chore: merge updates from staging (#13)

* - feat: add correct title links
- feat: dropdown for abstracts

* chore: update data

* fix: remove empty abstracts from data and UI

* fix: update jekyll and kramdown

* feat: academic_title for people cards (#14)

* summer social news update

* updated file format

* updated publications

* pjp picture updated

* feat: add academic_title field

---------

Co-authored-by: cassieperry <116086692+cassieperry@users.noreply.github.com>
Co-authored-by: ppark <peter_park@harvard.edu>

* feat: add support for current_position field for alumni

---------

Co-authored-by: cassieperry <116086692+cassieperry@users.noreply.github.com>
Co-authored-by: ppark <peter_park@harvard.edu>

Author: 3 people

Gemfile

@@ -2,19 +2,8 @@ source "https://rubygems.org"
 
 ruby '3.1.3'
 
-# gem "webrick"
-
 gem 'rexml', '~> 3.2', '>= 3.2.4'
-
-# Hello! This is where you manage which Jekyll version is used to run.
-# When you want to use a different version, change it below, save the
-# file and run `bundle install`. Run Jekyll with `bundle exec`, like so:
-#
-#     bundle exec jekyll serve
-#
-# This will help ensure the proper Jekyll version is running.
-# Happy Jekylling!
-gem "jekyll", "~> 3.8.6"
+gem "jekyll", "~> 4.4.1"
 gem "liquid", "~> 4.0"
 
 # This is the default theme for new Jekyll sites. You may change this to anything you like.
@@ -44,3 +33,6 @@ gem "wdm", "~> 0.1.0", :install_if => Gem.win_platform?
 # gem "rexml", "~> 3.2"
 
 gem "webrick", "~> 1.8"
+
+# Upgrade kramdown
+gem "kramdown", ">= 2.3.1"

Gemfile.lock

@@ -3,84 +3,86 @@ GEM
   specs:
     addressable (2.8.7)
       public_suffix (>= 2.0.2, < 7.0)
-    bulma-clean-theme (0.9.2)
-      jekyll (~> 3.8)
-      jekyll-feed (~> 0.11)
+    base64 (0.2.0)
+    bulma-clean-theme (0.14.0)
+      jekyll (>= 3.9, < 5.0)
+      jekyll-feed (~> 0.15)
       jekyll-paginate (~> 1.1)
-      jekyll-seo-tag (~> 2.5)
-      jekyll-sitemap (~> 1.2)
-      kramdown (~> 1.17)
-      rouge (~> 3.3)
+      jekyll-seo-tag (~> 2.7)
+      jekyll-sitemap (~> 1.4)
+      kramdown-parser-gfm (~> 1.1)
     colorator (1.1.0)
     concurrent-ruby (1.3.5)
+    csv (3.3.5)
     em-websocket (0.5.3)
       eventmachine (>= 0.12.9)
       http_parser.rb (~> 0)
     eventmachine (1.2.7)
-    ffi (1.17.1)
-    ffi (1.17.1-aarch64-linux-gnu)
-    ffi (1.17.1-aarch64-linux-musl)
-    ffi (1.17.1-arm-linux-gnu)
-    ffi (1.17.1-arm-linux-musl)
-    ffi (1.17.1-arm64-darwin)
-    ffi (1.17.1-x86-linux-gnu)
-    ffi (1.17.1-x86-linux-musl)
-    ffi (1.17.1-x86_64-darwin)
-    ffi (1.17.1-x86_64-linux-gnu)
-    ffi (1.17.1-x86_64-linux-musl)
+    ffi (1.17.2-arm64-darwin)
     forwardable-extended (2.6.0)
+    google-protobuf (3.25.4-arm64-darwin)
     http_parser.rb (0.8.0)
-    i18n (0.9.5)
+    i18n (1.14.7)
       concurrent-ruby (~> 1.0)
-    jekyll (3.8.7)
+    jekyll (4.4.1)
       addressable (~> 2.4)
+      base64 (~> 0.2)
       colorator (~> 1.0)
+      csv (~> 3.0)
       em-websocket (~> 0.5)
-      i18n (~> 0.7)
-      jekyll-sass-converter (~> 1.0)
+      i18n (~> 1.0)
+      jekyll-sass-converter (>= 2.0, < 4.0)
       jekyll-watch (~> 2.0)
-      kramdown (~> 1.14)
+      json (~> 2.6)
+      kramdown (~> 2.3, >= 2.3.1)
+      kramdown-parser-gfm (~> 1.0)
       liquid (~> 4.0)
-      mercenary (~> 0.3.3)
+      mercenary (~> 0.3, >= 0.3.6)
       pathutil (~> 0.9)
-      rouge (>= 1.7, < 4)
+      rouge (>= 3.0, < 5.0)
       safe_yaml (~> 1.0)
+      terminal-table (>= 1.8, < 4.0)
+      webrick (~> 1.7)
     jekyll-feed (0.17.0)
       jekyll (>= 3.7, < 5.0)
     jekyll-paginate (1.1.0)
-    jekyll-sass-converter (1.5.2)
-      sass (~> 3.4)
+    jekyll-sass-converter (3.0.0)
+      sass-embedded (~> 1.54)
     jekyll-seo-tag (2.8.0)
       jekyll (>= 3.8, < 5.0)
     jekyll-sitemap (1.4.0)
       jekyll (>= 3.7, < 5.0)
     jekyll-watch (2.2.1)
       listen (~> 3.0)
-    kramdown (1.17.0)
+    json (2.12.2)
+    kramdown (2.5.1)
+      rexml (>= 3.3.9)
+    kramdown-parser-gfm (1.1.0)
+      kramdown (~> 2.0)
     liquid (4.0.4)
     listen (3.9.0)
       rb-fsevent (~> 0.10, >= 0.10.3)
       rb-inotify (~> 0.9, >= 0.9.10)
-    mercenary (0.3.6)
+    mercenary (0.4.0)
     pathutil (0.16.2)
       forwardable-extended (~> 2.6)
-    public_suffix (6.0.1)
+    public_suffix (6.0.2)
     rb-fsevent (0.11.2)
     rb-inotify (0.11.1)
       ffi (~> 1.0)
     rexml (3.4.1)
     rouge (3.30.0)
     safe_yaml (1.0.5)
-    sass (3.7.4)
-      sass-listen (~> 4.0.0)
-    sass-listen (4.0.0)
-      rb-fsevent (~> 0.9, >= 0.9.4)
-      rb-inotify (~> 0.9, >= 0.9.7)
+    sass-embedded (1.77.5-arm64-darwin)
+      google-protobuf (>= 3.25, < 5.0)
+    terminal-table (3.0.2)
+      unicode-display_width (>= 1.1.1, < 3)
     thread_safe (0.3.6)
     tzinfo (1.2.11)
       thread_safe (~> 0.1)
     tzinfo-data (1.2025.1)
       tzinfo (>= 1.0.0)
+    unicode-display_width (2.6.0)
     wdm (0.1.1)
     webrick (1.9.1)
 
@@ -99,8 +101,9 @@ PLATFORMS
 
 DEPENDENCIES
   bulma-clean-theme
-  jekyll (~> 3.8.6)
+  jekyll (~> 4.4.1)
   jekyll-feed (~> 0.6)
+  kramdown (>= 2.3.1)
   liquid (~> 4.0)
   rexml (~> 3.2, >= 3.2.4)
   tzinfo (~> 1.2)

_layouts/people-category.html

@@ -18,16 +18,53 @@ <h2 class="category-header">{{ category }}</h2>
         {% assign currentPositionCategory = people_by_category | where: "name" , category | first %}
 
         <div class="category-body">
+
             {% for person in currentPositionCategory.items %}
             <div class="person-container" data-person="{{ person.name }}">
+
+              {% assign academic_subtitle = "" %}
+
+              <!-- Isolate the PhD part of the professional_title -->
+              {% assign split_professional_title = person.professional_title | split: "," %}
+              
+              {% for i in (0..max_index) %}
+                {% assign current = split_professional_title[i] | strip %}
+
+                {% if current contains "PhD" %}
+                  {% assign next_index = i | plus: 1 %}
+                  {% if next_index <= split_professional_title.size %}
+                    {% assign academic_subtitle = current | append: split_professional_title[next_index] %}
+                  {% endif %}
+                {% endif %}
+              {% endfor %}
+
+              {% comment %} Use professional_title if academic_subtitle is not available {% endcomment %}
+              {% if academic_subtitle == "" %}
+                {% if person.professional_title != person.subtitle %}
+                  {% assign academic_subtitle = person.professional_title %}
+                {% endif %}
+              {% endif %}
+
               {% if person.image %}
               <div class="person-card">
                 <img src="{{ person.image }}" alt="{{ person.name }}" />
                 <div class="person-information">
                   <p class="title">{{ person.person_title }}</p>
-                  <p class="subtitle">{{ person.subtitle }}</p>
-                  <p class="professional_title">{{ person.professional_title }}</p>
-                  {% comment %} <a class="read-more" href="{{ person.id }}">Read more</a> {% endcomment %}
+                  
+                  {% comment %} Use academic_title if available, otherwise try calculated title {% endcomment %}
+                  {% if person.academic_title %}
+                  <p class="professional_title">{{ person.academic_title }}</p>
+                  {% elsif academic_subtitle != "" %}
+                  <p class="professional_title">{{ academic_subtitle }}</p>
+                  {% else %}
+                  <p class="professional_title">{{ person.subtitle }}</p>
+                  {% endif %}
+
+                  {% comment %} Additional line for current_position if provided {% endcomment %}
+                  {% if person.status == "Alumni" and person.current_position %}
+                  <p class="current_position">{{ person.current_position }}</p>
+                  {% endif %}
+
                   {% if person.additional_links %}
                     <div class="additional-links-container">
                         {% if person.additional_links.github %}

_people/alexander-veit.md

@@ -3,7 +3,8 @@ person_title: <a href="/people/alexander-veit">Alexander Veit</a>
 name: Alexander Veit
 subtitle: Software Engineer  # Set subtitle to position_link_text
 professional_title: "Research Associate, PhD in Mathematics, University of Zurich"
-description: "Alexander Veit is part of the 4D Nucleome Data Coordination and Integration Center where he develops visualization tools for genomic data.Prior to joining Harvard, Alexander was a postdoctoral researcher at the University of Chicago, the Max Planck Institute for Mathematics in the Sciences (Leipzig) and the University of Zurich where he worked on numerical methods for partial differential equations.Before that, he completed his PhD in applied mathematics at the University of Zurich. His research involved the efficient approximation of time-domain boundary integral equations."
+academic_title: "PhD in Applied Mathematics, University of Zurich"
+description: "Alexander Veit is part of the 4D Nucleome Data Coordination and Integration Center where he develops visualization tools for genomic data. Prior to joining Harvard, Alexander was a postdoctoral researcher at the University of Chicago, the Max Planck Institute for Mathematics in the Sciences (Leipzig) and the University of Zurich where he worked on numerical methods for partial differential equations. Before that, he completed his PhD in applied mathematics at the University of Zurich. His research involved the efficient approximation of time-domain boundary integral equations."
 layout: person
 status: "Active Member"
 image: ./img/alexander-veit.jpg

_people/allen-lynch.md

@@ -3,6 +3,7 @@ person_title: <a href="/people/allen-lynch">Allen Lynch</a>
 name: Allen Lynch
 subtitle: Graduate Student  # Set subtitle to position_link_text
 professional_title: "PhD student, Bioinformatics and Integrative Genomics (BIG)"
+academic_title: "BA in Biochemistry, University of Minnesota - Twin Cities"
 description: "Allen received his Bachelor's degree in Biochemistry from the University of Minnesota-Twin Cities, then worked with Shirley Liu at the Dana-Farber Cancer Institute developing computational models of gene regulatory dynamics. He joined the Park lab as a graduate student in Harvard's Bioinformatics and Integrative Genomics PhD program."
 layout: person
 status: "Active Member"

_people/andy-schroeder.md

@@ -3,7 +3,8 @@ person_title: <a href="/people/andy-schroeder">Andy Schroeder</a>
 name: Andy Schroeder
 subtitle: Data Curator  # Set subtitle to position_link_text
 professional_title: "Senior Data Curator, 4D Nucleome DCIC"
-description: "Andrew Schroeder is currently working as part of the 4D Nucleome Data Coordination and Integration Center, assisting with project management and focusing on data management.Andrew received his PhD in Molecular and Cellular Biology from UMass, Amherst, followed by postdoctoral research at Tufts Medical School on circadian rhythms and neurobiology in Drosophila.  Andrew then joined FlyBase, a database of Drosophila Genes and Genomes as a data curator and software developer at Harvard University, shifting from wet lab research to computational biology before joining the Park lab and the 4DN-DCIC."
+academic_title: "PhD in Molecular and Cellular Biology, University of Massachusetts Amherst"
+description: "Andrew Schroeder is currently working as part of the 4D Nucleome Data Coordination and Integration Center, assisting with project management and focusing on data management. Andrew received his PhD in Molecular and Cellular Biology from UMass, Amherst, followed by postdoctoral research at Tufts Medical School on circadian rhythms and neurobiology in Drosophila. Andrew then joined FlyBase, a database of Drosophila Genes and Genomes as a data curator and software developer at Harvard University, shifting from wet lab research to computational biology before joining the Park lab and the 4DN-DCIC."
 layout: person
 status: "Active Member"
 image: ./img/andy-schroeder.jpg

_people/ann-caplin.md

@@ -3,6 +3,7 @@ person_title: <a href="/people/ann-caplin">Ann Caplin</a>
 name: Ann Caplin
 subtitle: Graduate Student  # Set subtitle to position_link_text
 professional_title: "PhD student, Bioinformatics and Integrative Genomics (BIG)"
+academic_title: "BS in Information and Data Sciences, California Institute of Technology"
 description: "Ann earned her BS in Information and Data Sciences from Caltech in 2022. While there she did research with Vineet Bafna at UCSD on detecting breakage-fusion-bridge (BFB) genomic rearrangements in cancer cells and did a senior thesis with Leonard Schulman on causal identification algorithms. She is currently working on studying mutational signatures in circulating tumor DNA with Doga Gulhan."
 layout: person
 status: "Active Member"

_people/anna-chung.md

@@ -4,6 +4,7 @@ name: Anna Chung
 subtitle: Project Coordinator  # Set subtitle to position_link_text
 position_category: "Alumni: Staff"
 professional_title: "Project Coordinator (2016-2019)"
+academic_title: "BS in Psychology, Boston College"
 description: "Anna graduated with a Bachelor's degree in Psychology from Boston College in 2014. Thereafter, she worked as a Coordinating Paralegal at Fragomen, Del Rey, Bernsen, & Loewy, LLP. for over two years. She is particularly interested in the administrative and project management aspects of health sciences. She is currently a nursing student at MGH IHP."
 layout: person
 status: "Alumni"

_people/cassie-perry.md

@@ -3,6 +3,7 @@ person_title: <a href="/people/cassie-perry">Cassie Perry</a>
 name: Cassie Perry
 subtitle: Research and Administrative Coordinator  # Set subtitle to position_link_text
 professional_title: "Research and Administrative Coordinator"
+academic_title: "BS in Neurobiology, BA in English, UW-Madison"
 description: "Cassie graduated from UW-Madison in 2022 with a Bachelor's degree in Neurobiology and English and a minor in Digital Studies. While completing her undergraduate degree, Cassie worked in a research lab at the Wisconsin Institute for Medical Research (WIMR) studying the role of the mechanistic target of rapamycin (mTOR) signaling pathway in heart regeneration."
 layout: person
 status: "Active Member"

_people/cesar-ferreyra-mansilla.md

@@ -3,6 +3,7 @@ person_title: <a href="/people/cesar-ferreyra-mansilla">Cesar Ferreyra-Mansilla<
 name: Cesar Ferreyra-Mansilla
 subtitle: Software Engineer  # Set subtitle to position_link_text
 professional_title: "Front End Engineer"
+academic_title: "BA in Information Science, Cornell University"
 layout: person
 status: "Active Member"
 image: ./img/cesar-ferreyra-mansilla.jpg