feat: populate the template with Park Lab information and links

.github/workflows/deploy.yml

@@ -0,0 +1,32 @@
+name: Deploy Jekyll site to GitHub Pages
+
+on:
+  push:
+    branches: []  # (currently disabled) Trigger on pushes to the source branch
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v2
+
+      - name: Set up Ruby
+        uses: ruby/setup-ruby@v1
+        with:
+          ruby-version: '3.1.3' # Use your required Ruby version
+
+      - name: Install dependencies
+        run: |
+          gem install bundler
+          bundle install
+
+      - name: Build Jekyll site
+        run: bundle exec jekyll build
+
+      - name: Deploy to GitHub Pages
+        uses: peaceiris/actions-gh-pages@v3
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./_site

Gemfile

@@ -1,5 +1,7 @@
 source "https://rubygems.org"
 
+ruby '3.1.3'
+
 # gem "webrick"
 
 gem 'rexml', '~> 3.2', '>= 3.2.4'

_config.yml

@@ -13,7 +13,7 @@
 # you will see them accessed via {{ site.title }}, {{ site.email }}, and so on.
 # You can create any custom variable you would like, and they will be accessible
 # in the templates via {{ site.myvariable }}.
-title: Site title
+title: PARK LAB
 tagline: Site tagline
 email: [email protected]
 description: >- # this means to ignore newlines until "baseurl:"
@@ -23,15 +23,14 @@ url: "http://example.com" # the base hostname & protocol for your site, e.g. htt
 permalink: pretty
 twitter_username: twitter_username
 github_username:  github_username
-favicon: favicon.ico
+favicon: favicon.svg
 author: Author
 twitter:
   username: twitter_username
   card: summary
 
 # Build settings
 markdown: kramdown
-#theme: minima
 theme: bulma-clean-theme
 plugins:
   - jekyll-feed
@@ -54,8 +53,13 @@ paginate: 10
 paginate_path: "/news/page:num"
 
 collections:
-  products:
+  people:
     output: true
-    layout: product
+    layout: person
     image: https://via.placeholder.com/800x600
     show_sidebar: false
+  supplements:
+    output: true
+    layout: supplement
+    image: https://via.placeholder.com/800x600
+    show_sidebar: false

_data/carousel-items.yml

@@ -0,0 +1,160 @@
+- caption:
+    header: A New Tool for Mutational Signature Analysis
+    nested_link: https://www.nature.com/articles/s41588-024-01659-0
+    body: Hu and Doga describe MuSiCal (Mutational Signature Calculator) for analysis
+      of somatic mutations (Nat Genetics 2024)
+  image: carousel-images/musical.png
+  link: https://www.nature.com/articles/s41588-024-01659-0
+- caption:
+    header: Tissue-specific proliferative effects underlie tumor CNA patterns
+    nested_link: https://www.nature.com/articles/s41588-024-01665-2
+    body: Chromosome evolution screens using single cell genome sequencing (Emma/Jake,
+      Nat Genetics, 2024)
+  image: carousel-images/chromosome_evolution.png
+  link: https://www.nature.com/articles/s41588-024-01665-2
+- caption:
+    header: Chromoscope for SV analysis
+    nested_link: https://www.nature.com/articles/s41592-023-02056-x
+    body: Interactive multiscale visualization for structural variation by Sehi and Dominik
+      (Nat Methods, 2023)
+  image: carousel-images/chromoscope.png
+  link: https://www.nature.com/articles/s41592-023-02056-x
+- caption:
+    header: Widespread emergence of mosaic CNVs in normal human tissues
+    nested_link: https://www.nature.com/articles/s41588-023-01537-1
+    body: A pan-tissue survey of mosaic chromosomal alterations in 948 individuals (Teng/Kharchenko
+      Lab, Nat Genetics, 2023)
+  image: carousel-images/mcnas.png
+  link: https://www.nature.com/articles/s41588-023-01537-1
+- caption:
+    header: A new mechanism for breast cancers
+    nested_link: https://rdcu.be/ddh89
+    body: Jake discovers Translocation-Bridge Amplification that generates focal amplifications
+      (Nature, 2023)
+  image: carousel-images/tbamplificationfig2.jpg
+  link: https://rdcu.be/ddh89
+- caption:
+    header: Single-cell genome sequencing of human neurons
+    nested_link: https://www.nature.com/articles/s41588-022-01180-2
+    body: Joe finds enrichment of somatic SNVs and indels in regulatory elements (Nat
+      Genetics, 2022)
+  image: carousel-images/thumbnail_image001.png
+  link: https://www.nature.com/articles/s41588-022-01180-2
+- caption:
+    header: Computational analysis of Cancer Genome Sequencing Data
+    nested_link: https://rdcu.be/cCQki
+    body: Isidro et al discuss recent advances in cancer genome analysis (Nature Reviews
+      Genetics, 2022)
+  image: carousel-images/slide-NRG_figure1.png
+  link: https://rdcu.be/cCQki
+- caption:
+    header: Landmarks of embryonic development inscribed in somatic mutations
+    nested_link: https://science.sciencemag.org/content/371/6535/1249
+    body: Mosaic variants in multiple organs resolve post-zygotic lineages (Science,
+      2021)
+  image: carousel-images/untitled-1-01.png
+  link: https://science.sciencemag.org/content/371/6535/1249
+- caption:
+    header: Origins/genetic interactions of KRAS mutations are allele- and tissue-specific
+    nested_link: https://www.nature.com/articles/s41467-021-22125-z
+    body: Analysis of KRAS mutations at the allele level using >13K samples (Nat Comm,
+      2021)
+  image: carousel-images/untitled-2.png
+  link: https://www.nature.com/articles/s41467-021-22125-z
+- caption:
+    header: Comprehensive analysis of chromothripsis using whole-genome data
+    nested_link: https://www.nature.com/articles/s41588-019-0576-7
+    body: Analysis of >2500 cancer genomes shows that chromothripsis events are prevalent
+      across multiple tumor types (Nat Genetics, 2020)
+  image: carousel-images/screenshot_2020-03-08_20.28.59.png
+  link: https://www.nature.com/articles/s41588-019-0576-7
+- caption:
+    header: Detecting mosaic mutations using a ML algorithm (MosaicForecast)
+    nested_link: https://www.nature.com/articles/s41587-019-0368-8
+    body: Yanmei et al develop MosaicForecast, a machine learning-based variant caller
+      for mosaic mutations (Nat Biotech, 2020)
+  image: carousel-images/image.png
+  link: https://www.nature.com/articles/s41587-019-0368-8
+- caption:
+    header: Detecting the mutational signature of homologous recombination deficiency
+    nested_link: https://www.nature.com/articles/s41588-019-0390-2
+    body: Doga et al develop SigMA to identify patients who may benefit from PARP inhibitor
+      treatment (Nat Genetics, 2019)
+  image: carousel-images/gulhan_2019.png
+  link: https://www.nature.com/articles/s41588-019-0390-2
+- caption:
+    header: LiRA identifies mutations in scDNA-seq data
+    nested_link: https://rdcu.be/brEMK
+    body: Craig develops a method for detection of somatic variants in single cells (Nat
+      Genetics, 2019)
+  image: carousel-images/bohrson_NG_fig1.jpg
+  link: https://rdcu.be/brEMK
+- caption:
+    header: 'Review: Detecting somatic mutations in normal cells'
+    nested_link: https://www.cell.com/trends/genetics/fulltext/S0168-9525(18)30073-8
+    body: Yanmei, Heather, Joe, and Peter discuss issues in detection of somatic variants
+      (Trends in Genetics, 2018)
+  image: carousel-images/figure_1.jpg
+  link: https://www.cell.com/trends/genetics/fulltext/S0168-9525(18)30073-8
+- caption:
+    header: Aging & neurodegeneration assoc. with increased mutations in neurons
+    nested_link: httbody://science.sciencemag.org/content/early/2017/12/06/science.aao4426
+    body: Analysis of the largest single cell WGS dataset to date (Science, 2018)
+  image: carousel-images/untitled.001.jpeg
+  link: httbody://science.sciencemag.org/content/early/2017/12/06/science.aao4426
+- caption:
+    header: 'PaSD-qc: quality control for single cell whole-genome sequencing data'
+    nested_link: https://academic-oup-com.ezp-prod1.hul.harvard.edu/nar/advance-article/doi/10.1093/nar/gkx1195/4658833
+    body: Sherman et al. (Nucleic Acids Research, 2017) develop a QC method based on
+      power density estimation
+  image: carousel-images/untitled.001_01.jpeg
+  link: https://academic-oup-com.ezp-prod1.hul.harvard.edu/nar/advance-article/doi/10.1093/nar/gkx1195/4658833
+- caption:
+    header: Analysis of microsatellite instability identifies patients that may benefit
+      from immunotherapy
+    nested_link: httbody://www.nature.com/articles/ncomms15180
+    body: Cortes-Ciriano et al,Nat Comm, June, 2017
+  image: carousel-images/isidro_figure.png
+  link: httbody://www.nature.com/articles/ncomms15180
+- caption:
+    header: Impact of mutation in a chromatin remodeling protein complex
+    nested_link: https://hms.harvard.edu/news/agent-mischief
+    body: Three papers from a collaboration with the Roberts lab inNature GeneticsandNature
+      Communications
+  image: carousel-images/smarcb1-deficient_g401_cell_line_before_and_after_smarcb1_re-expression.jpg
+  link: https://hms.harvard.edu/news/agent-mischief
+- caption:
+    header: Detecting structural variants from exome data
+    nested_link: null
+    body: Yang et al (AJHG, 2016) analyze nearly 5000 cancer exomes and identify thousands
+      of rearrangements.
+  image: carousel-images/slide1.jpg
+  link: null
+- caption:
+    header: Sequencing single neurons
+    nested_link: httbody://science.sciencemag.org/content/350/6256/94.short
+    body: Lineage tracing of neurons using mutational analysis of single cell whole-genome
+      sequencing data (Science, 2015; cover)
+  image: carousel-images/phylogenycircle.jpg
+  link: httbody://science.sciencemag.org/content/350/6256/94.short
+- caption:
+    header: 4D Nucleome project to understand higher-order nuclear organization
+    nested_link: httbody://4dn-dcic.hms.harvard.edu
+    body: The Park lab, along with the Kharchenko and Gehlenborg labs at DBMI, are leading
+      the Data Coordination and Integration Center
+  image: carousel-images/4C_interactome.png
+  link: httbody://4dn-dcic.hms.harvard.edu
+- caption:
+    header: Cell lineage analysis in human brain using endogenous retroelements
+    nested_link: httbody://www.cell.com/neuron/abstract/S0896-6273(14)01137-4
+    body: Gilad Evrony, Alice Lee, et al. inNeuron, 2015 (Collaboration with the Chris
+      Walsh lab)
+  image: carousel-images/brain-teinsertion-new.jpg
+  link: httbody://www.cell.com/neuron/abstract/S0896-6273(14)01137-4
+- caption:
+    header: Comparative analysis of metazoan chromatin organization
+    nested_link: httbody://www.nature.com/nature/journal/v512/n7515/full/nature13415.html
+    body: A cross-species analysis from the ENCODE and modENCODE consortia, led by Park
+      lab members,Nature, 2014
+  image: carousel-images/front_page.jpg
+  link: httbody://www.nature.com/nature/journal/v512/n7515/full/nature13415.html

_data/categories-order.yml

@@ -0,0 +1,12 @@
+- "Principal Investigator"
+- "Research Scientists"
+- "Staff"
+- "Postdoctoral Fellows"
+- "Students"
+- "Staff Scientists and Software Engineers"
+- "Alumni: Research Scientists"
+- "Alumni: Staff"
+- "Alumni: Postdoctoral Fellows"
+- "Alumni: Students"
+- "Alumni: Staff Scientists and Software Engineers"
+- "Alumni: Visiting Scholars"

_data/navigation.yml

@@ -11,8 +11,8 @@
 - name: Software
   link: /software/
 - name: Positions
-  link: /jobs/
-- name: Galleries
-  link: /galleries/
+  link: /positions/
 - name: Contact
-  link: /contact/
+  link: /contact/
+- name: Gallery
+  link: /gallery/

_includes/carousel.html

@@ -0,0 +1,33 @@
+<div class="carousel-container">
+    <div class="carousel">
+        <ul>
+            {% for item in site.data.carousel-items %}
+            {% assign index = forloop.index0 %}
+                <li class="carousel-item{% if index == 0 %} active{% endif %}" data-carousel-item="{{ index }}">
+                    <div class="content">
+                        <div class="image">
+                            <img src="/img/{{ item.image }}" alt="{{ item.caption.header }}">
+                        </div>
+                        <div class="text">
+                            <a href="{{ item.link }}" target="_blank"><h2>{{ item.caption.header }}</h2></a>
+                            <p>{{ item.caption.body }}</p>
+                        </div>
+                    </div>
+                </li>
+            {% endfor %}
+        </ul>
+        <div class="carousel-indicators">
+            <button class="carousel-control prev">
+                <img src="/img/chevron-left.svg" />
+            </button>
+            {% for item in site.data.carousel-items %}
+            {% assign index = forloop.index0 %}
+            <span class="indicator{% if index == 0 %} active{% endif %}" data-carousel-indicator="{{ index }}"></span>
+            {% endfor %}
+            <button class="carousel-control next">
+                <img src="/img/chevron-left.svg" />
+            </button>
+        </div>
+
+    </div>
+</div>

_includes/footer-scripts.html

@@ -1,5 +1,5 @@
 <!-- footer scripts -->
-<div style="background-color:#A41034">
+<div class="footer">
         <div class="content is-normal has-text-centered">
             <p style="color:white;padding-top:20px;padding-bottom:20px;"><a href="" style="color:white"><b>Lab title</b></a>
                 &nbsp;&middot;&nbsp; <a href="#" style="color:white"><b>Lab Description</b></a>

_includes/footer.html

@@ -1,16 +1,3 @@
 <footer class="footer">
-    <div class="container">
-
-        {% if site.footer_menu %}
-        <div class="columns is-multiline">
-            {% for item in site.data[site.footer_menu] %}
-            <div class="column has-text-centered">
-                <div>
-                    <a href="{{ item.link | prepend: site.baseurl }}" class="link">{{ item.name }}</a>
-                </div>
-            </div>
-            {% endfor %}
-        </div>
-        {% endif %}
-    </div>
+    <span class="footer-text"><b>Park Lab</b>, Department of Biomedical Informatics, Harvard Medical School, 10 Shattuck St, 3rd Floor, Boston, MA 02115</span>
 </footer>

_includes/head.html

@@ -1,10 +1,12 @@
 <head>
     <meta charset="utf-8">
     <meta name="viewport" content="width=device-width, initial-scale=1">
-    <title>{{ page.title }} - {{ site.title }}</title>
+    <title>{{ page.title }} | Park Lab | Computational Genomics | Harvard</title>
     <link rel="stylesheet" href="{{ site.baseurl }}/assets/css/app.css">
-    <link rel="shortcut icon" type="image/png"
-          {% if site.favicon %} href="{{ site.favicon | prepend: site.baseurl }}" {% else %} href="{{ site.baseurl }}/favicon.png" {% endif %}
+    <link rel="shortcut icon" type="image/png" href="/img/favicon.svg" />
+    <link
+        href="https://fonts.googleapis.com/css2?family=Inter:wght@400;500;600;700&family=Montserrat:wght@800&display=swap"
+        rel="stylesheet"
     />
     <script defer src="https://use.fontawesome.com/releases/v5.3.1/js/all.js"></script>
     {% seo %}

_includes/header.html

@@ -12,21 +12,27 @@
             </a>
         </div>
         <div class="navbar-menu" id="navMenu">
-            <div class="navbar-start">
-<!--                <a href="{{ site.baseurl }}/" class="navbar-item {% if page.url == "/" %}is-active{% endif %}"><b>Home</b></a>-->
+            <div class="navbar-content">
                 {% if site.data.navigation %}
                 {% for item in site.data.navigation %}
-                    {% if item.dropdown %}
-                    <div class="navbar-item has-dropdown is-hoverable">
+                    <!-- {% if item.dropdown %}
+                    <div class="navbar-item has-dropdown is-hoverable link-underline-animate">
                         <a href="{{ item.link | prepend: site.baseurl }}" class="navbar-link {% if item.link == page.url %}is-active{% endif %}"><b>{{ item.name }}</b></a>
                         <div class="navbar-dropdown">
                             {% for subitem in item.dropdown %}
                             <a href="{{ subitem.link | prepend: site.baseurl }}" class="navbar-item {% if subitem.link == page.url %}is-active{% endif %}"><b>{{ subitem.name }}</b></a>
                             {% endfor %}
                         </div>
                     </div>
-                    {% else %}
-                <a href="{{ item.link | prepend: site.baseurl }}" class="navbar-item {% if item.link == page.url %}is-active{% endif %}"><b>{{ item.name }}</b></a>
+                    {% else %} -->
+                    <div class="navbar-item">
+                        <a href="{{ item.link | prepend: site.baseurl }}" class="navbar-item-link link-underline-animate {% if item.link == page.url %}is-active {% endif %}">
+                            <span class="navbar-item-text">
+                                {{ item.name }}
+                            </span>
+                        </a>
+                        <div class="disc"></div>
+                    </div>
                     {% endif %}
                 {% endfor %}
                 {% endif %}