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Pages, layouts, and shared components

Rendering model

Most primary pages use:

---
title: Page title
layout: default
---

_layouts/default.html assembles the common shell in this order:

  1. _includes/header.html
  2. _includes/nav.html
  3. Page content inside #main-wrap .container
  4. _includes/footer.html

Individual people records use _layouts/member.html. News posts use _layouts/post.html. Both layouts include the same header, navigation, and footer directly.

Primary pages

Homepage: index.html

The homepage contains three sections:

  • A concise “Exploring the Genome” introduction.
  • “Our Work,” generated from the three newest records in site.papers.
  • “News,” containing the five newest posts and one randomly sampled event or conference teaser from the preceding year.

The event image is selected at Jekyll build time. No browser JavaScript is used.

Research: research.html

The Research page contains an overview and alternating illustrated research-program panels. Add a new program by copying a <article class="research-program"> block and placing its image in assets/images/.

People: people.html

The People page reads _people. A person may appear in more than one section because status is a list. Ph.D. alumni are ordered by the end date of the Ph.D. student entry in prior_lab_roles, newest first. See PEOPLE.md.

Software: software.html

Software is maintained directly as card markup. Each card may contain a purpose statement and resource links such as website, source code, documentation, publication, or download.

Publications: publications.html

This file intentionally remains a small wrapper around _includes/publications_page.html. The page uses generated _papers records, shows four curated featured papers, groups the full list by year, displays complete author lists, and loads live citation counts. See PUBLICATIONS.md.

News: news/index.html

The News index uses jekyll-paginate and displays eight posts per page. Individual stories use _layouts/post.html. See NEWS_POSTS.md.

Jobs: jobs.html

The page renders published _jobs records and an empty-state message when no opening is active. See JOBS.md.

Contact: contact.html

The page contains office and wet-lab locations, maps, and building imagery. Edit the address and map links directly in this file.

BibTeX browser: pub_bib.html

This page lists the embedded bibtex field from every generated paper and links to /pub.bib. Do not maintain a second bibliography here.

Header and navigation

_includes/header.html owns document metadata and dependencies. nav.html owns the visible site header. The current navigation links are Home, Research, People, Software, Publications, Jobs, News, and Contact.

At widths of 720 px or less, mobile_navigation.css and assets/js/site-navigation.js replace the horizontal menu with an accessible Menu button and two-column link panel. Keep the aria-controls, aria-expanded, and hidden attributes when changing the button.

Footer

_includes/footer.html is intentionally compact. It contains the lab identity, three university affiliation links, a generated copyright year, and Contact. Add only high-value links; the footer should not duplicate the entire primary navigation.

Reusable includes

Use the existing includes rather than copying their markup:

{% include person_card.html person=person %}
{% include publication_citation.html paper=paper compact=true %}
{% include publication_featured.html paper=paper %}

The publication citation accepts these principal parameters:

  • paper: required generated publication record.
  • compact=true: tighter member/news presentation.
  • member_id: shows that member’s non-byline role, when present.
  • show_abstract=true: allows an expandable abstract.
  • show_metrics=true: renders a live citation badge when DOI or PMID exists.
  • show_consortium=true: displays a Consortium badge if any member_roles value is consortium.

Page style conventions

Primary pages use .site-page, .site-page-header, .section-eyebrow, .section-heading, .site-action-links, and component-specific classes. Avoid inline styles. Add component CSS to main_style.css; reserve mobile_navigation.css for navigation behavior only.