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Atlas Analytics Lab Website

Official website for the Atlas Analytics Lab at Concordia University, Montreal. We focus on AI research in computational pathology, foundation models, and medical imaging.

🌐 Live Site: https://atlasanalyticslab.github.io
📧 Contact: mahdi.hosseini@concordia.ca
📊 Site Stats: 8 layouts · 10 includes · 3 JS modules · 10 pages · Clean codebase (Dec 2025 audit)

About

The Atlas Analytics Lab operates within Concordia University's Department of Computer Science and Software Engineering (CSSE). Dr. Mahdi S. Hosseini serves as Gina Cody Research Chair, Adjunct Professor in Pathology at McGill University, and Affiliate Member of Mila – Quebec AI Institute.

Research Areas:

  • Computational Pathology & Digital Pathology
  • Foundation Models & Vision-Language Models
  • Self-Supervised Learning & Representation Learning
  • Medical Image Analysis & Clinical AI

Affiliations:

Quick Start

Requirements

  • Ruby: 3.4.7+ (latest stable version)
  • Bundler: 2.7.2+ (gem install bundler)
  • Build Tools: GCC/Clang, Make (for native gem compilation)

Installation (macOS):

brew install ruby

Installation (Ubuntu/Debian):

sudo apt install ruby-full build-essential zlib1g-dev

Running Locally

  1. Clone the repository:

    git clone https://github.com/AtlasAnalyticsLab/AtlasAnalyticsLab.github.io.git
cd AtlasAnalyticsLab.github.io

  2. Install dependencies:

    gem install bundler
bundle install

  3. Start the development server:

    bundle exec jekyll serve --livereload

  4. Visit: http://127.0.0.1:4000

Changes to files are automatically reloaded. Restart the server after editing _config.yml or plugin files.

Useful Commands

# Production build
bundle exec jekyll build

# Clean cache and generated files
bundle exec jekyll clean

# Check configuration
bundle exec jekyll doctor

Updating Content

News & Announcements

File: _data/news.yml

Add new items to the top of the file. Supports Markdown formatting:

- date: November 27, 2025
  headline: "🎓 **New achievement!** [Link to details](/path)"

Team Members

Files:

  • _data/principal_investigator.yml - PI information
  • _data/postdocs.yml - Postdoctoral fellows
  • _data/phd_students.yml - PhD students
  • _data/masters.yml - Master's students
  • _data/team_collaborators.yml - External collaborators
  • _data/alumni_members.yml - Former members

Photos: Place headshots in images/teampic/ (use JPG or PNG)

Publications

File: _data/publications.yml

Add new publications to the top of the file:

- title: "Your Paper Title"
  authors: "Author1, Author2, Author3"
  venue: "Conference/Journal Name"
  year: 2025
  link:
    url: "https://arxiv.org/abs/..."
    display: "arXiv preprint"
  image: your-image.png  # Place in images/pubpic/
  highlight: 1  # Set to 1 to feature in "Group Highlights"
  description: "Brief description of the paper"

Images: Place publication thumbnails in images/pubpic/

Job Openings

File: _pages/openings.md

Edit the markdown file directly. Add position announcement PDFs to assets/openings/.

Homepage Carousel

Directory: images/homepic/

Simply add images to this directory - they automatically appear in the carousel. No configuration needed.

Supported formats: JPG, JPEG, PNG, GIF, WebP

Lab Life Gallery

Directory: images/picpic/
Layout: CSS Grid Masonry (auto-reordering for tight packing)

Add photos of lab events, conferences, and activities. They automatically appear on the /gallery/ page.

Features:

  • Automatic image loading - Just drop images in images/picpic/
  • Masonry layout - Images automatically reorder to minimize gaps
  • Responsive grid - 1 column (mobile) → 2 (tablet) → 3 (desktop) → 4 (large screens)
  • Respects layout_wide setting - Adapts to site-wide layout configuration
  • Supported formats: JPG, JPEG, PNG

How it works:

  • Images sorted by filename in reverse order (newest first)
  • CSS Grid masonry with JavaScript fallback for browser compatibility
  • No code changes needed when adding/removing photos

Project Structure

├── _config.yml           # Site configuration (includes layout_wide setting)
├── _data/                # YAML data files (news, team, publications)
├── _includes/            # Reusable components (header, footer, etc.)
├── _layouts/             # Page templates
├── _pages/               # Website pages (home, team, publications, etc.)
├── _plugins/             # Custom Jekyll plugins
├── _sass/                # SCSS stylesheets
├── assets/               # Static files (PDFs, documents)
├── css/                  # Compiled stylesheets
├── images/               # All images organized by type
│   ├── homepic/         # Homepage carousel
│   ├── teampic/         # Team member photos
│   ├── pubpic/          # Publication thumbnails
│   ├── logopic/         # Organization logos
│   └── picpic/          # Lab activities gallery
├── js/                   # JavaScript files
└── _site/                # Generated site (auto-generated, don't edit)

Layout Configuration

The website supports two layout modes configured in _config.yml:

  • layout_wide: true - Full viewport width with responsive padding (default)
  • layout_wide: false - Fixed 1000px max-width, centered layout

This setting affects the entire site including header, footer, and content areas.

Page Navigation

Page URL Edit
Home / _pages/home.md
Team /team _pages/team.md + _data/ files
Publications /publications _data/publications.yml
Openings /openings _pages/openings.md
Funding /funding _pages/funding.md
Contact /contact _pages/contact.md
All News /allnews _data/news.yml
Gallery /gallery _pages/gallery.md + images/picpic/

Deployment

The site automatically deploys via GitHub Actions when you push to the main branch.

Deployment Workflow:

  1. Push changes to main branch
  2. GitHub Actions runs .github/workflows/deploy.yml
  3. Site builds with JEKYLL_ENV=production using official GitHub Pages actions
  4. Build artifact uploaded and deployed to GitHub Pages
  5. Site updates in 1-2 minutes

GitHub Actions Workflow:

  • Uses actions/configure-pages@v4 for Pages configuration
  • Uses actions/upload-pages-artifact@v3 for build artifact
  • Uses actions/deploy-pages@v4 for deployment
  • Ruby 3.4.7 with bundler cache for faster builds

Manual Deployment:

bundle exec jekyll build
yes | bash bin/deploy --src main --deploy gh-pages

Architecture & Technology

Core Technologies

Static Site Generator:

  • Jekyll 4.4.1 (Ruby-based)
  • Liquid templating engine
  • Kramdown Markdown processor

Frontend Framework:

  • Bootstrap 5 (Lumen theme)
  • Custom SCSS modules (5 partials)
  • Responsive design (5 breakpoints: 576px, 768px, 992px, 1200px, 1400px)

JavaScript Modules (3 files):

  1. theme-toggle.js - Three-state theme switcher (light/dark/auto)
  2. gallery-masonry.js - CSS Grid masonry fallback
  3. external-links.js - Auto-opens external links in new tabs

Layout System:

  • 8 layout templates (_layouts/)
  • 10 reusable components (_includes/)
  • Layout-wide mode: configurable full-width or fixed 1000px

File Structure Overview

├── _layouts/          # 8 page layouts (default, homelay, textlay, etc.)
├── _includes/         # 10 reusable components (header, footer, etc.)
├── _pages/            # 10 content pages (Markdown)
├── _data/             # 8 YAML data files (team, publications, news)
├── _sass/             # 5 SCSS modules (variables, components, themes, etc.)
├── _plugins/          # 1 Ruby plugin (BibTeX filter)
├── css/               # Main stylesheet entry point
├── js/                # 3 JavaScript modules
├── images/            # 5 subdirectories (team, publications, gallery, etc.)
└── assets/            # Additional resources (PDFs, documents)

Code Quality:

  • Comprehensive inline documentation (all files)
  • Standardized comment headers
  • Zero unused/redundant code (Dec 2025 audit)
  • Clean, maintainable codebase

Support & Maintenance

Troubleshooting

Problem: Gem compilation fails
Solution: Install missing OS libraries:

# macOS
brew install libffi zlib openssl

# Ubuntu/Debian
sudo apt install libffi-dev zlib1g-dev libssl-dev

Problem: Changes don't appear
Solution: Clear cache and rebuild:

bundle exec jekyll clean
bundle exec jekyll serve

Problem: Broken links or configuration issues
Solution: Run diagnostics:

bundle exec jekyll doctor

Updates

Pull latest changes regularly:

git pull origin main
bundle install

Security Features

  • ✅ Crawler Protection: robots.txt controls search engine access
  • ✅ Custom 404 Page: User-friendly error handling with navigation
  • ✅ DDoS Protection: GitHub Pages + Cloudflare CDN
  • ✅ Security Headers: Content security and XSS protection

Technology Stack

  • Static Site Generator: Jekyll 4.4.1
  • Hosting: GitHub Pages (automatic deployment)
  • Frontend Framework: Bootstrap 5 (Lumen theme via jsDelivr CDN)
  • Template Engine: Liquid (Jekyll's templating system)
  • Styling: SCSS/SASS with 5 modular partials
  • JavaScript: 3 vanilla JS modules (theme switcher, gallery masonry, external links)
  • Theme: Light/Dark/Auto mode with CSS custom properties
  • Ruby Plugin: 1 custom Liquid filter (BibTeX keyword hiding)

Build Stats:

  • 8 layouts, 10 includes, 10 pages
  • 8 YAML data files
  • 5+ image directories with auto-loading
  • Clean codebase (0 unused files as of Dec 2025)

Contributing

For lab members and collaborators, see DEVELOPMENT.md for detailed development documentation including:

  • Git workflow and branching strategy
  • Detailed file structure and architecture
  • Comment standardization guidelines
  • Development history and changelog
  • Code cleanup reports
  • Maintenance tasks and verification commands
  • URL management and configuration

Quick member instructions: .github/Instructions_members.md

License & Attribution

License: MIT License

Original Design: Allan Lab
Adapted From: Uppsala Security Lab & Cloud (USLC)
Customized For: Atlas Analytics Lab, Concordia University

Development: This website was developed with assistance from AI tools for code generation, documentation, and maintenance.

Contact

Dr. Mahdi S. Hosseini
Assistant Professor Department of Computer Science and Software Engineering
Concordia University, Montreal, QC, Canada

📧 Email: mahdi.hosseini@concordia.ca
🔗 Website: https://atlasanalyticslab.github.io
💻 GitHub: https://github.com/AtlasAnalyticsLab/AtlasAnalyticsLab.github.io

Last Updated: December 2, 2025

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