update publication, show github and paper websites

cremerlab · Jan 1, 2024 · ed59208 · ed59208
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diff --git a/.bundle/config b/.bundle/config
@@ -0,0 +1,2 @@
+---
+BUNDLE_CLEAN: "true"
diff --git a/Gemfile b/Gemfile
@@ -1,8 +1,13 @@
 source 'https://rubygems.org'
 
-gem 'jekyll', '3.8.5'
+gem 'github-pages'
 
-group :jekyll_plugins do
-  gem 'jekyll-paginate'
-  gem 'jekyll-sitemap'
-end
+#gem 'jekyll', '3.8.5'
+
+#group :jekyll_plugins do
+#  gem 'jekyll-paginate'
+#  gem 'jekyll-sitemap'
+#end
+
+
+gem "webrick", "~> 1.8"
diff --git a/Gemfile.lock b/Gemfile.lock
@@ -1,66 +1,287 @@
 GEM
   remote: https://rubygems.org/
   specs:
-    addressable (2.7.0)
-      public_suffix (>= 2.0.2, < 5.0)
+    activesupport (7.1.2)
+      base64
+      bigdecimal
+      concurrent-ruby (~> 1.0, >= 1.0.2)
+      connection_pool (>= 2.2.5)
+      drb
+      i18n (>= 1.6, < 2)
+      minitest (>= 5.1)
+      mutex_m
+      tzinfo (~> 2.0)
+    addressable (2.8.6)
+      public_suffix (>= 2.0.2, < 6.0)
+    base64 (0.2.0)
+    bigdecimal (3.1.5)
+    coffee-script (2.4.1)
+      coffee-script-source
+      execjs
+    coffee-script-source (1.11.1)
     colorator (1.1.0)
-    concurrent-ruby (1.1.8)
-    em-websocket (0.5.2)
+    commonmarker (0.23.10)
+    concurrent-ruby (1.2.2)
+    connection_pool (2.4.1)
+    dnsruby (1.70.0)
+      simpleidn (~> 0.2.1)
+    drb (2.2.0)
+      ruby2_keywords
+    em-websocket (0.5.3)
       eventmachine (>= 0.12.9)
-      http_parser.rb (~> 0.6.0)
+      http_parser.rb (~> 0)
+    ethon (0.16.0)
+      ffi (>= 1.15.0)
     eventmachine (1.2.7)
-    ffi (1.13.1)
+    execjs (2.9.1)
+    faraday (2.8.1)
+      base64
+      faraday-net_http (>= 2.0, < 3.1)
+      ruby2_keywords (>= 0.0.4)
+    faraday-net_http (3.0.2)
+    ffi (1.16.3)
     forwardable-extended (2.6.0)
-    http_parser.rb (0.6.0)
-    i18n (0.9.5)
+    gemoji (3.0.1)
+    github-pages (228)
+      github-pages-health-check (= 1.17.9)
+      jekyll (= 3.9.3)
+      jekyll-avatar (= 0.7.0)
+      jekyll-coffeescript (= 1.1.1)
+      jekyll-commonmark-ghpages (= 0.4.0)
+      jekyll-default-layout (= 0.1.4)
+      jekyll-feed (= 0.15.1)
+      jekyll-gist (= 1.5.0)
+      jekyll-github-metadata (= 2.13.0)
+      jekyll-include-cache (= 0.2.1)
+      jekyll-mentions (= 1.6.0)
+      jekyll-optional-front-matter (= 0.3.2)
+      jekyll-paginate (= 1.1.0)
+      jekyll-readme-index (= 0.3.0)
+      jekyll-redirect-from (= 0.16.0)
+      jekyll-relative-links (= 0.6.1)
+      jekyll-remote-theme (= 0.4.3)
+      jekyll-sass-converter (= 1.5.2)
+      jekyll-seo-tag (= 2.8.0)
+      jekyll-sitemap (= 1.4.0)
+      jekyll-swiss (= 1.0.0)
+      jekyll-theme-architect (= 0.2.0)
+      jekyll-theme-cayman (= 0.2.0)
+      jekyll-theme-dinky (= 0.2.0)
+      jekyll-theme-hacker (= 0.2.0)
+      jekyll-theme-leap-day (= 0.2.0)
+      jekyll-theme-merlot (= 0.2.0)
+      jekyll-theme-midnight (= 0.2.0)
+      jekyll-theme-minimal (= 0.2.0)
+      jekyll-theme-modernist (= 0.2.0)
+      jekyll-theme-primer (= 0.6.0)
+      jekyll-theme-slate (= 0.2.0)
+      jekyll-theme-tactile (= 0.2.0)
+      jekyll-theme-time-machine (= 0.2.0)
+      jekyll-titles-from-headings (= 0.5.3)
+      jemoji (= 0.12.0)
+      kramdown (= 2.3.2)
+      kramdown-parser-gfm (= 1.1.0)
+      liquid (= 4.0.4)
+      mercenary (~> 0.3)
+      minima (= 2.5.1)
+      nokogiri (>= 1.13.6, < 2.0)
+      rouge (= 3.26.0)
+      terminal-table (~> 1.4)
+    github-pages-health-check (1.17.9)
+      addressable (~> 2.3)
+      dnsruby (~> 1.60)
+      octokit (~> 4.0)
+      public_suffix (>= 3.0, < 5.0)
+      typhoeus (~> 1.3)
+    html-pipeline (2.14.3)
+      activesupport (>= 2)
+      nokogiri (>= 1.4)
+    http_parser.rb (0.8.0)
+    i18n (1.14.1)
       concurrent-ruby (~> 1.0)
-    jekyll (3.8.5)
+    jekyll (3.9.3)
       addressable (~> 2.4)
       colorator (~> 1.0)
       em-websocket (~> 0.5)
-      i18n (~> 0.7)
+      i18n (>= 0.7, < 2)
       jekyll-sass-converter (~> 1.0)
       jekyll-watch (~> 2.0)
-      kramdown (~> 1.14)
+      kramdown (>= 1.17, < 3)
       liquid (~> 4.0)
       mercenary (~> 0.3.3)
       pathutil (~> 0.9)
       rouge (>= 1.7, < 4)
       safe_yaml (~> 1.0)
+    jekyll-avatar (0.7.0)
+      jekyll (>= 3.0, < 5.0)
+    jekyll-coffeescript (1.1.1)
+      coffee-script (~> 2.2)
+      coffee-script-source (~> 1.11.1)
+    jekyll-commonmark (1.4.0)
+      commonmarker (~> 0.22)
+    jekyll-commonmark-ghpages (0.4.0)
+      commonmarker (~> 0.23.7)
+      jekyll (~> 3.9.0)
+      jekyll-commonmark (~> 1.4.0)
+      rouge (>= 2.0, < 5.0)
+    jekyll-default-layout (0.1.4)
+      jekyll (~> 3.0)
+    jekyll-feed (0.15.1)
+      jekyll (>= 3.7, < 5.0)
+    jekyll-gist (1.5.0)
+      octokit (~> 4.2)
+    jekyll-github-metadata (2.13.0)
+      jekyll (>= 3.4, < 5.0)
+      octokit (~> 4.0, != 4.4.0)
+    jekyll-include-cache (0.2.1)
+      jekyll (>= 3.7, < 5.0)
+    jekyll-mentions (1.6.0)
+      html-pipeline (~> 2.3)
+      jekyll (>= 3.7, < 5.0)
+    jekyll-optional-front-matter (0.3.2)
+      jekyll (>= 3.0, < 5.0)
     jekyll-paginate (1.1.0)
+    jekyll-readme-index (0.3.0)
+      jekyll (>= 3.0, < 5.0)
+    jekyll-redirect-from (0.16.0)
+      jekyll (>= 3.3, < 5.0)
+    jekyll-relative-links (0.6.1)
+      jekyll (>= 3.3, < 5.0)
+    jekyll-remote-theme (0.4.3)
+      addressable (~> 2.0)
+      jekyll (>= 3.5, < 5.0)
+      jekyll-sass-converter (>= 1.0, <= 3.0.0, != 2.0.0)
+      rubyzip (>= 1.3.0, < 3.0)
     jekyll-sass-converter (1.5.2)
       sass (~> 3.4)
+    jekyll-seo-tag (2.8.0)
+      jekyll (>= 3.8, < 5.0)
     jekyll-sitemap (1.4.0)
       jekyll (>= 3.7, < 5.0)
+    jekyll-swiss (1.0.0)
+    jekyll-theme-architect (0.2.0)
+      jekyll (> 3.5, < 5.0)
+      jekyll-seo-tag (~> 2.0)
+    jekyll-theme-cayman (0.2.0)
+      jekyll (> 3.5, < 5.0)
+      jekyll-seo-tag (~> 2.0)
+    jekyll-theme-dinky (0.2.0)
+      jekyll (> 3.5, < 5.0)
+      jekyll-seo-tag (~> 2.0)
+    jekyll-theme-hacker (0.2.0)
+      jekyll (> 3.5, < 5.0)
+      jekyll-seo-tag (~> 2.0)
+    jekyll-theme-leap-day (0.2.0)
+      jekyll (> 3.5, < 5.0)
+      jekyll-seo-tag (~> 2.0)
+    jekyll-theme-merlot (0.2.0)
+      jekyll (> 3.5, < 5.0)
+      jekyll-seo-tag (~> 2.0)
+    jekyll-theme-midnight (0.2.0)
+      jekyll (> 3.5, < 5.0)
+      jekyll-seo-tag (~> 2.0)
+    jekyll-theme-minimal (0.2.0)
+      jekyll (> 3.5, < 5.0)
+      jekyll-seo-tag (~> 2.0)
+    jekyll-theme-modernist (0.2.0)
+      jekyll (> 3.5, < 5.0)
+      jekyll-seo-tag (~> 2.0)
+    jekyll-theme-primer (0.6.0)
+      jekyll (> 3.5, < 5.0)
+      jekyll-github-metadata (~> 2.9)
+      jekyll-seo-tag (~> 2.0)
+    jekyll-theme-slate (0.2.0)
+      jekyll (> 3.5, < 5.0)
+      jekyll-seo-tag (~> 2.0)
+    jekyll-theme-tactile (0.2.0)
+      jekyll (> 3.5, < 5.0)
+      jekyll-seo-tag (~> 2.0)
+    jekyll-theme-time-machine (0.2.0)
+      jekyll (> 3.5, < 5.0)
+      jekyll-seo-tag (~> 2.0)
+    jekyll-titles-from-headings (0.5.3)
+      jekyll (>= 3.3, < 5.0)
     jekyll-watch (2.2.1)
       listen (~> 3.0)
-    kramdown (1.17.0)
-    liquid (4.0.3)
-    listen (3.4.0)
+    jemoji (0.12.0)
+      gemoji (~> 3.0)
+      html-pipeline (~> 2.2)
+      jekyll (>= 3.0, < 5.0)
+    kramdown (2.3.2)
+      rexml
+    kramdown-parser-gfm (1.1.0)
+      kramdown (~> 2.0)
+    liquid (4.0.4)
+    listen (3.8.0)
       rb-fsevent (~> 0.10, >= 0.10.3)
       rb-inotify (~> 0.9, >= 0.9.10)
     mercenary (0.3.6)
+    minima (2.5.1)
+      jekyll (>= 3.5, < 5.0)
+      jekyll-feed (~> 0.9)
+      jekyll-seo-tag (~> 2.1)
+    minitest (5.20.0)
+    mutex_m (0.2.0)
+    nokogiri (1.16.0-aarch64-linux)
+      racc (~> 1.4)
+    nokogiri (1.16.0-arm-linux)
+      racc (~> 1.4)
+    nokogiri (1.16.0-arm64-darwin)
+      racc (~> 1.4)
+    nokogiri (1.16.0-x86-linux)
+      racc (~> 1.4)
+    nokogiri (1.16.0-x86_64-darwin)
+      racc (~> 1.4)
+    nokogiri (1.16.0-x86_64-linux)
+      racc (~> 1.4)
+    octokit (4.25.1)
+      faraday (>= 1, < 3)
+      sawyer (~> 0.9)
     pathutil (0.16.2)
       forwardable-extended (~> 2.6)
-    public_suffix (4.0.6)
-    rb-fsevent (0.10.4)
+    public_suffix (4.0.7)
+    racc (1.7.3)
+    rb-fsevent (0.11.2)
     rb-inotify (0.10.1)
       ffi (~> 1.0)
+    rexml (3.2.6)
     rouge (3.26.0)
+    ruby2_keywords (0.0.5)
+    rubyzip (2.3.2)
     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)
+    sawyer (0.9.2)
+      addressable (>= 2.3.5)
+      faraday (>= 0.17.3, < 3)
+    simpleidn (0.2.1)
+      unf (~> 0.1.4)
+    terminal-table (1.8.0)
+      unicode-display_width (~> 1.1, >= 1.1.1)
+    typhoeus (1.4.1)
+      ethon (>= 0.9.0)
+    tzinfo (2.0.6)
+      concurrent-ruby (~> 1.0)
+    unf (0.1.4)
+      unf_ext
+    unf_ext (0.0.9.1)
+    unicode-display_width (1.8.0)
+    webrick (1.8.1)
 
 PLATFORMS
-  universal-darwin-21
+  aarch64-linux
+  arm-linux
+  arm64-darwin
+  x86-linux
+  x86_64-darwin
+  x86_64-linux
 
 DEPENDENCIES
-  jekyll (= 3.8.5)
-  jekyll-paginate
-  jekyll-sitemap
+  github-pages
+  webrick (~> 1.8)
 
 BUNDLED WITH
-   2.2.4
+   2.5.3
diff --git a/Gemfileold b/Gemfileold
@@ -0,0 +1,9 @@
+source 'https://rubygems.org'
+
+gem 'jekyll', '3.8.5'
+
+group :jekyll_plugins do
+  gem 'jekyll-paginate'
+  gem 'jekyll-sitemap'
+end
+
diff --git a/_data/publications.yml b/_data/publications.yml
@@ -15,12 +15,14 @@
       The differing prevalences of propionate and butyrate-producing bacteria in the human gut microbiota
   authors: Rebecca Christensen, Yu Han Daisy Wang, Markus Arnoldini, and Jonas Cremer
   journal: bioRxiv
+  github: https://github.com/rchristensen26/Butyrate_Propionate_Comparative_Analysis
   doi: 10.1101/2023.11.27.568948
 - title: >
       hplc-py: A Python Package For Rapid Peak Quantification in Complex Chromatograms
   authors: Griffin Chure and Jonas Cremer
   journal: chemRxiv
   doi: 10.26434/chemrxiv-2023-m2n4r
+  paper_website: https://cremerlab.github.io/hplc-py/
   github: https://github.com/cremerlab/hplc-py
 - title: >
       Conditionally unutilized proteins and their profound effects on growth and adaptation across microbial species
@@ -38,7 +40,7 @@
   doi: 10.7554/eLife.84878
   github: https://github.com/cremerlab/flux_parity
   paper_website: https://cremerlab.github.io/flux_parity/
-  notes: "Featured as a Spotlight Article by Avi Flamholz and Akshit Goyal: Matching metabolic supply to demand optimizes microbial growth. Trends in Microbiology, 2023."
+  notes: 'Featured as a Spotlight Article by Avi Flamholz and Akshit Goyal: Matching metabolic supply to demand optimizes microbial growth. <a href="https://doi.org/10.1016/j.tim.2023.06.003"> Trends in Microbiology, 2023 </a>'
 
 2022: 
   - title: >
@@ -48,6 +50,7 @@
     journal: PRL
     volume: 129
     doi: 10.1103/PhysRevLett.129.138101
+    notes: 'Editor suggestion and featured in <a href="https://physics.aps.org/articles/v15/146" Physics>Physics</a>'
   - title: >
       Coordination of gene expression with cell size enables <i>Escherichia coli</i>
       to efficiently maintain motility across conditions

diff --git a/_pages/publications.md b/_pages/publications.md
@@ -16,10 +16,7 @@ featured_image: /images/blackboard.jpg
 {% for paper in year[1] %}
 <a href="https://doi.org/{{paper.doi}}"><b>{{paper.title}}</b></a><br/>
 {{paper.authors}}<br/>
-<i>{{paper.journal}}</i> {{paper.volume}}<b>{{paper.issue}}</b> ({{year[0]}}) doi: `{{paper.doi}}`
-{% if paper.github != "" %}
-<a href={{paper.github}}>GitHub Repository</a><br/>
-{% endif %}
+<i>{{paper.journal}}</i> {{paper.volume}}<b>{{paper.issue}}</b> ({{year[0]}}) doi: `{{paper.doi}}`<br/>{% if paper.github|default() %} <a href="{{paper.github}}"> GitHub Repository</a>{% endif %}{% if paper.paper_website|default() %} <a href="{{paper.paper_website}}">Paper Website</a> {% endif %}{% if paper.notes|default() %}{{paper.notes}} {% endif %}
 
 {% endfor %}
 {% endfor %}