Functional Genomics Lab Website

Static academic website for Yuanqing Feng’s lab, built with Jekyll and deployed via GitHub Pages.

Live site: <fenglab-cpu.github.io>

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1. Tech Stack

• Jekyll – static site generator.
• HTML / CSS – custom page layout and styling.
• Font Awesome – icons in header/footer.
• GitHub Pages – hosting.

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2. Run the Site Locally

Prerequisites: Ruby, Bundler, Git.

1. Clone the repo

   git clone https://github.com/fenglab-cpu/fenglab-cpu.github.io/.git
   cd fenglab-cpu.github.io

2. Install dependencies

   bundle install

3. Serve the site

   bundle exec jekyll serve

4. Open in browser
   • Visit http://localhost:4000

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3. Content Editing Cheat Sheet

This section covers the content that changes most often: People, News, and Publications.

3.1 People Page – people.md

Current lab members

• Cards live under the <!-- Current Lab Members --> section inside:

  <div class="people-grid">
      ... person-card blocks ...
  </div>

• To add a member, copy an existing <div class="person-card">...</div> block and update the fields:

  <div class="person-card">
      <div class="person-photo">
          <img src="/assets/images/alice.jpg" alt="Alice Zhang"
               style="width: 100%; height: 100%; object-fit: cover;">
      </div>
      <div class="person-info">
          <div class="person-name">Alice Zhang</div>
          <div class="person-title">PhD Student</div>
          <div class="person-contact">
              <a href="mailto:alice@example.edu">alice@example.edu</a>
          </div>
      </div>
  </div>

• Photos:
  • Save images to assets/images/ (e.g. assets/images/alice.jpg).
  • Use <img src="/assets/images/..."> and set a descriptive alt attribute.
  • Or keep using emoji avatars: <div class="person-photo">👩‍🔬</div>.

Lab alumni

• In people.md, scroll to the <!-- Lab Alumni --> section and the <tbody> of .alumni-table.
• Add a new row:

  <tr>
      <td><strong>Jane Doe</strong></td>
      <td>PhD Student</td>
      <td class="year-cell">2024</td>
      <td class="current-cell">Postdoc, XYZ University</td>
  </tr>

Delete / rename people

• Delete a member: remove the entire <div class="person-card">...</div> block.
• Delete an alumni: remove the corresponding <tr>...</tr> row.
• Rename or update roles/contact: edit text inside .person-name, .person-title, and the email link.
  The grid layout will adjust automatically.

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3.2 News – news.md

News items are stored in the front-matter YAML list under news_items: at the top of news.md.

Example entry:

- date: "FEB 2024"
  title: "Nature Genetics Publication"
  excerpt: "Short description of the news."
  link: "https://example.com/paper-or-article"   # optional
  pmid: "12345678"                               # optional
  category: "publication"                        # publication | award | position | presentation

• Add news
  • Add a new - block at the top of news_items: (latest first).
  • Choose category from publication, award, position, presentation to control the badge color.
  • link/pmid are optional.
• Edit / delete news
  • Edit fields in-place to rename/update.
  • To delete, remove the entire YAML block from - date: through category: ....
• This list powers:
  • The /news/ page cards, and
  • The homepage hero “What’s New” ticker.

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3.3 Publications – publications.md

The Publications page is grouped by year and has a year filter.

Year headings

• Each year section starts with:

  <h2 class="pub-year-heading" data-year="2024">2024</h2>

• For a new year (e.g. 2025), add a similar heading with data-year="2025" and text 2025.

Publication cards

• Each publication is a .publication-item with a data-year attribute:

  <div class="publication-item fade-in" data-year="2024">
      <div class="pub-figure">
          <img src="../assets/pub_images/2025_newpaper_cover.jpg"
               alt="Cover or schematic for the paper"
               style="width: 100%; height: auto; object-fit: contain;">
      </div>
      <div class="pub-content">
          <div class="pub-title">
              <a href="https://doi.org/10.1234/example.doi">Full paper title goes here</a>
          </div>
          <div class="pub-authors">
              <span class="author-highlight">Feng Y</span>, Lastname A, Lastname B, ...
          </div>
          <div class="pub-venue">
              <em>Journal Name</em>. 2025; volume(issue):pages.
          </div>
          <div class="pub-links">
              PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/12345678/">12345678</a> |
              DOI: <a href="https://doi.org/10.1234/example.doi">10.1234/example.doi</a>
          </div>
      </div>
  </div>

Images for publications

• Store images in assets/pub_images/ (e.g. assets/pub_images/2025_newpaper_cover.jpg).
• Within publications.md, reference them as src="../assets/pub_images/..." (note the ..).
• Use clear alt text (e.g. “Nature Genetics cover showing skin pigmentation diversity in Africans”).

Year filter buttons

• Filter buttons at the top are inside <div class="pub-filter-bar">:

  <button class="pub-filter-btn" data-year-filter="2025">2025</button>

• When adding a new year:
  • Add a matching button with data-year-filter="YYYY".
  • Ensure each publication for that year has data-year="YYYY" and a matching year heading.

Delete / move publications

• Delete: remove the whole <div class="publication-item ...">...</div> block.
• Edit: change title/authors/journal/links in .pub-title, .pub-authors, .pub-venue, .pub-links.
• Move to another year:
  • Change data-year="YYYY" on the block.
  • Move it under the corresponding year heading.
  • Add/update the filter button if this is a new year.

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4. Helper Script – tools/new_snippet.py

This script directly edits the site files to add new entries.

Run from the repo root:

python tools/new_snippet.py

You’ll be asked for a type:

• news
  • Updates news.md.
  • Asks for date, title, excerpt, optional link/PMID, and category.
  • Inserts a new YAML block at the top of news_items: so it becomes the latest news.
• publication
  • Updates publications.md.
  • Asks for year, title, authors, journal, citation, DOI/PMID, and optional image file name.
  • Ensures a year filter button exists for that year.
  • Inserts a new .publication-item under the correct year heading; if the year doesn’t exist yet, it creates the heading for you.
• person
  • Updates people.md.
  • Asks for name, role/title, optional email, and optional image file (or emoji avatar).
  • Inserts a new person-card into the Current Members people-grid.

After each operation the script prints the exact block it inserted, so you can review it before committing.

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5. Git Workflow

Typical workflow after editing content or using the helper script:

1. Check status

   git status

2. Stage changes

   # Add specific files
   git add README.md news.md publications.md people.md
   # or add everything
   git add .

3. Commit and push

   git commit -m "Update content"
   git pull --rebase origin main   # optional but recommended
   git push origin main

Quick one-liner:

git add . && git commit -m "update site content" && git pull --rebase origin main && git push origin main

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6. Contributing, License, Contact

• Contributing – Suggestions and pull requests are welcome.
• License – This project uses the MIT License (see LICENSE).
• Contact – For questions, email:
  Fengyuanqing2010@gmail.com

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