Jekyll migration

.gitignore

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+_site
+.sass-cache
+.jekyll-cache
+.jekyll-metadata
+vendor

404.html

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+---
+permalink: /404.html
+layout: default
+---
+
+<style type="text/css" media="screen">
+  .container {
+    margin: 10px auto;
+    max-width: 600px;
+    text-align: center;
+  }
+  h1 {
+    margin: 30px 0;
+    font-size: 4em;
+    line-height: 1;
+    letter-spacing: -1px;
+  }
+</style>
+
+<div class="container">
+  <h1>404</h1>
+
+  <p><strong>Page not found :(</strong></p>
+  <p>The requested page could not be found.</p>
+</div>

Gemfile

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+source "https://rubygems.org"
+# 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", "~> 4.3.3"
+# This is the default theme for new Jekyll sites. You may change this to anything you like.
+gem "minima", "~> 2.5"
+# If you want to use GitHub Pages, remove the "gem "jekyll"" above and
+# uncomment the line below. To upgrade, run `bundle update github-pages`.
+gem "github-pages", "~> GITHUB-PAGES-VERSION", group: :jekyll_plugins
+# If you have any plugins, put them here!
+group :jekyll_plugins do
+  gem "jekyll-feed", "~> 0.12"
+end
+
+# Windows and JRuby does not include zoneinfo files, so bundle the tzinfo-data gem
+# and associated library.
+platforms :mingw, :x64_mingw, :mswin, :jruby do
+  gem "tzinfo", ">= 1", "< 3"
+  gem "tzinfo-data"
+end
+
+# Performance-booster for watching directories on Windows
+gem "wdm", "~> 0.1.1", :platforms => [:mingw, :x64_mingw, :mswin]
+
+# Lock `http_parser.rb` gem to `v0.6.x` on JRuby builds since newer versions of the gem
+# do not have a Java counterpart.
+gem "http_parser.rb", "~> 0.6.0", :platforms => [:jruby]

Gemfile.lock

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+GEM
+  remote: https://rubygems.org/
+  specs:
+    addressable (2.8.6)
+      public_suffix (>= 2.0.2, < 6.0)
+    colorator (1.1.0)
+    concurrent-ruby (1.2.3)
+    em-websocket (0.5.3)
+      eventmachine (>= 0.12.9)
+      http_parser.rb (~> 0)
+    eventmachine (1.2.7)
+    ffi (1.16.3-x64-mingw-ucrt)
+    forwardable-extended (2.6.0)
+    google-protobuf (4.26.1-x64-mingw-ucrt)
+      rake (>= 13)
+    http_parser.rb (0.8.0)
+    i18n (1.14.5)
+      concurrent-ruby (~> 1.0)
+    jekyll (4.3.3)
+      addressable (~> 2.4)
+      colorator (~> 1.0)
+      em-websocket (~> 0.5)
+      i18n (~> 1.0)
+      jekyll-sass-converter (>= 2.0, < 4.0)
+      jekyll-watch (~> 2.0)
+      kramdown (~> 2.3, >= 2.3.1)
+      kramdown-parser-gfm (~> 1.0)
+      liquid (~> 4.0)
+      mercenary (>= 0.3.6, < 0.5)
+      pathutil (~> 0.9)
+      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-sass-converter (3.0.0)
+      sass-embedded (~> 1.54)
+    jekyll-seo-tag (2.8.0)
+      jekyll (>= 3.8, < 5.0)
+    jekyll-watch (2.2.1)
+      listen (~> 3.0)
+    kramdown (2.4.0)
+      rexml
+    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 (0.4.0)
+    minima (2.5.1)
+      jekyll (>= 3.5, < 5.0)
+      jekyll-feed (~> 0.9)
+      jekyll-seo-tag (~> 2.1)
+    pathutil (0.16.2)
+      forwardable-extended (~> 2.6)
+    public_suffix (5.0.5)
+    rake (13.2.1)
+    rb-fsevent (0.11.2)
+    rb-inotify (0.10.1)
+      ffi (~> 1.0)
+    rexml (3.2.6)
+    rouge (4.2.1)
+    safe_yaml (1.0.5)
+    sass-embedded (1.77.1-x64-mingw-ucrt)
+      google-protobuf (>= 3.25, < 5.0)
+    terminal-table (3.0.2)
+      unicode-display_width (>= 1.1.1, < 3)
+    tzinfo (2.0.6)
+      concurrent-ruby (~> 1.0)
+    tzinfo-data (1.2024.1)
+      tzinfo (>= 1.0.0)
+    unicode-display_width (2.5.0)
+    wdm (0.1.1)
+    webrick (1.8.1)
+
+PLATFORMS
+  x64-mingw-ucrt
+
+DEPENDENCIES
+  http_parser.rb (~> 0.6.0)
+  jekyll (~> 4.3.3)
+  jekyll-feed (~> 0.12)
+  minima (~> 2.5)
+  tzinfo (>= 1, < 3)
+  tzinfo-data
+  wdm (~> 0.1.1)
+
+BUNDLED WITH
+   2.5.10

_config.yml

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+# Welcome to Jekyll!
+#
+# This config file is meant for settings that affect your whole blog, values
+# which you are expected to set up once and rarely edit after that. If you find
+# yourself editing this file very often, consider using Jekyll's data files
+# feature for the data you need to update frequently.
+#
+# For technical reasons, this file is *NOT* reloaded automatically when you use
+# 'bundle exec jekyll serve'. If you change this file, please restart the server process.
+#
+# If you need help with YAML syntax, here are some quick references for you:
+# https://learn-the-web.algonquindesign.ca/topics/markdown-yaml-cheat-sheet/#yaml
+# https://learnxinyminutes.com/docs/yaml/
+#
+# Site settings
+# These are used to personalize your new site. If you look in the HTML files,
+# 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: Ryan Amos
+description: >- # this means to ignore newlines until "baseurl:"
+  My personal website. Check out my work, both personal and professional.
+baseurl: "/" # the subpath of your site, e.g. /blog
+domain: "ryan-b-amos.com"
+url: "https://ryan-b-amos.com" # the base hostname & protocol for your site, e.g. http://example.com
+twitter_username: ryanbmamos
+github_username:  rbamos
+
+# Build settings
+theme: minima
+plugins:
+  - jekyll-feed
+
+header_pages:
+  - music.md
+  - resume.md
+
+
+# Exclude from processing.
+# The following items will not be processed, by default.
+# Any item listed under the `exclude:` key here will be automatically added to
+# the internal "default list".
+#
+# Excluded items can be processed by explicitly listing the directories or
+# their entries' file path in the `include:` list.
+#
+# exclude:
+#   - .sass-cache/
+#   - .jekyll-cache/
+#   - gemfiles/
+#   - Gemfile
+#   - Gemfile.lock
+#   - node_modules/
+#   - vendor/bundle/
+#   - vendor/cache/
+#   - vendor/gems/
+#   - vendor/ruby/

_posts/2024-05-11-welcome-to-jekyll.markdown

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+---
+layout: post
+title:  "Website migration"
+date:   2024-05-11 12:03:15 -0400
+categories: 
+---
+I've moved my website from a static HTML site to a Jekyll blog. We're still hosted on Github Pages. I've had some ideas kicking around in my head for things to write about, and I'm hopeful that setting up easier blog posting will help with that.

index.markdown

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+---
+# Feel free to add content and custom Front Matter to this file.
+# To modify the layout, see https://jekyllrb.com/docs/themes/#overriding-theme-defaults
+
+layout: home
+---
+
+<link rel="stylesheet" type="text/css" href="style.css" />
+
+<img class="photo" src="profile.png" width="200"/>
+
+Hello! I'm a Lead Software Engineer at Panorama Education on the Security Squad. My role involves implementing, improving, and coordinating platform security.
+
+I received my PhD from Princeton in April 2022. My PhD advisors were <a href="https://www.princeton.edu/~pmittal/">Prateek Mittal</a> and <a href="https://www.cs.princeton.edu/~felten/">Ed Felten</a>. My dissertation work focused on longitudinal internet measurements to address and understand consumer protection issues. I'm generally interested in cryptography, security, privacy, and tech policy. Additionally, I have experience in computational genomics and computational immunology.
+
+In my spare time, I [climb rocks](https://www.mountainproject.com/user/200319301/ryan-amos), I play the [guitar](/music/), and I ferment things (usually intentionally), I help run a [local board game group](https://www.highland-park.games/), and I run a D&D campaign. Previously, I founded [Princeton University Blacksmiths](https://materials.princeton.edu/education/student-organizations/princeton-blacksmiths), I was a director for the [New Jersey Blacksmiths Association](https://njblacksmiths.org), and I [taught rock climbing](https://amga.com/hire-a-guide/?page=CiviCRM&q=civicrm/profile/view&reset=1&id=21643&gid=32).
+
+My publications and ongoing projects can be found on my resume ([link](resume.pdf)).
+
+You can reach me at <a href='mail&#116;&#111;&#58;ry%61na&#109;os&#64;p&#114;oto&#110;&#109;&#37;&#54;1i%&#54;C&#46;c&#37;6Fm'>ryana&#109;o&#115;&#64;prot&#111;nm&#97;i&#108;&#46;&#99;&#111;m</a>.
+
+## Research
+Ryan Amos, Gunes Acar, Eli Lucherini, Mihir Kshirsagar, Arvind Narayanan, Jonathan Mayer.
+<i>Privacy Policies Over Time: Curation and Analysis of a Million Document Dataset.</i> WWW '21. <br/>
+<a href="https://arxiv.org/abs/2008.09159">Paper link</a>.<br/>
+<a href="https://privacypolicies.cs.princeton.edu/">Project page</a>.
+
+
+Ryan Amos, Roland Maio, Prateek Mittal. (Author list subject to change)
+<i>Reviews in motion: a large scale, longitudinal study of review recommendations on Yelp.</i> In submission.<br/>
+<a href="https://arxiv.org/abs/2202.09005">Paper link</a>.<br/>
+<a href="https://sites.google.com/princeton.edu/longitudinal-review-data/home">Project page</a>.
+
+Ryan Amos, Marios Georgiou, Aggelos Kiayias, Mark Zhandry.
+<i>One-shot signatures and applications to hybrid quantum/classical authentication.</i> STOC '20. <br/>
+<a href="https://par.nsf.gov/servlets/purl/10164786">Paper link</a>.
+
+Matthew J Salganik, et al.
+<i>Measuring the predictability of life outcomes with a scientific mass collaboration.</i> PNAS '20<br/>
+<a href="https://www.pnas.org/content/117/15/8398">Paper link</a>.<br/>
+<a href="https://www.fragilefamilieschallenge.org/">Project page</a>.
+
+Yoonjoo Choi, Jacob M Furlon, Ryan B Amos, Karl E Griswold, Chris Bailey-Kellogg.
+<i>DisruPPI: structure-based computational redesign algorithm for protein binding disruption.</i> Bioinformatics vol. 34.<br/>
+<a href="https://academic.oup.com/bioinformatics/article/34/13/i245/5045713">Paper link</a>.
+
+Jason H Moore, Ryan Amos, Jeff Kiralis, Peter C Andrews.
+<i>Heuristic Identification of Biological Architectures for Simulating Complex Hierarchical Genetic Interactions.</i> Genetic Epidemiology vol. 39<br/>
+<a href="https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/gepi.21865">Paper link</a>.
+
+### Incomplete works
+These are works that are incomplete, and are shown here as documentation of roads not fully travelled. Perhaps one day I can return to finish these.
+
+
+Ryan Amos, Samuel Ginzberg, Sameer Waugh, Edward W. Felten, Michael Freedman, Prateek Mittal.
+<i>Shuffling the Cards: An Information-Theoretic Defense Against Side Channel Attacks</i>
+<a href="papers/Side_Channel_Mitigation.pdf">Draft paper link</a>.
+
+Ryan Amos, Edward W. Felten.
+<i>Incentive-Driven Randomness Beacons</i>
+<a href="papers/Incentive_Driven_Randomness_Beacons.pdf">Draft paper link</a>.

music.md

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+---
+layout: page
+title: Music
+---
+<p>
+De Novo: <a href="DeNovo.mp3">MP3</a>, <a href="DeNovo.gp">Tab</a>
+</p>
+
+<p>
+Breaking the Ceiling: <a href="Breaking The Ceiling.mp3">MP3</a>, <a href="Breaking The Ceiling.gp">Tab</a>
+</p>
+
+<p>
+A couple covers: <a href="https://www.youtube.com/playlist?list=PLfeOBIG9tMi8_dlZvQHSQH-X4y92mn5vK">YouTube Playlist</a>
+</p>

resume.md

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+---
+layout: page
+title: Resume
+---
+
+<script type="text/javascript">
+    window.location.href = "/resume.pdf"
+</script>
+
+Redirecting you...