Site update.

Author: sjmgarnier

Gemfile.lock

@@ -1,143 +1,195 @@
 GEM
   remote: https://rubygems.org/
   specs:
-    RedCloth (4.2.9)
-    activesupport (4.2.6)
+    activesupport (4.2.7)
       i18n (~> 0.7)
       json (~> 1.7, >= 1.7.7)
       minitest (~> 5.1)
       thread_safe (~> 0.3, >= 0.3.4)
       tzinfo (~> 1.1)
-    addressable (2.4.0)
-    blankslate (2.1.2.4)
-    classifier-reborn (2.0.4)
-      fast-stemmer (~> 1.0)
+    addressable (2.5.0)
+      public_suffix (~> 2.0, >= 2.0.2)
     coffee-script (2.4.1)
       coffee-script-source
       execjs
-    coffee-script-source (1.10.0)
-    colorator (0.1)
-    ethon (0.9.0)
+    coffee-script-source (1.12.2)
+    colorator (1.1.0)
+    ethon (0.10.1)
       ffi (>= 1.3.0)
     execjs (2.7.0)
-    faraday (0.9.2)
+    faraday (0.10.1)
       multipart-post (>= 1.2, < 3)
-    fast-stemmer (1.0.2)
-    ffi (1.9.10)
+    ffi (1.9.14)
+    forwardable-extended (2.6.0)
     gemoji (2.1.0)
-    github-pages (43)
-      RedCloth (= 4.2.9)
-      github-pages-health-check (= 0.6.0)
-      jekyll (= 2.4.0)
+    github-pages (114)
+      activesupport (= 4.2.7)
+      github-pages-health-check (= 1.3.0)
+      jekyll (= 3.3.1)
+      jekyll-avatar (= 0.4.2)
       jekyll-coffeescript (= 1.0.1)
-      jekyll-feed (= 0.3.1)
+      jekyll-default-layout (= 0.1.4)
+      jekyll-feed (= 0.8.0)
       jekyll-gist (= 1.4.0)
-      jekyll-mentions (= 0.2.1)
+      jekyll-github-metadata (= 2.3.0)
+      jekyll-mentions (= 1.2.0)
+      jekyll-optional-front-matter (= 0.1.2)
       jekyll-paginate (= 1.1.0)
-      jekyll-redirect-from (= 0.9.1)
+      jekyll-readme-index (= 0.0.3)
+      jekyll-redirect-from (= 0.11.0)
+      jekyll-relative-links (= 0.2.1)
       jekyll-sass-converter (= 1.3.0)
-      jekyll-seo-tag (= 0.1.4)
-      jekyll-sitemap (= 0.9.0)
-      jemoji (= 0.5.0)
-      kramdown (= 1.9.0)
-      liquid (= 2.6.2)
-      maruku (= 0.7.0)
+      jekyll-seo-tag (= 2.1.0)
+      jekyll-sitemap (= 0.12.0)
+      jekyll-swiss (= 0.4.0)
+      jekyll-theme-architect (= 0.0.3)
+      jekyll-theme-cayman (= 0.0.3)
+      jekyll-theme-dinky (= 0.0.3)
+      jekyll-theme-hacker (= 0.0.3)
+      jekyll-theme-leap-day (= 0.0.3)
+      jekyll-theme-merlot (= 0.0.3)
+      jekyll-theme-midnight (= 0.0.3)
+      jekyll-theme-minimal (= 0.0.3)
+      jekyll-theme-modernist (= 0.0.3)
+      jekyll-theme-primer (= 0.1.5)
+      jekyll-theme-slate (= 0.0.3)
+      jekyll-theme-tactile (= 0.0.3)
+      jekyll-theme-time-machine (= 0.0.3)
+      jekyll-titles-from-headings (= 0.1.4)
+      jemoji (= 0.7.0)
+      kramdown (= 1.11.1)
+      liquid (= 3.0.6)
+      listen (= 3.0.6)
       mercenary (~> 0.3)
-      pygments.rb (= 0.6.3)
-      rdiscount (= 2.1.8)
-      redcarpet (= 3.3.3)
+      minima (= 2.0.0)
+      nokogiri (= 1.6.8.1)
+      rouge (= 1.11.1)
       terminal-table (~> 1.4)
-    github-pages-health-check (0.6.0)
+    github-pages-health-check (1.3.0)
       addressable (~> 2.3)
       net-dns (~> 0.8)
-      public_suffix (~> 1.4)
+      octokit (~> 4.0)
+      public_suffix (~> 2.0)
       typhoeus (~> 0.7)
-    html-pipeline (1.9.0)
+    html-pipeline (2.4.2)
       activesupport (>= 2)
-      nokogiri (~> 1.4)
+      nokogiri (>= 1.4)
     i18n (0.7.0)
-    jekyll (2.4.0)
-      classifier-reborn (~> 2.0)
-      colorator (~> 0.1)
-      jekyll-coffeescript (~> 1.0)
-      jekyll-gist (~> 1.0)
-      jekyll-paginate (~> 1.0)
+    jekyll (3.3.1)
+      addressable (~> 2.4)
+      colorator (~> 1.0)
       jekyll-sass-converter (~> 1.0)
       jekyll-watch (~> 1.1)
       kramdown (~> 1.3)
-      liquid (~> 2.6.1)
+      liquid (~> 3.0)
       mercenary (~> 0.3.3)
-      pygments.rb (~> 0.6.0)
-      redcarpet (~> 3.1)
+      pathutil (~> 0.9)
+      rouge (~> 1.7)
       safe_yaml (~> 1.0)
-      toml (~> 0.1.0)
+    jekyll-avatar (0.4.2)
+      jekyll (~> 3.0)
     jekyll-coffeescript (1.0.1)
       coffee-script (~> 2.2)
-    jekyll-feed (0.3.1)
+    jekyll-default-layout (0.1.4)
+      jekyll (~> 3.0)
+    jekyll-feed (0.8.0)
+      jekyll (~> 3.3)
     jekyll-gist (1.4.0)
       octokit (~> 4.2)
-    jekyll-mentions (0.2.1)
-      html-pipeline (~> 1.9.0)
-      jekyll (~> 2.0)
+    jekyll-github-metadata (2.3.0)
+      jekyll (~> 3.1)
+      octokit (~> 4.0, != 4.4.0)
+    jekyll-mentions (1.2.0)
+      activesupport (~> 4.0)
+      html-pipeline (~> 2.3)
+      jekyll (~> 3.0)
+    jekyll-optional-front-matter (0.1.2)
+      jekyll (~> 3.0)
     jekyll-paginate (1.1.0)
-    jekyll-redirect-from (0.9.1)
+    jekyll-readme-index (0.0.3)
+      jekyll (~> 3.0)
+    jekyll-redirect-from (0.11.0)
       jekyll (>= 2.0)
+    jekyll-relative-links (0.2.1)
+      jekyll (~> 3.3)
     jekyll-sass-converter (1.3.0)
       sass (~> 3.2)
-    jekyll-seo-tag (0.1.4)
-      jekyll (>= 2.0)
-    jekyll-sitemap (0.9.0)
-    jekyll-watch (1.4.0)
+    jekyll-seo-tag (2.1.0)
+      jekyll (~> 3.3)
+    jekyll-sitemap (0.12.0)
+      jekyll (~> 3.3)
+    jekyll-swiss (0.4.0)
+    jekyll-theme-architect (0.0.3)
+      jekyll (~> 3.3)
+    jekyll-theme-cayman (0.0.3)
+      jekyll (~> 3.3)
+    jekyll-theme-dinky (0.0.3)
+      jekyll (~> 3.3)
+    jekyll-theme-hacker (0.0.3)
+      jekyll (~> 3.3)
+    jekyll-theme-leap-day (0.0.3)
+      jekyll (~> 3.3)
+    jekyll-theme-merlot (0.0.3)
+      jekyll (~> 3.3)
+    jekyll-theme-midnight (0.0.3)
+      jekyll (~> 3.3)
+    jekyll-theme-minimal (0.0.3)
+      jekyll (~> 3.3)
+    jekyll-theme-modernist (0.0.3)
+      jekyll (~> 3.3)
+    jekyll-theme-primer (0.1.5)
+      jekyll (~> 3.3)
+    jekyll-theme-slate (0.0.3)
+      jekyll (~> 3.3)
+    jekyll-theme-tactile (0.0.3)
+      jekyll (~> 3.3)
+    jekyll-theme-time-machine (0.0.3)
+      jekyll (~> 3.3)
+    jekyll-titles-from-headings (0.1.4)
+      jekyll (~> 3.3)
+    jekyll-watch (1.5.0)
       listen (~> 3.0, < 3.1)
-    jemoji (0.5.0)
+    jemoji (0.7.0)
+      activesupport (~> 4.0)
       gemoji (~> 2.0)
-      html-pipeline (~> 1.9)
-      jekyll (>= 2.0)
-    json (1.8.3)
-    kramdown (1.9.0)
-    liquid (2.6.2)
-    listen (3.0.8)
-      rb-fsevent (~> 0.9, >= 0.9.4)
-      rb-inotify (~> 0.9, >= 0.9.7)
-    maruku (0.7.0)
+      html-pipeline (~> 2.2)
+      jekyll (>= 3.0)
+    json (1.8.6)
+    kramdown (1.11.1)
+    liquid (3.0.6)
+    listen (3.0.6)
+      rb-fsevent (>= 0.9.3)
+      rb-inotify (>= 0.9.7)
     mercenary (0.3.6)
     mini_portile2 (2.1.0)
-    minitest (5.9.0)
+    minima (2.0.0)
+    minitest (5.10.1)
     multipart-post (2.0.0)
     net-dns (0.8.0)
-    nokogiri (1.6.8)
+    nokogiri (1.6.8.1)
       mini_portile2 (~> 2.1.0)
-      pkg-config (~> 1.1.7)
-    octokit (4.3.0)
-      sawyer (~> 0.7.0, >= 0.5.3)
-    parslet (1.5.0)
-      blankslate (~> 2.0)
-    pkg-config (1.1.7)
-    posix-spawn (0.3.11)
-    public_suffix (1.5.3)
-    pygments.rb (0.6.3)
-      posix-spawn (~> 0.3.6)
-      yajl-ruby (~> 1.2.0)
-    rb-fsevent (0.9.7)
+    octokit (4.6.2)
+      sawyer (~> 0.8.0, >= 0.5.3)
+    pathutil (0.14.0)
+      forwardable-extended (~> 2.6)
+    public_suffix (2.0.5)
+    rb-fsevent (0.9.8)
     rb-inotify (0.9.7)
       ffi (>= 0.5.0)
-    rdiscount (2.1.8)
-    redcarpet (3.3.3)
-    rouge (1.11.0)
+    rouge (1.11.1)
     safe_yaml (1.0.4)
-    sass (3.4.22)
-    sawyer (0.7.0)
-      addressable (>= 2.3.5, < 2.5)
-      faraday (~> 0.8, < 0.10)
-    terminal-table (1.6.0)
+    sass (3.4.23)
+    sawyer (0.8.1)
+      addressable (>= 2.3.5, < 2.6)
+      faraday (~> 0.8, < 1.0)
+    terminal-table (1.7.3)
+      unicode-display_width (~> 1.1.1)
     thread_safe (0.3.5)
-    toml (0.1.2)
-      parslet (~> 1.5.0)
     typhoeus (0.8.0)
       ethon (>= 0.8.0)
     tzinfo (1.2.2)
       thread_safe (~> 0.1)
-    yajl-ruby (1.2.1)
+    unicode-display_width (1.1.3)
 
 PLATFORMS
   ruby
@@ -148,4 +200,4 @@ DEPENDENCIES
   rouge
 
 BUNDLED WITH
-   1.12.5
+   1.13.7

_config.yml

@@ -57,7 +57,7 @@ people:
 
 - name: Subash Ray
   pic: subash
-  position: Graduate Student
+  position: Graduate Student (PhD candidate)
   social:
     - title: twitter
       url: https://twitter.com/skrRay
@@ -144,6 +144,10 @@ people:
   pic: default
   position: Undergraduate Student
 
+- name: Mitali Shah
+  pic: default
+  position: Undergraduate Student
+
 - name: Purva Shah
   pic: purva
   position: Undergraduate Student, Lab Assistant

_posts/2015-06-01-shiny-teachR.md

@@ -1,25 +1,25 @@
 ---
 title: <code>teachR</code> package
-subtitle: All our educational Shiny apps in one place 
+subtitle: All our educational Shiny apps in one place
 layout: default
 modal-id: teachR
 date: 2015-06-01
 img: r_teachr.png
 thumbnail: r_teachr-thumbnail.png
 alt: image-alt
-category: 
+category:
     - shiny-portfolio
     - r-portfolio
-description: 
-    <b>Description:</b> <code>teachR</code> is a convenience R package that makes it easy to install and run all our 
+description:
+    <b>Description:</b> <code>teachR</code> is a convenience R package that makes it easy to install and run all our
     educational Shiny apps on your computer. It also contains a function to export self-contained versions of our apps
-    for installing them on your personal <a href="https://www.rstudio.com/products/shiny/shiny-server/">Shiny Server</a>
-    or on your <a href="https://www.shinyapps.io/">shinyapps.io</a> account. 
+    for installing them on your personal <a href="https://www.rstudio.com/products/shiny/shiny-server/">Shiny Server</a>, <a href="http://www.shinyproxy.io/">ShinyProxy Server</a>,
+    or on your <a href="https://www.shinyapps.io/">shinyapps.io</a> account.
     <br><br>
-    We are also welcoming contributions to <code>teachR</code>. If you would like your Shiny educational app to be 
+    We are also welcoming contributions to <code>teachR</code>. If you would like your Shiny educational app to be
     included in <code>teachR</code>, just fork our <a href="https://github.com/swarm-lab/teachR/">GitHub repository</a>,
     add your app to your copy of <code>teachR</code>, and submit a pull request. Make sure to include an <code>info</code>
-    file following the model included in each of <code>teachR</code>'s apps. 
+    file following the model included in each of <code>teachR</code>'s apps.
     <br><br>
     <b>Source code and installation instructions:</b> <a href="https://github.com/swarm-lab/teachR/">Click here</a>
 

_posts/2015-06-02-biol-337.md

@@ -8,15 +8,15 @@ img: biol337.png
 thumbnail: biol337-thumbnail.png
 alt: image-alt
 category: teaching-portfolio
-description: 
+description:
     Understanding collective intelligence is one of the main challenges of contemporary science. Social dynamics are
     essential for the organization of gregarious and social organisms, and they are an important part of many human
     activities including the selection of social and industrial norms, the growing use of crowd-sourcing and viral
-    marketing in social networks, and the influence of media and entourage on the outcome of democratic processes. This 
-    course will provide an overview of the fundamental principles underlying the organization of animal societies. It 
-    will include detailed consideration of the behavioral, social and physical processes that are responsible for the 
-    coordination of activities in large animal and human groups. 
+    marketing in social networks, and the influence of media and entourage on the outcome of democratic processes. This
+    course will provide an overview of the fundamental principles underlying the organization of animal societies. It
+    will include detailed consideration of the behavioral, social and physical processes that are responsible for the
+    coordination of activities in large animal and human groups.
     <br><br>
-    <a href="http://biology.njit.edu/docs/biol_337-S15.pdf">Latest syllabus</a>
+    <a href="http://biology.njit.edu/sites/biology/files/lcms/docs/biol_337-S17_0.pdf">Latest syllabus</a>
 
 ---

_posts/2015-06-02-shiny-agg-seg.md

@@ -7,10 +7,10 @@ date: 2015-06-02
 img: agg_seg.png
 thumbnail: agg_seg-thumbnail.png
 alt: image-alt
-category: 
+category:
     - shiny-portfolio
-description: 
-    <b>Description:</b> ...
+description:
+    <b>Description:</b> This app lets you explore a simple model of aggregation and segregation between two types of particles. 
     <br><br>
     <b>Demo:</b> <a href="/shiny/aggregation_segregation/">Click here</a>
     <br><br>

_posts/2015-06-03-biol-320.md

@@ -11,6 +11,6 @@ category: teaching-portfolio
 description:
     Success in the constantly evolving fields of biology and medicine necessitates staying current in scientific literature. This requires competency in skills such as analysis of primary sources, synthesis of information from multiple sources, and oral and written communication skills. This course focuses on these competencies. Students will develop skills needed to read and analyze scientific literature, and to communicate science through the making of short educational movies, scientific podcasts, and popular science articles.
     <br><br><a href="/biol320/">Course webpage</a>
-    <br><br><a href="http://biology.njit.edu/docs/biol_320-F14.pdf">Latest syllabus</a>
+    <br><br><a href="http://biology.njit.edu/sites/biology/files/lcms/docs/F16_BIOL_320_1.pdf">Latest syllabus</a>
 
 ---

_posts/2015-07-26-shiny-ant-coll-dec.md

@@ -7,10 +7,10 @@ date: 2015-07-26
 img: ant_coll_dec.png
 thumbnail: ant_coll_dec-thumbnail.png
 alt: image-alt
-category: 
+category:
     - shiny-portfolio
-description: 
-    <b>Description:</b> ...
+description:
+    <b>Description:</b> This app let's you explore a model of collective decision-making in ants. This model combines ideas from <a href="http://link.springer.com/article/10.1007%2FBF00462870">Goss et al. (1989)</a> and <a href="http://link.springer.com/article/10.1007%2FBF02224053">Beckers et al. (1990)</a>.
     <br><br>
     <b>Demo:</b> <a href="/shiny/ant_collective_decision/">Click here</a>
     <br><br>