier Lab (Ocean Recoveries Lab) in the Department of Ecology, Evolution, and Marine Biology at UC Santa Barbara.

Read the manual: stier-lab.github.io/lab-manual

What's in here

The manual covers everything a new or current lab member needs: onboarding, safety, communication norms, graduate program guidance, funding, mentoring, authorship, data management, fieldwork in Mo'orea, and more. It is written in first person by Adrian Stier and is intended as a living document that evolves with the lab.

Structure

sections/           30 markdown files, one per topic
onboarding-checklist.md
working-agreement.md
config.json         Section metadata (IDs, titles, nav groups)
template.html       HTML shell with CSS, JS, sidebar, placeholders
build.js            Build script: markdown → HTML

The source of truth is the markdown in sections/. Everything else is generated.

Editing content

1. Edit any markdown file in sections/ (or onboarding-checklist.md / working-agreement.md).
2. Run npm run build.
3. Open Stier_Lab_Manual.html in a browser to check your changes.
4. Commit and push. GitHub Pages serves index.html automatically.

Adding a new section

1. Create a new markdown file in sections/ (e.g., 31-new-topic.md). Start with an # H1 heading.
2. Add an entry to config.json in the appropriate nav group:

   { "file": "31-new-topic.md", "id": "new-topic", "title": "New Topic", "num": "31" }

3. Run npm run build.

Changing the design

Edit template.html (CSS, JavaScript, layout). The build script replaces three placeholders:

• {{NAV_ITEMS}} — sidebar navigation links
• {{SECTIONS}} — section HTML content
• {{DATE}} — current date string

Setup

Requires Node.js.

npm install
npm run build

Build output

• Stier_Lab_Manual.html — standalone HTML file (can be opened directly)
• index.html — identical copy for GitHub Pages
• Stier_Lab_Manual_YYYY-MM-DD.md — combined markdown snapshot

License

This manual is specific to the Stier Lab at UCSB. You are welcome to use it as a template for your own lab manual with attribution.