grnsight 4.0.0 → 6.0.0

package/_gh_pages/documents/abstracts/SIGGRAPH 2017 Abstract/siggraph-abstract-review.out

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package/_gh_pages/encryption/server.cert

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+-----END CERTIFICATE-----

package/_gh_pages/encryption/server.key

@@ -0,0 +1,28 @@
+-----BEGIN PRIVATE KEY-----
+MIIEvgIBADANBgkqhkiG9w0BAQEFAASCBKgwggSkAgEAAoIBAQC/g1FrTdrWyCcy
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+M1O6nwbvDbHOFQ9PsCxV23hP
+-----END PRIVATE KEY-----

package/_gh_pages/index.html

@@ -3,28 +3,23 @@
 
     <head>
         <title>GRNsight - Home</title>
-        <link rel="stylesheet" type="text/css" href="/GRNsight/assets/css/bootstrap.min.css">
+        <link rel="shortcut icon" type="image/x-icon" href="favicon.ico">
+        <link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/4.5.2/css/bootstrap.min.css" integrity="sha384-JcKb8q3iqJ61gNV9KGb8thSsNjpSL0n8PARn9HuZOnIxN0hoP+VmmDGMN5t9UJ0Z" crossorigin="anonymous">
         <link rel="stylesheet" type="text/css" href="/GRNsight/assets/css/main.css">
         <meta charset="utf-8">
-        <!-- Begin Jekyll SEO tag v2.0.0 -->
+        <!-- Begin Jekyll SEO tag v2.6.1 -->
+<meta name="generator" content="Jekyll v3.9.0" />
 <meta property="og:title" content="Home" />
+<meta property="og:locale" content="en_US" />
 <meta name="description" content="GRNsight is an open source web application and service for visualizing models of small- to medium-scale gene regulatory networks." />
 <meta property="og:description" content="GRNsight is an open source web application and service for visualizing models of small- to medium-scale gene regulatory networks." />
-<link rel="canonical" href="http://dondi.github.io/GRNsight/" />
-<meta property="og:url" content="http://dondi.github.io/GRNsight/" />
+<link rel="canonical" href="http://localhost:3001/GRNsight/" />
+<meta property="og:url" content="http://localhost:3001/GRNsight/" />
 <meta property="og:site_name" content="GRNsight" />
 <script type="application/ld+json">
-  {
-    "@context": "http://schema.org",
-    "@type": "WebSite",
-    "name": "GRNsight",
-    "headline": "Home",
-    "description": "GRNsight is an open source web application and service for visualizing models of small- to medium-scale gene regulatory networks.",
-    "logo": "http://dondi.github.io/GRNsight/assets/images/GRNsight_logo_20140710_main_resized.jpg",
-    "url": "http://dondi.github.io/GRNsight/"
-  }
-</script>
+{"@type":"WebSite","url":"http://localhost:3001/GRNsight/","name":"GRNsight","description":"GRNsight is an open source web application and service for visualizing models of small- to medium-scale gene regulatory networks.","publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"http://localhost:3001/GRNsight/assets/images/GRNsight_logo_20140710_main_resized.jpg"}},"headline":"Home","@context":"https://schema.org"}</script>
 <!-- End Jekyll SEO tag -->
+
     </head>
 
 
@@ -39,7 +34,7 @@
             </div>
             <p id="title"><a href="/GRNsight">GRNsight</a></p>
             <p id="subtext">Web app and service for visualizing models of gene regulatory networks.</p>
-            <div class="alert alert-success hidden" id="cookie-notice" role="alert">
+            <div class="alert alert-success d-none" id="cookie-notice" role="alert">
                 <div>This site uses Google Analytics to count pageviews and file uploads to demonstrate usage of our software to interested parties such as our employers and funding agencies. Information about your use of this site is shared with Google. By using this site, you agree to its use of cookies.</div>
                 <button class="cookie-action" data-dismiss="alert" aria-label="Got It">
                     <strong>Got It</strong>
@@ -69,17 +64,18 @@
 
                 </ul>
                 <p id="modText" class="modNav">
-                    Last modified: 9/6/15
+                    Last modified: 6/9/2019
                 </p>
             </div>
+
         </div>
 
         <div id="mainContent">
-            <p id="pageTitle">GRNsight <span id="version">v1.12</span></p>
-            <div id="pageContent">
+            <p id="pageTitle">GRNsight <span id="version">v4.0.0</span></p>
+            <div id="graphPageContent">
                 Welcome to GRNsight. Please select a file to upload.
                 <br><br>
-                <iframe class="embedded-demo" src="http://grnsight.cs.lmu.edu/client"></iframe>
+                <iframe class="embedded-demo" src="https://grnsight.cs.lmu.edu/client"></iframe>
             </div>
 
             <div id="footer">
@@ -120,7 +116,7 @@
             </div>
         </div>
 
-        <script>
+          <script>
             (function(i,s,o,g,r,a,m){i["GoogleAnalyticsObject"]=r;i[r]=i[r]||function(){
                 (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
                 m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
@@ -129,10 +125,37 @@
             ga("create", "UA-54882218-1", "auto");
             ga("send", "pageview");
         </script>
-        <script src="https://code.jquery.com/jquery.js"></script>
-        <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.2.0/js/bootstrap.min.js"></script>
+        <script src="https://code.jquery.com/jquery-3.5.1.min.js"></script>
+        <script src="https://cdn.jsdelivr.net/npm/popper.js@1.16.1/dist/umd/popper.min.js" integrity="sha384-9/reFTGAW83EW2RDu2S0VKaIzap3H66lZH81PoYlFhbGU+6BZp6G7niu735Sk7lN" crossorigin="anonymous"></script>
+        <script src="https://stackpath.bootstrapcdn.com/bootstrap/4.5.2/js/bootstrap.min.js" integrity="sha384-B4gt1jrGC7Jh4AgTPSdUtOBvfO8shuf57BaghqFfPlYxofvL8/KUEfYiJOMMV+rV" crossorigin="anonymous"></script>
         <script src="/GRNsight/assets/js/main.js"></script>
         <script src="/GRNsight/assets/js/ga-report.js"></script>
+    
+        <!-- Placeholder for whatever the final iframe management solution will be. -->
+    
+    
+        <script>
+            var $window = $(window);
+            // https://stackoverflow.com/questions/20125340/can-i-use-jquery-to-resize-an-iframe-to-fill-the-remaining-window-space
+            $window.on('load resize', function(){
+                var HEIGHT_OFFSET = 53;
+                var HEIGHT_PADDING = 20;
+                var SMALL_HEIGHT = 648 + HEIGHT_OFFSET;
+                var MEDIUM_HEIGHT = 840 + HEIGHT_OFFSET;
+                var LARGE_HEIGHT = 1080 + HEIGHT_OFFSET;
+                $('iframe').height(function() {
+                    var display = $window.height() - $(this).offset().top;
+                    if (display < SMALL_HEIGHT) {
+                      display = SMALL_HEIGHT;
+                    } else if (display > SMALL_HEIGHT && display < LARGE_HEIGHT) {
+                      display = MEDIUM_HEIGHT;
+                    }
+                    return display + HEIGHT_PADDING;
+                });
+            });
+        </script>
+    
+    
 
 
     </body>

package/_gh_pages/links.html

@@ -3,27 +3,23 @@
 
     <head>
         <title>GRNsight - Links</title>
-        <link rel="stylesheet" type="text/css" href="/GRNsight/assets/css/bootstrap.min.css">
+        <link rel="shortcut icon" type="image/x-icon" href="favicon.ico">
+        <link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/4.5.2/css/bootstrap.min.css" integrity="sha384-JcKb8q3iqJ61gNV9KGb8thSsNjpSL0n8PARn9HuZOnIxN0hoP+VmmDGMN5t9UJ0Z" crossorigin="anonymous">
         <link rel="stylesheet" type="text/css" href="/GRNsight/assets/css/main.css">
         <meta charset="utf-8">
-        <!-- Begin Jekyll SEO tag v2.0.0 -->
+        <!-- Begin Jekyll SEO tag v2.6.1 -->
+<meta name="generator" content="Jekyll v3.9.0" />
 <meta property="og:title" content="Links" />
-<meta name="description" content="GRNsight is an open source web application and service for visualizing models of small- to medium-scale gene regulatory networks." />
-<meta property="og:description" content="GRNsight is an open source web application and service for visualizing models of small- to medium-scale gene regulatory networks." />
-<link rel="canonical" href="http://dondi.github.io/GRNsight/links.html" />
-<meta property="og:url" content="http://dondi.github.io/GRNsight/links.html" />
+<meta property="og:locale" content="en_US" />
+<meta name="description" content="Useful links for GRNsight, an open source web application and service for visualizing models of small- to medium-scale gene regulatory networks." />
+<meta property="og:description" content="Useful links for GRNsight, an open source web application and service for visualizing models of small- to medium-scale gene regulatory networks." />
+<link rel="canonical" href="http://localhost:3001/GRNsight/links.html" />
+<meta property="og:url" content="http://localhost:3001/GRNsight/links.html" />
 <meta property="og:site_name" content="GRNsight" />
 <script type="application/ld+json">
-  {
-    "@context": "http://schema.org",
-    "@type": "WebPage",
-    "headline": "Links",
-    "description": "GRNsight is an open source web application and service for visualizing models of small- to medium-scale gene regulatory networks.",
-    "logo": "http://dondi.github.io/GRNsight/assets/images/GRNsight_logo_20140710_main_resized.jpg",
-    "url": "http://dondi.github.io/GRNsight/links.html"
-  }
-</script>
+{"@type":"WebPage","url":"http://localhost:3001/GRNsight/links.html","description":"Useful links for GRNsight, an open source web application and service for visualizing models of small- to medium-scale gene regulatory networks.","publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"http://localhost:3001/GRNsight/assets/images/GRNsight_logo_20140710_main_resized.jpg"}},"headline":"Links","@context":"https://schema.org"}</script>
 <!-- End Jekyll SEO tag -->
+
     </head>
 
 
@@ -38,7 +34,7 @@
             </div>
             <p id="title"><a href="/GRNsight">GRNsight</a></p>
             <p id="subtext">Web app and service for visualizing models of gene regulatory networks.</p>
-            <div class="alert alert-success hidden" id="cookie-notice" role="alert">
+            <div class="alert alert-success d-none" id="cookie-notice" role="alert">
                 <div>This site uses Google Analytics to count pageviews and file uploads to demonstrate usage of our software to interested parties such as our employers and funding agencies. Information about your use of this site is shared with Google. By using this site, you agree to its use of cookies.</div>
                 <button class="cookie-action" data-dismiss="alert" aria-label="Got It">
                     <strong>Got It</strong>
@@ -68,30 +64,40 @@
 
                 </ul>
                 <p id="modText" class="modNav">
-                    Last modified: 5/11/16
+                    Last modified: 9/25/19
                 </p>
             </div>
+
         </div>
 
         <div id="mainContent">
             <p id="pageTitle">Links</p>
+
+                <h4 class="linkHeader">Principal Investigators</h4>
+                <ul class="linkInfo">
+                    <li><a href="http://kdahlquist.github.io/DahlquistLab/" target="_blank">Kam D. Dahlquist, Ph.D.</a></li>
+                    <li><a href="http://dondi.lmu.build/" target="_blank">John David N. Dionisio, Ph.D.</a></li>
+                    <li><a href="https://cse.lmu.edu/department/math/facultyandstaff/?expert=ben.fitzpatrick" target="_blank">Ben G. Fitzpatrick, Ph.D.</a></li>
+                </ul>
+
+                <h4 class="linkHeader">Courses Using GRNsight</h4>
+                <ul class="linkInfo">
+                  <li><a href="http://www.openwetware.org/wiki/BIOL398-04/S15" target="_blank">BIOL 398-04: Biomathematical Modeling/MATH 388-01: Survey of Biomathematics - Spring 2015</a></li>
+                  <li><a href="https://openwetware.org/wiki/BIOL398-05/S17" target="_blank">BIOL 398-05: Biomathematical Modeling/MATH 388-01: Survey of Biomathematics - Spring 2017</a></li>
+                  <li><a href="https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Main_Page" target="_blank">BIOL/CMSI 367-01: Biological Databases - Fall 2017</a></li>
+                </ul>
+
             <div id="pageContent">
                 <h4 class="linkHeader">Gene Regulatory Networks</h4>
                 <ul class="linkInfo">
                   <li><a href="http://www.yeastract.com/" target="_blank">YEASTRACT</a></li>
                   <li><a href="http://jaspar.genereg.net/" target="_blank">JASPAR</a></li>
-                  <li><a href="http://www.yeastgenome.org/help/function-help/regulation" target="_blank">Regulation Help at the <span style="font-style:italic;">Saccharomyces</span> Genome Database</a></li>
-                </ul>
-                <h4 class="linkHeader">Principal Investigators</h4>
-                <ul class="linkInfo">
-                    <li><a href="http://myweb.lmu.edu/kdahlqui" target="_blank">Kam D. Dahlquist, Ph.D.</a></li>
-                    <li><a href="http://myweb.lmu.edu/dondi" target="_blank">John David N. Dionisio, Ph.D.</a></li>
-                    <li><a href="http://myweb.lmu.edu/bfitzpatrick/" target="_blank">Ben G. Fitzpatrick, Ph.D.</a></li>
+                  <li><a href="https://sites.google.com/view/yeastgenome-help/function-help/regulation" target="_blank">Regulation Help at the <span style="font-style:italic;">Saccharomyces</span> Genome Database</a></li>
                 </ul>
+
                 <h4 class="linkHeader">Software</h4>
                 <ul class="linkInfo">
                   <li><a href="https://github.com/dondi/GRNsight" target="_blank">GRNSight @ GitHub</a></li>
-                  <li><a href="http://www.bioinformatics.org/wiki/GRNsight" target="_blank">GRNSight @ Bioinformatics.Org wiki</a></li>
                   <li><a href="http://kdahlquist.github.io/GRNmap/index.html" target="blank">GRNmap</a></li>
                   <li><a href="http://nodejs.org/" target="_blank">Node.js</a></li>
                   <li><a href="http://expressjs.com/" target="_blank">Express Framework</a></li>
@@ -100,6 +106,15 @@
                   <li><a href="http://getbootstrap.com" target="_blank">Bootstrap</a></li>
                   <li><a href="https://github.com/dondi/GRNsight/wiki/Jekyll-Tutorial" target="_blank">Jekyll Tutorial</a></li>
                 </ul>
+
+                <h4 class="linkHeader">Bioinformatics Tools Registries</h4>
+                <ul class="linkInfo">
+                  <li><a href="https://links.bioinformatics.ca/links_directory/resource/83363/grnsight-web-application-and-service-visualizing-models-small-medium-scale-gene" target="_blank">GRNsight</a> @ <a href="https://links.bioinformatics.ca/links_directory/">bioinformatics.ca Links Directory</a></li>
+                  <li><a href="http://www.bioinformatics.org/wiki/GRNsight" target="_blank">GRNsight</a> @ <a href="http://www.bioinformatics.org/" target="_blank">Bioinformatics.org</a></li>
+                  <li><a href="https://biojs.net/#/component/grnsight" target="_blank">GRNsight</a> @ <a href="https://biojs.net" target="_blank">BioJS Registry</a></li>
+                  <li><a href="https://bio.tools/tool/GRNsight" target="_blank">GRNsight</a> @ <a href="https://bio.tools/" target="_blank">Elixir Tools and Data Services Registry</a></li>
+                  <li><a href="https://www.npmjs.com/package/grnsight" target="_blank">GRNsight</a> @ <a href="https://www.npmjs.com/" target="_blank">npm</a></li>
+                </ul>
             </div>
 
             <div id="footer">
@@ -138,7 +153,7 @@
             </div>
         </div>
 
-        <script>
+          <script>
             (function(i,s,o,g,r,a,m){i["GoogleAnalyticsObject"]=r;i[r]=i[r]||function(){
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@@ -147,10 +162,14 @@
             ga("create", "UA-54882218-1", "auto");
             ga("send", "pageview");
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-        <script src="https://code.jquery.com/jquery.js"></script>
-        <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.2.0/js/bootstrap.min.js"></script>
+        <script src="https://code.jquery.com/jquery-3.5.1.min.js"></script>
+        <script src="https://cdn.jsdelivr.net/npm/popper.js@1.16.1/dist/umd/popper.min.js" integrity="sha384-9/reFTGAW83EW2RDu2S0VKaIzap3H66lZH81PoYlFhbGU+6BZp6G7niu735Sk7lN" crossorigin="anonymous"></script>
+        <script src="https://stackpath.bootstrapcdn.com/bootstrap/4.5.2/js/bootstrap.min.js" integrity="sha384-B4gt1jrGC7Jh4AgTPSdUtOBvfO8shuf57BaghqFfPlYxofvL8/KUEfYiJOMMV+rV" crossorigin="anonymous"></script>
         <script src="/GRNsight/assets/js/main.js"></script>
         <script src="/GRNsight/assets/js/ga-report.js"></script>
+    
+    
+    
 
 
     </body>

package/_gh_pages/news.html

@@ -3,27 +3,23 @@
 
     <head>
         <title>GRNsight - News</title>
-        <link rel="stylesheet" type="text/css" href="/GRNsight/assets/css/bootstrap.min.css">
+        <link rel="shortcut icon" type="image/x-icon" href="favicon.ico">
+        <link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/4.5.2/css/bootstrap.min.css" integrity="sha384-JcKb8q3iqJ61gNV9KGb8thSsNjpSL0n8PARn9HuZOnIxN0hoP+VmmDGMN5t9UJ0Z" crossorigin="anonymous">
         <link rel="stylesheet" type="text/css" href="/GRNsight/assets/css/main.css">
         <meta charset="utf-8">
-        <!-- Begin Jekyll SEO tag v2.0.0 -->
+        <!-- Begin Jekyll SEO tag v2.6.1 -->
+<meta name="generator" content="Jekyll v3.9.0" />
 <meta property="og:title" content="News" />
-<meta name="description" content="GRNsight is an open source web application and service for visualizing models of small- to medium-scale gene regulatory networks." />
-<meta property="og:description" content="GRNsight is an open source web application and service for visualizing models of small- to medium-scale gene regulatory networks." />
-<link rel="canonical" href="http://dondi.github.io/GRNsight/news.html" />
-<meta property="og:url" content="http://dondi.github.io/GRNsight/news.html" />
+<meta property="og:locale" content="en_US" />
+<meta name="description" content="News and updates about the GRNsight gene regulatory network visualization web app, including new releases and conference presentations." />
+<meta property="og:description" content="News and updates about the GRNsight gene regulatory network visualization web app, including new releases and conference presentations." />
+<link rel="canonical" href="http://localhost:3001/GRNsight/news.html" />
+<meta property="og:url" content="http://localhost:3001/GRNsight/news.html" />
 <meta property="og:site_name" content="GRNsight" />
 <script type="application/ld+json">
-  {
-    "@context": "http://schema.org",
-    "@type": "WebPage",
-    "headline": "News",
-    "description": "GRNsight is an open source web application and service for visualizing models of small- to medium-scale gene regulatory networks.",
-    "logo": "http://dondi.github.io/GRNsight/assets/images/GRNsight_logo_20140710_main_resized.jpg",
-    "url": "http://dondi.github.io/GRNsight/news.html"
-  }
-</script>
+{"@type":"WebPage","url":"http://localhost:3001/GRNsight/news.html","description":"News and updates about the GRNsight gene regulatory network visualization web app, including new releases and conference presentations.","publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"http://localhost:3001/GRNsight/assets/images/GRNsight_logo_20140710_main_resized.jpg"}},"headline":"News","@context":"https://schema.org"}</script>
 <!-- End Jekyll SEO tag -->
+
     </head>
 
 
@@ -38,7 +34,7 @@
             </div>
             <p id="title"><a href="/GRNsight">GRNsight</a></p>
             <p id="subtext">Web app and service for visualizing models of gene regulatory networks.</p>
-            <div class="alert alert-success hidden" id="cookie-notice" role="alert">
+            <div class="alert alert-success d-none" id="cookie-notice" role="alert">
                 <div>This site uses Google Analytics to count pageviews and file uploads to demonstrate usage of our software to interested parties such as our employers and funding agencies. Information about your use of this site is shared with Google. By using this site, you agree to its use of cookies.</div>
                 <button class="cookie-action" data-dismiss="alert" aria-label="Got It">
                     <strong>Got It</strong>
@@ -68,15 +64,80 @@
 
                 </ul>
                 <p id="modText" class="modNav">
-                    Last modified: 6/6/16
+                    Last modified: 6/7/19
                 </p>
             </div>
+
         </div>
 
         <div id="mainContent">
             <p id="pageTitle">News</p>
             <div id="pageContent">
                 <div class="panel-group">
+
+                  <div class="panel panel-default">
+                      <div class="panel-heading">
+                          <p class="panel-title aboutHeaders">
+                              <a href="#news2019" data-toggle="collapse">
+                                  2019
+                              </a>
+                          </p>
+                      </div>
+                      <div id="news2019" class="panel-collapse collapse in">
+                          <div class="panel-body">
+                            <p class="newsDate">June 7, 2019</p>
+                            <p class="newsHeader">GRNsight v4.0.0 Released</p>
+                            <p class="newsInfo">For a description of the new features, please see the <a href="/GRNsight/about.html#v4_0_0Content">About page</a>.</p>
+                          </div>
+                      </div>
+                  </div>
+
+                  <div class="panel panel-default">
+                      <div class="panel-heading">
+                          <p class="panel-title aboutHeaders">
+                              <a href="#news2018" data-toggle="collapse">
+                                  2018
+                              </a>
+                          </p>
+                      </div>
+                      <div id="news2018" class="panel-collapse collapse in">
+                          <div class="panel-body">
+                            <p class="newsDate">June 1, 2018</p>
+                            <p class="newsHeader">GRNsight v3.1.0 Released</p>
+                            <p class="newsInfo">For a description of the new features, please see the <a href="/GRNsight/about.html#v3_1_0Content">About page</a>.</p>
+
+                            <p class="newsDate">April 29, 2018</p>
+                            <p class="newsHeader">GRNsight v3.0.0 Released</p>
+                            <p class="newsInfo">For a description of the new features, please see the <a href="/GRNsight/about.html#v3_0_0Content">About page</a>.</p>
+
+                            <p class="newsDate">January 22, 2018</p>
+                            <p class="newsHeader">GRNsight v2.3.0 Released</p>
+                            <p class="newsInfo">For a description of the new features, please see the <a href="/GRNsight/about.html#v2_3_0Content">About page</a>.</p>
+                          </div>
+                      </div>
+                  </div>
+
+                    <div class="panel panel-default">
+                        <div class="panel-heading">
+                            <p class="panel-title aboutHeaders">
+                                <a href="#news2017" data-toggle="collapse">
+                                    2017
+                                </a>
+                            </p>
+                        </div>
+                        <div id="news2017" class="panel-collapse collapse in">
+                            <div class="panel-body">
+                                <p class="newsDate">June 2, 2017</p>
+                                <p class="newsHeader">GRNsight v2.1.11 Released</p>
+                                <p class="newsInfo">For a description of the new features, please see the <a href="/GRNsight/about.html#v2_1_11Content">About page</a>.</p>
+
+                                <p class="newsDate">May 10, 2017</p>
+                                <p class="newsHeader">GRNsight v2.0.20 Released</p>
+                                <p class="newsInfo">For a description of the new features, please see the <a href="/GRNsight/about.html#v2_0_20Content">About page</a>.</p>
+                            </div>
+                        </div>
+                    </div>
+
                     <div class="panel panel-default">
                         <div class="panel-heading">
                             <p class="panel-title aboutHeaders">
@@ -88,9 +149,26 @@
 
                         <div id="news2016" class="panel-collapse collapse in">
                             <div class="panel-body">
+
+                                <p class="newsDate">September 12, 2016</p>
+                                <p class="newsHeader">GRNsight article published in <i>PeerJ Computer Science</i></p>
+                                <p class="newsInfo">Kam D. Dahlquist, John David N. Dionisio, Ben G. Fitzpatrick, Nicole A. Anguiano, Anindita Varshneya, Britain J. Southwick, Mihir Samdarshi. (2016) GRNsight: a web application and service for visualizing models of small- to medium-scale gene regulatory networks. <em>PeerJ Computer Science</em> 2:e85 <a href="https://doi.org/10.7717/peerj-cs.85" target="_blank">https://doi.org/10.7717/peerj-cs.85</a></p>
+
+                                <p class="newsDate">August 18, 2016</p>
+                                <p class="newsHeader">Revision to article describing GRNsight is posted online in <i>PeerJ Preprints</i></p>
+                                <p class="newsInfo">Kam D. Dahlquist, John David N. Dionisio, Ben G. Fitzpatrick, Nicole A. Anguiano, Anindita Varshneya, Britain J. Southwick, Mihir Samdarshi. (2016) GRNsight: a web application and service for visualizing models of small- to medium-scale gene regulatory networks. <em>PeerJ Preprints</em> 4:e2068v2 <a href="https://doi.org/10.7287/peerj.preprints.2068v2" target="_blank">https://doi.org/10.7287/peerj.preprints.2068v2</a></p>
+
+                                <p class="newsDate">August 12, 2016</p>
+                                <p class="newsHeader">GRNsight v1.18.1 Released</p>
+                                <p class="newsInfo">For a description of the new features, please see the <a href="/GRNsight/about.html#v1_18Content">About page</a>.</p>
+
+                                <p class="newsDate">July 9, 2016</p>
+                                <p class="newsHeader">GRNsight and GRNmap presented at BOSC and ISMB</p>
+                                <p class="newsInfo">Kam D. Dahlquist gave a lightning talk and poster about GRNsight and <a href="http://kdahlquist.github.io/GRNmap/index.html">GRNmap</a> at the <a href="https://www.open-bio.org/wiki/BOSC_2016">Bioinformatics Open Source Conference (BOSC) 2016</a> held on July 8-9, 2016 in Orlando, Florida.  <a href="https://www.open-bio.org/w/images/2/24/BOSC2016-program4.pdf">Click here to view the complete BOSC program with abstracts.</a>  The poster was also presented at the <a href="https://www.iscb.org/ismb2016">Intelligent Systems for Molecular Biology Conference (ISMB)</a> immediately following BOSC on July 10-12, 2016. <a href="http://f1000research.com/posters/5-1618">Click here to view the poster</a> on F1000Research.  <a href="http://f1000research.com/slides/5-1637">Click here to view the slides</a> on F1000Research.</p>
+
                                 <p class="newsDate">May 23, 2016</p>
                                 <p class="newsHeader">Article describing GRNsight is posted online in <i>PeerJ Preprints</i></p>
-                                <p class="newsInfo">Kam D. Dahlquist, John David N. Dionisio, Ben G. Fitzpatrick, Nicole A. Anguiano, Anindita Varshneya, Britain J. Southwick, Mihir Samdarshi. (2016) GRNsight: a web application and service for visualizing models of small- to medium-scale gene regulatory networks. <em>PeerJ Preprints</em> 4:e2068v1 <a href="https://doi.org/10.7287/peerj.preprints.2068v1">https://doi.org/10.7287/peerj.preprints.2068v1</a></p>
+                                <p class="newsInfo">Kam D. Dahlquist, John David N. Dionisio, Ben G. Fitzpatrick, Nicole A. Anguiano, Anindita Varshneya, Britain J. Southwick, Mihir Samdarshi. (2016) GRNsight: a web application and service for visualizing models of small- to medium-scale gene regulatory networks. <em>PeerJ Preprints</em> 4:e2068v1 <a href="https://doi.org/10.7287/peerj.preprints.2068v1" target="_blank">https://doi.org/10.7287/peerj.preprints.2068v1</a></p>
 
                                 <p class="newsDate">April 4, 2016</p>
                                 <p class="newsHeader">Experimental Biology</p>
@@ -265,7 +343,7 @@
             </div>
         </div>
 
-        <script>
+          <script>
             (function(i,s,o,g,r,a,m){i["GoogleAnalyticsObject"]=r;i[r]=i[r]||function(){
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@@ -274,10 +352,14 @@
             ga("create", "UA-54882218-1", "auto");
             ga("send", "pageview");
         </script>
-        <script src="https://code.jquery.com/jquery.js"></script>
-        <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.2.0/js/bootstrap.min.js"></script>
+        <script src="https://code.jquery.com/jquery-3.5.1.min.js"></script>
+        <script src="https://cdn.jsdelivr.net/npm/popper.js@1.16.1/dist/umd/popper.min.js" integrity="sha384-9/reFTGAW83EW2RDu2S0VKaIzap3H66lZH81PoYlFhbGU+6BZp6G7niu735Sk7lN" crossorigin="anonymous"></script>
+        <script src="https://stackpath.bootstrapcdn.com/bootstrap/4.5.2/js/bootstrap.min.js" integrity="sha384-B4gt1jrGC7Jh4AgTPSdUtOBvfO8shuf57BaghqFfPlYxofvL8/KUEfYiJOMMV+rV" crossorigin="anonymous"></script>
         <script src="/GRNsight/assets/js/main.js"></script>
         <script src="/GRNsight/assets/js/ga-report.js"></script>
+    
+    
+    
 
 
     </body>

package/_gh_pages/onlyfooter.html

@@ -0,0 +1,78 @@
+<!doctype html>
+<html>
+    <head>
+        <title>GRNsight - just the footer :3</title>
+        <link rel="stylesheet" type="text/css" href="/GRNsight/assets/css/bootstrap.min.css">
+        <link rel="stylesheet" type="text/css" href="/GRNsight/assets/css/main.css">
+        <link rel="stylesheet" type="text/css" href="/GRNsight/assets/css/footer.css">
+        <meta charset="utf-8">
+        <!-- Begin Jekyll SEO tag v2.6.1 -->
+<meta name="generator" content="Jekyll v3.9.0" />
+<meta property="og:title" content="just the footer :3" />
+<meta property="og:locale" content="en_US" />
+<meta name="description" content="GRNsight is an open source web application and service for visualizing models of small- to medium-scale gene regulatory networks." />
+<meta property="og:description" content="GRNsight is an open source web application and service for visualizing models of small- to medium-scale gene regulatory networks." />
+<link rel="canonical" href="http://localhost:3001/GRNsight/onlyfooter.html" />
+<meta property="og:url" content="http://localhost:3001/GRNsight/onlyfooter.html" />
+<meta property="og:site_name" content="GRNsight" />
+<script type="application/ld+json">
+{"@type":"WebPage","url":"http://localhost:3001/GRNsight/onlyfooter.html","description":"GRNsight is an open source web application and service for visualizing models of small- to medium-scale gene regulatory networks.","publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"http://localhost:3001/GRNsight/assets/images/GRNsight_logo_20140710_main_resized.jpg"}},"headline":"just the footer :3","@context":"https://schema.org"}</script>
+<!-- End Jekyll SEO tag -->
+
+    </head>
+    <body>
+
+        <div>
+            <div id="footer">
+  <hr id="separate">
+  <ul id="footerNav">
+    <li><a href="/GRNsight/" target="_blank">Home</a></li>
+    <li><a href="/GRNsight/about.html" target="_blank">About</a></li>
+    <li><a href="/GRNsight/news.html" target="_blank">News</a></li>
+    <li><a href="https://github.com/dondi/GRNsight" target="_blank">Developers</a></li>
+    <li><a href="/GRNsight/documentation.html" target="_blank">Documentation</a></li>
+    <li><a href="https://github.com/dondi/GRNsight/wiki" target="_blank">Wiki</a></li>
+    <li><a href="/GRNsight/publications.html" target="_blank">Publications</a></li>
+    <li><a href="/GRNsight/people.html" target="_blank">People</a></li>
+    <li><a href="/GRNsight/contact.html" target="_blank">Contact</a></li>
+    <li><a href="/GRNsight/links.html" target="_blank">Links</a></li>
+    <li><a href="/GRNsight/beta.html" target="_blank">Beta</a></li>
+    <li><a href="/GRNsight/about.html#privacy" target="_blank">Privacy</a></li>
+  </ul>
+  <p id="CCLicense">
+      This web site is free and open to all users and there is no login requirement.
+
+      Web site content is available under the <a href="http://creativecommons.org/licenses/by-nc-sa/3.0/" target="_blank">Creative Commons
+      <br>
+      Attribution Non-Commercial Share Alike 3.0 Unported License</a>.
+
+      GRNsight code is available under the open source <a href="http://opensource.org/licenses/BSD-3-Clause" target="_blank">BSD license</a>.
+
+  </p>
+</div>
+
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+        </div>
+
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+        <script src="https://stackpath.bootstrapcdn.com/bootstrap/4.5.2/js/bootstrap.min.js" integrity="sha384-B4gt1jrGC7Jh4AgTPSdUtOBvfO8shuf57BaghqFfPlYxofvL8/KUEfYiJOMMV+rV" crossorigin="anonymous"></script>
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+        <script src="/GRNsight/assets/js/ga-report.js"></script>
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+
+</html>