Sulkowska Lab Website

Static Jekyll source for the Interdisciplinary Laboratory of Biological Systems Modelling at the Centre of New Technologies, University of Warsaw. The site is for lab members, collaborators, applicants, funders, press, and scientific visitors who need current information about the group, research, software, publications, and contact details.

Quick Start

Requirements:

• Ruby 3.4.1, pinned in .ruby-version
• Bundler

bundle install
bundle exec jekyll serve

Open http://127.0.0.1:4000/.

Build

bundle exec jekyll build

The static output is written to _site/. Do not edit _site/ directly; it is generated.

Deploy

The repository remote is https://github.com/ilbsm/ilbsm.github.io.git. The expected host is GitHub Pages from the main branch because this is an organization pages repo. Confirm the Pages settings in GitHub before handoff.

No env vars are required for the Jekyll build. The publications page fetches live OpenAlex data in the browser and falls back to _data/publications.json if the API is unavailable.

Structure

_config.yml                 Site settings and Jekyll build options
_layouts/default.html       Shared page shell
_layouts/news_item.html     News article layout
_includes/head.html         Metadata, fonts, shared CSS
_includes/nav.html          Primary navigation
_includes/slideshow.html    Shared top banner
_includes/footer.html       Site footer
_includes/jump_nav.html     Reusable section jump menu
_data/                      Editable YAML/JSON content
_data/navigation.yml        Primary navigation links
_data/slideshow.yml         Shared top banner slides and labels
_data/footer.yml            Footer address and social links
_news/                      News collection items
assets/css/sulkowska.css    Shared CSS, currently grouped by page sections
assets/js/sulkowska.js      Shared behavior and page-specific initializers
assets/js/hero-knot.js      Home-page Three.js animation
assets/images/                 Images, logos, portraits, gallery media
scripts/                    Maintenance scripts

There are no Sass partials at handoff. If future work adds Sass, put partials in _sass/ and keep compiled site assets under assets/.

Editing Guide

Most content changes should happen in _data/:

• Group members: _data/group.yml
• Home sections: _data/home.yml
• Research topics: _data/topics.yml
• Funded projects: _data/research_projects.yml
• Projects and software: _data/projects.yml
• Media lists and gallery data: _data/media/*
• News summaries: _data/news.yml

Long-form news items live in _news/ and use layout: news_item.

The local publication fallback and figure metadata live in _data/publications.json and _data/publication_figures.yml. They can be rebuilt with:

python3 scripts/update_publication_figures.py

Review the generated diff before committing because the script pulls live OpenAlex and PubMed Central data.

Config Notes

• baseurl is empty for root-domain hosting.
• url is the production origin.
• The news collection outputs pages under /news/:path/.
• The Gemfile uses the github-pages gem so the default GitHub Pages action resolves the same Jekyll version as production.
• Do not commit a stale Gemfile.lock from a local Jekyll 4 install; GitHub Pages currently builds this site with Jekyll 3.10.0 through github-pages.

Ownership And Attribution

The repo history does not identify a third-party theme, upstream source URL, or license file. Treat the site code and content as lab-owned with all rights reserved until the owners add a license. Jekyll and bundled gems keep their own licenses through RubyGems.

If a reused upstream source is later confirmed, add its URL, license, and any required file headers before public handoff.

Domain And DNS

The production URL in _config.yml is https://jsulkowska.cent.uw.edu.pl.

The repo does not contain DNS ownership records, registrar access notes, or SSL renewal details. Add those to the private handoff packet, not to this public repository.

Known Issues

• Page CSS has been moved out of page templates, but assets/css/sulkowska.css is now a large monolithic stylesheet. A future pass should split it into Sass partials or clearer CSS modules.
• Page behavior has been moved into assets/js/sulkowska.js, but that file now mixes shared behavior with page-specific initializers. A future pass should split it into smaller files.
• The publications page prefers live OpenAlex data, then falls back to _data/publications.json if OpenAlex is temporarily unavailable. Refresh _data/publications.json periodically with the maintenance script.
• See docs/cleanup-audit.md for the current structural audit and proposed cleanup order.