BioJazz Lab website

Source for https://biojazz-lab.github.io, the website of the BioJazz Lab (Department of Biology, Baylor University).

It is a static site built with Zola 0.23 or later, using a design adapted from the researchlab theme, and published by GitHub Pages. Every push to main rebuilds and redeploys the site automatically (about 1 minute).

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Where things live

What you want to change	Where
Home page text, headline, tagline	content/_index.md
Research areas (one file per area)	content/research/*.md
Lab members (one file per person)	content/members/*.md
Publications	content/publications/feng.bib (BibTeX); preprints in content/publications/preprints/
News items (one file per item)	content/news/YYYY-MM-DD-title.md
Join Us / Contact pages	content/join.md, content/contact.md
Menu, colours, e-mail, social links	config.toml
Images	static/img/… (people photos in static/img/people/)
Page layouts (rarely needed)	templates/

Placeholder text that still needs your input is marked TODO, either in a yellow box on the page or in a comment in the file. To list all of them, run grep -rn TODO content config.toml.

Common tasks

Add a news item. Create content/news/2026-11-15-new-grant.md:

+++
title = "Lab receives NIH grant"
date = 2026-11-15
+++

Short description, with [links](https://example.org) if needed.

The three newest items appear on the home page automatically.

Add a lab member. Copy docs/new-member-template.md to content/members/<lastname>.md, fill it in, and add a photo at static/img/people/<lastname>.jpg (square crop, about 600 × 600 px). When a position is filled, delete the matching content/members/open-*.md placeholder. To link the new member's name in the publication list, add them to content/publications/members_mapping.json, for example "smith": ["Jane Smith"]. Alumni without a member page can be linked to another page instead, for example "smith": {"names": ["Jane Smith"], "url": "https://scholar.google.com/..."}.

Add a publication. Paste the BibTeX entry into content/publications/feng.bib and add a labels = {Topic A, Topic B} line. Then run python3 scripts/bib2json.py to update bib.json. GitHub Actions also runs this before every build, so a commit that changes only the .bib file still updates the site.

Add a preprint. Put preprints in content/publications/preprints/feng-preprints.bib (use journal = {bioRxiv (preprint)}); they appear in the Preprints section of the Selected Publications page. When a preprint is published, move its entry to content/publications/feng.bib and update the journal details. The sections on that page are listed in content/publications.md under [extra] sections.

Give a member a personal publication list. To show a member's own publications (for example, from before they joined) without mixing them into the lab's Publications page, put them in content/publications/members/<username>.bib. Then show them on that member's page with {{<list_publications data_file="content/publications/members/<username>.json" />}}. scripts/bib2json.py converts each of these files separately; see zjohnson.bib for an example.

Add a research area. Copy one of the files in content/research/, then change title, description, weight (its position in the order) and image.

Preview locally

brew install zola        # one time (macOS); needs Zola 0.23 or newer
zola serve               # then open http://127.0.0.1:1111

Zola version: the templates use Tera 2 syntax, so you need Zola 0.23 or newer. Older versions (0.22 and earlier) can't build the site. The deploy workflow pins the version in .github/workflows/deploy.yml (ZOLA_VERSION). To upgrade Zola later, change that number, then run zola check locally to make sure everything still builds.

Publish

git add -A
git commit -m "Describe your change"
git push

Watch progress in the repository's Actions tab.

One-time GitHub setup

1. Create the GitHub organization BioJazz-Lab and, inside it, a public repository named biojazz-lab.github.io.
2. In this folder, run:

   git init -b main
   git add -A
   git commit -m "Initial lab website"
   git remote add origin https://github.com/BioJazz-Lab/biojazz-lab.github.io.git
   git push -u origin main

3. On GitHub, open the repository's Settings → Pages → Build and deployment and set Source to GitHub Actions.
4. After the first workflow run finishes, the site is live at https://biojazz-lab.github.io.

How it's put together

• templates/ holds every page layout, written in Tera 2 syntax for Zola 0.23+. Shared pieces (header, footer, scroll-to-top button) are in templates/partials/.
• templates/components/list_publications.html is a component, the Zola 0.23 replacement for shortcodes. It's called from Markdown like this: {{<list_publications member="feng" />}} or {{<list_publications show_filters={true} />}}.
• Curly braces in Markdown: content files are now processed as templates, so if a page ever needs to show literal {{ }} or {% %} text, wrap that text in {% raw %} … {% endraw %}.
• scripts/bib2json.py converts the BibTeX file into bib.json for the publication list. It needs only Python 3.
• static/ holds the CSS (Tailwind, typography and css/site.css), JavaScript, icons and images.
• Styles use Baylor green (#154734) and gold (#FFB81C).
• The layout and publication list are adapted from the researchlab theme by Pierre-Louis Aublin, Dimitrios Giakatos and Jean-François Baffier, under the MIT licence; see docs/researchlab-theme-LICENSE. The theme is no longer loaded as a Zola theme, so the old themes/researchlab/ folder is unused and can be deleted.