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add jekyll site
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‎.github/workflows/deploy-jekyll.yml‎

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name: Deploy Jekyll site to GitHub Pages
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on:
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push:
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branches: [ main ]
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paths: [ 'jekyll-site/**' ]
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pull_request:
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branches: [ main ]
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paths: [ 'jekyll-site/**' ]
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workflow_dispatch:
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# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
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permissions:
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contents: read
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pages: write
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id-token: write
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# Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued.
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# However, do NOT cancel in-progress runs as we want to allow these production deployments to complete.
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concurrency:
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group: "pages"
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cancel-in-progress: false
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jobs:
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build:
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runs-on: ubuntu-latest
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steps:
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- name: Checkout
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uses: actions/checkout@v4
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- name: Setup Ruby
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uses: ruby/setup-ruby@v1
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with:
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ruby-version: '3.1'
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bundler-cache: true
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working-directory: ./jekyll-site
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- name: Setup Pages
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id: pages
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uses: actions/configure-pages@v3
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- name: Build with Jekyll
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run: |
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cd jekyll-site
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bundle exec jekyll build --baseurl "${{ steps.pages.outputs.base_path }}"
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env:
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JEKYLL_ENV: production
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- name: Upload artifact
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uses: actions/upload-pages-artifact@v2
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with:
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path: ./jekyll-site/_site
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# Deployment job
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deploy:
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environment:
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name: github-pages
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url: ${{ steps.deployment.outputs.page_url }}
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runs-on: ubuntu-latest
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needs: build
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if: github.ref == 'refs/heads/main' && github.event_name != 'pull_request'
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steps:
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- name: Deploy to GitHub Pages
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id: deployment
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uses: actions/deploy-pages@v2

‎jekyll-site/Gemfile‎

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source "https://rubygems.org"
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# Jekyll and dependencies
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gem "jekyll", "~> 4.3.0"
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gem "webrick", "~> 1.8"
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# Theme
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gem "just-the-docs", "~> 0.7.0"
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# Plugins
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group :jekyll_plugins do
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gem "jekyll-feed", "~> 0.12"
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gem "jekyll-sitemap"
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gem "jekyll-seo-tag"
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gem "jekyll-remote-theme"
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end
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# Windows and JRuby does not include zoneinfo files, so bundle the tzinfo-data gem
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# and associated library.
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platforms :mingw, :x64_mingw, :mswin, :jruby do
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gem "tzinfo", ">= 1", "< 3"
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gem "tzinfo-data"
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end
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# Performance-booster for watching directories on Windows
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gem "wdm", "~> 0.1.1", :platforms => [:mingw, :x64_mingw, :mswin]
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# Lock `http_parser.rb` gem to `v0.6.x` on JRuby builds since newer versions of the gem
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# do not have a Java counterpart.
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gem "http_parser.rb", "~> 0.6.0", :platforms => [:jruby]

‎jekyll-site/README.md‎

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# MIMIC Jekyll Website
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This is the Jekyll version of the MIMIC website, built using the [Just the Docs](https://just-the-docs.github.io/just-the-docs/) theme.
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## Local Development
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### Prerequisites
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- Ruby 3.1 or higher
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- Bundler gem
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### Setup
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1. Install dependencies:
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```bash
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cd jekyll-site
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bundle install
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```
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2. Run the development server:
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```bash
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bundle exec jekyll serve
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```
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3. Open your browser to `http://localhost:4000`
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### Building for Production
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```bash
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bundle exec jekyll build
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```
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The built site will be in the `_site` directory.
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## Site Structure
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```
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jekyll-site/
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├── _config.yml # Jekyll configuration
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├── _includes/ # Reusable content snippets
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│ └── database/ # Database column definitions
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├── _docs/ # Main documentation
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├── _tutorials/ # Step-by-step guides
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├── _concepts/ # Conceptual explanations
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├── _faqs/ # Frequently asked questions
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├── assets/ # Images, CSS, JS
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└── index.md # Homepage
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```
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## Key Features
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### Collections
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- **docs**: Main documentation organized by MIMIC version and module
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- **tutorials**: Step-by-step guides for common tasks
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- **concepts**: Explanatory content about database design and analysis
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- **faqs**: Common questions and answers
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### Includes System
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Reusable content snippets for database column definitions:
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```liquid
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{% include database/subject_id.md %}
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```
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### Navigation
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Hierarchical navigation with automatic menu generation based on front matter:
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```yaml
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---
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title: "Page Title"
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parent: "Parent Page"
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nav_order: 1
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---
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```
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## Content Guidelines
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### Front Matter
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All pages should include appropriate front matter:
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```yaml
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---
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title: "Page Title"
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layout: default
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parent: "Parent Page" # if applicable
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nav_order: 1 # for ordering in navigation
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permalink: /custom-url/ # if different from default
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description: "Page description for SEO"
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---
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```
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### Using Includes
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For database column definitions, use the includes system:
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```liquid
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{% include database/subject_id.md %}
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{% include database/hadm_id.md %}
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```
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### Code Blocks
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Use fenced code blocks with language specification:
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```sql
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SELECT subject_id, COUNT(*)
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FROM patients
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GROUP BY subject_id;
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```
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### Callouts
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Use Just the Docs callouts for important information:
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```markdown
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{: .note }
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> This is a note callout.
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{: .important }
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> This is an important callout.
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{: .highlight }
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> This is a highlight callout.
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```
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## Deployment
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The site is automatically deployed via GitHub Actions when changes are pushed to the main branch. See `.github/workflows/deploy-jekyll.yml` for the deployment configuration.
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## Theme Customization
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The site uses the Just the Docs theme. For customization options, see the [theme documentation](https://just-the-docs.github.io/just-the-docs/).
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## Migration from Hugo
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This Jekyll site replaces the previous Hugo-based website. Key differences:
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- **Includes**: `{{% include "file.md" %}}` → `{% include file.md %}`
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- **Front matter**: TOML → YAML
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- **Navigation**: Automatic based on front matter
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- **Collections**: Organized content types
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## Contributing
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1. Make changes to content files
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2. Test locally with `bundle exec jekyll serve`
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3. Submit pull request
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4. Changes will be automatically deployed after merge

‎jekyll-site/_concepts/index.md‎

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---
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title: "Concepts"
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layout: default
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nav_order: 4
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has_children: true
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permalink: /concepts/
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---
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# MIMIC Concepts
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Understanding the fundamental concepts behind MIMIC data organization, design principles, and analysis approaches.
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## Database Design Concepts
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Learn about the underlying structure:
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- **[Schema Overview](/concepts/schema-overview/)** - How MIMIC is organized
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- **[Data Provenance](/concepts/data-provenance/)** - Understanding data sources
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- **[Identifier Systems](/concepts/identifiers/)** - Patient, admission, and stay IDs
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- **[Temporal Organization](/concepts/time-concepts/)** - How time is handled
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## Data Integration Concepts
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Connect data across the database:
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- **[Cross-Module Linking](/concepts/cross-module-linking/)** - Join data from different modules
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- **[Patient Trajectories](/concepts/patient-trajectories/)** - Follow patients through care
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- **[Temporal Alignment](/concepts/temporal-alignment/)** - Synchronize different data streams
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## Data Quality Concepts
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Understand data characteristics:
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- **[Missingness Patterns](/concepts/missingness/)** - Understanding missing data
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- **[Data Validation](/concepts/validation/)** - Quality checks and validation
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- **[Known Limitations](/concepts/limitations/)** - Understanding data constraints
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## Privacy and Ethics
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Important considerations for research:
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- **[De-identification Process](/concepts/deidentification/)** - How privacy is protected
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- **[Data Use Agreements](/concepts/data-agreements/)** - Legal and ethical requirements
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- **[Responsible Use](/concepts/responsible-use/)** - Best practices for research
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## Analysis Concepts
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Fundamental analysis approaches:
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- **[Cohort Definition](/concepts/cohorts/)** - Defining patient populations
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- **[Outcome Measurement](/concepts/outcomes/)** - Measuring clinical outcomes
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- **[Statistical Considerations](/concepts/statistics/)** - Important statistical concepts
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- **[Reproducible Research](/concepts/reproducibility/)** - Ensuring reproducible results
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---
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{: .highlight }
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> These concepts provide the foundation for effective MIMIC research. Understanding these principles will help you design better studies and avoid common pitfalls.

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