npm - grnsight - Versions diffs - 4.0.0 → 6.0.0 - Mend

grnsight 4.0.0 → 6.0.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (458) hide show

package/_gh_pages/people.html CHANGED Viewed

@@ -3,27 +3,23 @@
     <head>
         <title>GRNsight - People</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="People" />
-<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/people.html" />
-<meta property="og:url" content="http://dondi.github.io/GRNsight/people.html" />
+<meta property="og:locale" content="en_US" />
+<meta name="description" content="Principal Investigators, current and former undergraduate research assistants for the GRNsight gene regulatory network visualization web app." />
+<meta property="og:description" content="Principal Investigators, current and former undergraduate research assistants for the GRNsight gene regulatory network visualization web app." />
+<link rel="canonical" href="http://localhost:3001/GRNsight/people.html" />
+<meta property="og:url" content="http://localhost:3001/GRNsight/people.html" />
 <meta property="og:site_name" content="GRNsight" />
 <script type="application/ld+json">
-  {
-    "@context": "http://schema.org",
-    "@type": "WebPage",
-    "headline": "People",
-    "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/people.html"
-  }
-</script>
+{"@type":"WebPage","url":"http://localhost:3001/GRNsight/people.html","description":"Principal Investigators, current and former undergraduate research assistants for the GRNsight gene regulatory network visualization web app.","publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"http://localhost:3001/GRNsight/assets/images/GRNsight_logo_20140710_main_resized.jpg"}},"headline":"People","@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>
@@ -68,51 +64,140 @@
                 </ul>
                 <p id="modText" class="modNav">
-                    Last modified: 6/4/15
+                    Last modified: 9/17/20
                 </p>
             </div>
         </div>
         <div id="mainContent">
-            <div class="fixWidthforImage">
-                <div class="pull-left">
-                    <p id="pageTitle">People</p>
+<div class="container carousel-container">
+  <div class="row">
+    <div id="carouselControls" class="carousel slide" data-ride="carousel">
+      <div class="carousel-inner" role="listbox">
+        <div class="item carousel-item active">
+          <!-- Temporary hardcoded width pending final carousel styles. -->
+          <img
+            class="w-100"
+            style="width: 1024px"
+            src="/GRNsight/assets/images/grnsight2020.png"
+            alt="GRNsight 2020"
+          />
+          <div class="carousel-caption d-none d-mid-block">
+            <p>
+              The remote/online GRNsight team at one of our weekly meetings
+              on 11 September 2020<!-- 10:43 am -->. <em>Clockwise from top left:</em>
+              Ian M. Green, John David N. Dionisio, Kam Dahlquist, Ona O. Igbinedion,
+              and Lauren L. Amparo.
+            </p>
+          </div>
+        </div>
+<!-- TODO Full Bootstrap CSS must be activated for this to work.
+        <div class="item carousel-item">
+          <img
+            class="w-100"
+            src="/GRNsight/assets/images/LMUSymposium_Group_20150321-2_resized.jpg"
+            alt="UGRS 7"
+          />
+          <div class="carousel-caption d-none d-mid-block">
+            <p>
+              The Dahlquist Lab along with the LMU Bioinformatics and
+              Biomathematics Groups at the
+              <a href="http://academics.lmu.edu/symposium/"
+                >7th Annual Loyola Marymount University Undergraduate Research
+                Symposium</a
+              >
+              on 21 March 2015. <em>Back row, left to right:</em> Juan Carrillo,
+              Natalie Williams, K. Grace Johnson, Kevin Wyllie, Kevin McGee, Kam
+              Dahlquist, Ben Fitzpatrick.
+              <em>Front row, left to right:</em> Monica Hong, Nicole Anguiano,
+              Anindita Varshneya, Trixie Roque, John David N. Dionisio.
+            </p>
+          </div>
+        </div>
+        <div class="item carousel-item">
+          <img class="w-100"
+          src="/GRNsight/assets/images/Choe-Shin_CMSI402-poster-session_20180430.jpg"
+          alt="Eileen Choe and Jen Shin"/>
+          <div class="carousel-caption d-none d-mid-block">
+            <p>
+              Eileen Choe and Jen Shin
+            </p>
+          </div>
+        </div>
+-->
+      </div>
+      <a
+        class="left carousel-control carousel-control-prev"
+        href="#carouselControls"
+        role="button"
+        data-slide="prev"
+      >
+        <span class="glyphicon glyphicon-chevron-left carousel-control-prev-icon" aria-hidden="true"></span>
+        <span class="sr-only">Previous</span>
+      </a>
+      <a
+        class="right carousel-control carousel-control-next"
+        href="#carouselControls"
+        role="button"
+        data-slide="next"
+      >
+        <span class="glyphicon glyphicon-chevron-right carousel-control-next-icon" aria-hidden="true"></span>
+        <span class="sr-only">Next</span>
+      </a>
+    </div>
+  </div>
+</div>
+            <div class="people-section">
+              <p id="pageTitle">People</p>
-                    <div id="pageContent">
+              <div id="pageContent" class="people-columns">
+                <section>
                         <h2>Principal Investigators</h2>
                           <p class="name">Kam D. Dahlquist, Ph.D.</p>
                             <p class="personInfo">
-                              <a href="http://myweb.lmu.edu/kdahlqui" target="_blank">http://myweb.lmu.edu/kdahlqui</a> <br>
+                              <a href="http://kdahlquist.github.io/DahlquistLab/" target="_blank">http://kdahlquist.github.io/DahlquistLab/</a> <br>
                               Department of Biology</p><br>
                           <p class="name">John David N. Dionisio, Ph.D.</p>
                             <p class="personInfo">
-                              <a href="http://myweb.lmu.edu/dondi" target="_blank">http://myweb.lmu.edu/dondi</a> <br>
-                          Department of Electrical Engineering and Computer Science</p> <br>
+                              <a href="http://dondi.lmu.build/" target="_blank">http://dondi.lmu.build/</a> <br>
+                          Department of Computer Science</p> <br>
                         <p class="name">Ben G. Fitzpatrick, Ph.D.</p>
                         <p class="personInfo">
-                            <a href="http://myweb.lmu.edu/bfitzpatrick/" target="_blank">http://myweb.lmu.edu/bfitzpatrick</a> <br>
                             Department of Mathematics
                         </p>
                         <h2>Manager of Laboratory Facilities</h2>
                           <p class="name">Masao Kitamura</p>
-                            <p class="personInfo">Department of Electrical Engineering and Computer Science</p>
+                            <p class="personInfo">Department of Computer Science</p>
+                </section>
+                <section>
                         <h2>Research Assistants</h2>
                           <p class="name">Current Students</p>
-                            <p class="studentName">Mihir Samdarshi (LMU Biology '19) Fall 2015 - Present</p>
-                            <p class="studentName">Anindita Varshneya (LMU Biology '17), Fall 2014 - Present</p>
+                            <p class="studentName">Ona O. Igbinedion (LMU Computer Science '22) Spring 2020 - Present</p>
+                            <p class="studentName">Ian M. Green (LMU Computer Science '22) Fall 2020 - Present</p>
+                            <p class="studentName">Lauren L. Amparo (LMU Biology '24) Fall 2020 - Present</p>
                           <p class="name">Former Students</p>
-                            <p class="studentName">Nicole Anguiano (LMU Computer Science '16), Spring 2014 - Fall 2015</p>
+                            <p class="studentName">Alexia M. Filler (LMU Computer Science '20) Spring 2019 - Spring 2020</p>
+                            <p class="studentName">Kevin B. Patterson (LMU Computer Science '20) Spring 2020 - Spring 2020</p>
+                            <p class="studentName">Mihir Samdarshi (LMU Biology '19) Fall 2015 - Fall 2019</p>
+                            <p class="studentName">John L. Lopez (LMU Computer Science '20) Spring 2018 - Spring 2019</p>
+                            <p class="studentName">Justin Kyle T. Torres (LMU Computer Science '19) Fall 2018</p>
+                            <p class="studentName">Eileen J. Choe (LMU Computer Science '18) Spring 2017 - Spring 2018</p>
+                            <p class="studentName">Yeon-Soo (Jen) Shin (LMU Computer Science '19), Fall 2016 - Spring 2018</p>
+                            <p class="studentName">Edward B. Bachoura (LMU Computer Science '19) Spring 2017 - Fall 2017</p>
+                            <p class="studentName">Nicole A. Anguiano (LMU Computer Science '16), Spring 2014 - Spring 2017</p>
+                            <p class="studentName">Anindita Varshneya (LMU Biology '17), Fall 2014 - Spring 2017</p>
                             <p class="studentName">Katrina Sherbina (LMU Biomathematics, '14), Spring 2014</p>
-                            <p class="studentName">Britain Southwick (LMU Computer Science '14), Spring 2014</p>
-                    </div>
-                </div>
-                <div class="pull-right">
-                    <img src="/GRNsight/assets/images/LMUSymposium_Group_20150321-2_resized.jpg"/>
-                    <p>The Dahlquist Lab along with the LMU Bioinformatics and Biomathematics Groups at the <a href="http://academics.lmu.edu/symposium/">7th Annual Loyola Marymount University Undergraduate Research Symposium</a> on 21 March 2015. <em>Back row, left to right:</em> Juan Carrillo, Natalie Williams, K. Grace Johnson, Kevin Wyllie, Kevin McGee, Kam Dahlquist, Ben Fitzpatrick. <em>Front row, left to right:</em> Monica Hong, Nicole Anguiano, Anindita Varshneya, Trixie Roque, John David N. Dionisio.</p>
-                </div>
+                            <p class="studentName">Britain J. Southwick (LMU Computer Science '14), Spring 2014</p>
+                </section>
+              </div>
             </div>
             <div id="footer">
@@ -151,7 +236,7 @@
             </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),
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@@ -160,10 +245,14 @@
             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/privacy.html CHANGED Viewed

@@ -3,27 +3,23 @@
     <head>
         <title>GRNsight - Beta</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="Beta" />
+<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/privacy.html" />
-<meta property="og:url" content="http://dondi.github.io/GRNsight/privacy.html" />
+<link rel="canonical" href="http://localhost:3001/GRNsight/privacy.html" />
+<meta property="og:url" content="http://localhost:3001/GRNsight/privacy.html" />
 <meta property="og:site_name" content="GRNsight" />
 <script type="application/ld+json">
-  {
-    "@context": "http://schema.org",
-    "@type": "WebPage",
-    "headline": "Beta",
-    "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/privacy.html"
-  }
-</script>
+{"@type":"WebPage","url":"http://localhost:3001/GRNsight/privacy.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":"Beta","@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>
@@ -71,6 +67,7 @@
                     Last modified: 3/9/15
                 </p>
             </div>
         </div>
         <div id="mainContent">
@@ -121,7 +118,7 @@
             </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)
@@ -130,10 +127,19 @@
             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 src="/GRNsight/assets/js/iframeResizer.min.js"></script>
+        <script src="https://grnsight.cs.lmu.edu/beta/client/js/iframe-coordination.js"></script>
     </body>

package/_gh_pages/publications.html CHANGED Viewed

@@ -3,27 +3,23 @@
     <head>
         <title>GRNsight - Publications</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="Publications" />
-<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/publications.html" />
-<meta property="og:url" content="http://dondi.github.io/GRNsight/publications.html" />
+<meta property="og:locale" content="en_US" />
+<meta name="description" content="Papers, talks, and posters about GRNsight, a web application and service for visualizing models of small- to medium-scale gene regulatory networks." />
+<meta property="og:description" content="Papers, talks, and posters about GRNsight, a web application and service for visualizing models of small- to medium-scale gene regulatory networks." />
+<link rel="canonical" href="http://localhost:3001/GRNsight/publications.html" />
+<meta property="og:url" content="http://localhost:3001/GRNsight/publications.html" />
 <meta property="og:site_name" content="GRNsight" />
 <script type="application/ld+json">
-  {
-    "@context": "http://schema.org",
-    "@type": "WebPage",
-    "headline": "Publications",
-    "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/publications.html"
-  }
-</script>
+{"@type":"WebPage","url":"http://localhost:3001/GRNsight/publications.html","description":"Papers, talks, and posters about GRNsight, a 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":"Publications","@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>
@@ -68,9 +64,10 @@
                 </ul>
                 <p id="modText" class="modNav">
-                    Last modified: 6/7/16
+                    Last modified: 6/24/18
                 </p>
             </div>
         </div>
         <div id="mainContent">
@@ -89,16 +86,21 @@
                         <div id="papers" class="panel-collapse collapse in">
                             <div class="panel-body">
                                 <p class="publication">
-                                    <b>May 23, 2016</b><br>
-                                    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><br><br>
+                                    <b>September 12, 2016</b><br>
+                                    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><br><br>
-                                    <a href="https://peerj.com/preprints/2068v1/">View HTML with embedded PDF</a><br>
-                                    <a href="https://peerj.com/preprints/2068v1.pdf">Download PDF (2.4 MB)</a><br><br>
+                                    <a href="https://doi.org/10.7717/peerj-cs.85" target="_blank">View HTML with embedded PDF</a><br>
+                                    <a href="https://peerj.com/articles/cs-85.pdf" target="_blank">Download PDF (2.7 MB)</a><br>
+                                    <a href="https://peerj.com/articles/cs-85/reviews/" target="_blank">See peer review history</a><br><br>
+                                    <i>Note that preprints of this article were posted in PeerJ Preprints on <a href="https://peerj.com/preprints/2068v1/" target="_blank">May 23</a> and <a href="https://peerj.com/preprints/2068v2/" target="_blank">August 18</a>, 2016.</i><br><br>
                                     <b>Abstract</b><br>
-                                    GRNsight is a web application and service for visualizing models of gene regulatory networks (GRNs). A gene regulatory network consists of genes, transcription factors, and the regulatory connections between them which govern the level of expression of mRNA and protein from genes. The original motivation to create GRNsight came from our efforts to perform parameter estimation and forward simulation of the dynamics of a differential equations model of a small GRN with 21 nodes and 31 edges. We wanted a quick and easy way to visualize the weight parameters from the model which represent the direction and magnitude of the influence of a transcription factor on its target gene, so we created GRNsight. GRNsight automatically lays out either an unweighted or weighted network graph based on an Excel input spreadsheet containing an adjacency matrix where regulators are named in the columns and target genes in the rows. When a user uploads a spreadsheet with an unweighted adjacency matrix, GRNsight automatically lays out the graph using black lines and pointed arrowheads. When a user uploads a spreadsheet with a weighted adjacency matrix, GRNsight uses pointed and blunt arrowheads, and colors the edges and adjusts their thicknesses based on the sign (positive for activation or negative for repression) and magnitude of the weight parameter. GRNsight is written in JavaScript, with diagrams facilitated by D3.js, a data visualization library. Node.js and the Express framework handle server-side functions. GRNsight’s diagrams are based on D3.js’s force graph layout algorithm, which was then extensively customized to support the specific needs of GRN visualization. Nodes are rectangular and support gene labels of up to 12 characters. The edges are arcs, which become straight lines when the nodes are close together. Self-regulatory edges are indicated by a loop on the lower-right side of a node. When a user mouses over an edge, the numerical value of the weight parameter is displayed. Visualizations can be modified by sliders that adjust D3.js’s force graph layout parameters and through manual node dragging. GRNsight is best-suited for visualizing networks of fewer than 35 nodes and 70 edges, although it accepts networks of up to 75 nodes or 150 edges. Although originally designed for GRNs, GRNsight has general applicability for displaying any small, unweighted or weighted network with directed edges for systems biology or other application domains. GRNsight serves as an example of following and teaching best practices for scientific computing, using an open and test-driven development model with rigorous documentation of requirements and issues on GitHub. An exhaustive unit testing framework using Mocha and the Chai assertion library consists of over 130 automated unit tests that examine over 520 test files to ensure that the program is running as expected. GRNsight is available under the open source BSD license at <a href="http://dondi.github.io/GRNsight/">http://dondi.github.io/GRNsight/</a>.
+                                    GRNsight is a web application and service for visualizing models of gene regulatory networks (GRNs). A gene regulatory network consists of genes, transcription factors, and the regulatory connections between them which govern the level of expression of mRNA and protein from genes. The original motivation came from our efforts to perform parameter estimation and forward simulation of the dynamics of a differential equations model of a small GRN with 21 nodes and 31 edges. We wanted a quick and easy way to visualize the weight parameters from the model which represent the direction and magnitude of the influence of a transcription factor on its target gene, so we created GRNsight. GRNsight automatically lays out either an unweighted or weighted network graph based on an Excel spreadsheet containing an adjacency matrix where regulators are named in the columns and target genes in the rows, a Simple Interaction Format (SIF) text file, or a GraphML XML file. When a user uploads an input file specifying an unweighted network, GRNsight automatically lays out the graph using black lines and pointed arrowheads.  For a weighted network, GRNsight uses pointed and blunt arrowheads, and colors the edges and adjusts their thicknesses based on the sign (positive for activation or negative for repression) and magnitude of the weight parameter. GRNsight is written in JavaScript, with diagrams facilitated by D3.js, a data visualization library. Node.js and the Express framework handle server-side functions. GRNsight’s diagrams are based on D3.js’s force graph layout algorithm, which was then extensively customized to support the specific needs of GRNs. Nodes are rectangular and support gene labels of up to 12 characters.  The edges are arcs, which become straight lines when the nodes are close together.  Self-regulatory edges are indicated by a loop.  When a user mouses over an edge, the numerical value of the weight parameter is displayed. Visualizations can be modified by sliders that adjust the force graph layout parameters and through manual node dragging. GRNsight is best-suited for visualizing networks of fewer than 35 nodes and 70 edges, although it accepts networks of up to 75 nodes or 150 edges. GRNsight has general applicability for displaying any small, unweighted or weighted network with directed edges for systems biology or other application domains. GRNsight serves as an example of following and teaching best practices for scientific computing and complying with FAIR Principles, using an open and test-driven development model with rigorous documentation of requirements and issues on GitHub. An exhaustive unit testing framework using Mocha and the Chai assertion library consists of around 160 automated unit tests that examine nearly 530 test files to ensure that the program is running as expected. The GRNsight application (<a href="http://dondi.github.io/GRNsight/">http://dondi.github.io/GRNsight/</a>) and code (<a href="https://github.com/dondi/GRNsight">https://github.com/dondi/GRNsight</a>) are available under the open source BSD license.
                                 </p>
                             </div>
                         </div>
                     </div>
@@ -114,6 +116,32 @@
                         <div id="presentations" class="panel-collapse collapse">
                             <div class="panel-body">
+                                <p class="abstract">
+                                    <b>LMU Department of Biology Seminar Series</b><br><br>
+                                    September 16, 2016<br>
+                                    GRNmap and GRNsight: Using the power of genomics, mathematics,and open source visualization software to understand gene regulatory networks in yeast<br>
+                                    <b>Kam D. Dahlquist</b><br><br>
+                                </p>
+<br>
+                                <p class="abstract">
+                                    <b><a href="https://www.open-bio.org/wiki/BOSC_2016">Bioinformatics Open Source Conference (BOSC) 2016, Orlando, FL</a></b><br><br>
+                                    July 9, 2016<br>
+                                    GRNmap and GRNsight: open source software for dynamical systems modeling and visualization of medium-scale gene regulatory networks<br>
+                                    <b>Kam D. Dahlquist</b>, Ben G. Fitzpatrick, John David N. Dionisio, Nicole A. Anguiano, Juan S. Carrillo, Trixie Anne M. Roque, Anindita Varshneya, Mihir Samdarshi, and Chukwuemeka Azinge<br><br>
+                                    Abstract: A gene regulatory network (GRN) consists of genes, transcription factors, and the regulatory connections between them that govern the level of expression of mRNA and proteins from those genes. Over a period of several years, our group has developed a MATLAB software package, called GRNmap, that uses ordinary differential equations to model the dynamics of medium-scale GRNs. The program uses a penalized least squares approach (Dahlquist et al. 2015, DOI: 10.1007/s11538-015-0092-6) to estimate production rates, expression thresholds, and regulatory weights for each transcription factor in the network based on gene expression data, and then performs a forward simulation of the dynamics of the network. GRNmap has options for using a sigmoidal or Michaelis-Menten production function.  The large number of developers and time span of development led to a code base that was difficult to revise and adjust. We therefore brought the code under version control in a GitHub repository and refactored the script-based software with global variables into a function-based package that uses an object to carry relevant information from function to function. This modular approach allows for cleaner, less ambiguous code and increased maintainability. We standardized the format of the input and output Excel workbooks, making them more readable. We also added an optimization diagnostics output worksheet which includes both the actual and theoretical minimum least squared error overall, and the mean squared errors for the individual genes. The MATLAB compiler was used to create an executable that can be run on any Windows machine without the need of a MATLAB license, increasing the accessibility of our program. Finally, we have implemented test-driven development, creating unit tests for all new features to speed up debugging and to prevent future code regressions.  We are improving the test coverage of previous code.<br><br>
+                                    GRNsight is an open source web application for visualizing such models of gene regulatory networks. GRNsight accepts GRNmap- or user-generated spreadsheets containing an adjacency matrix representation of the GRN and automatically lays out the graph of the GRN model. It is written in JavaScript, with diagrams facilitated by D3.js. Node.js and the Express framework handle server-side functions. GRNsight’s diagrams are based on D3.js’s force graph layout algorithm, which was then extensively customized. GRNsight uses pointed and blunt arrowheads, and colors the edges and adjusts their thicknesses based on the sign (activation or repression) and magnitude of the GRNmap weight parameter. Visualizations can be modified through manual node dragging and sliders that adjust the force graph parameters. From the early stages, GRNsight has had a unit testing framework using Mocha and the Chai assertion library to perform test-driven development where unit tests are written before new functionality is coded. This framework consists of over 160 automated unit tests that examine over 450 test files to ensure that the program is running as expected. Error and warning messages inform the user what happened, the source of the problem, and possible solutions. <br><br>
+                                    Together, the life cycle of these two programs illustrate the differences between the cultures of mathematics and computing, the challenges and benefits of bringing an existing code base up to open development standards (GRNmap), and the advantages of starting a project using best practices from the beginning (GRNsight).  Our goal is to facilitate reproducible research.<br><br>
+                                     <a href="http://f1000research.com/slides/5-1637">Click here to view the slides on F1000Research.</a><br><br>
+                                     <iframe src="//www.slideshare.net/GRNsight/slideshelf" width="615px" height="470px" frameborder="0" marginwidth="0" marginheight="0" scrolling="no" style="border:none;" allowfullscreen webkitallowfullscreen mozallowfullscreen></iframe>
+                                     <!--<figcaption><a href="http://www.slideshare.net/GRNsight/dahlquist-bosc-20160709-64224474" target="_blank">Slides</a> from <a href="//www.slideshare.net/GRNsight" target="_blank">GRNsight</a> on SlideShare</figcaption>-->
+                                </p>
+<br>
                                 <p class="abstract">
                                     <b><a href="http://experimentalbiology.org/PDFS/2016/EB-2016-Program-Web-FullProgram.aspx">Experimental Biology 2016, San Diego, CA</a></b><br><br>
                                     April 4, 2016<br>
@@ -139,7 +167,7 @@
                                 </p>
                                 <figure class="publication">
-                                    <iframe src="http://www.slideshare.net/slideshow/embed_code/44236648" width="425" height="355" frameborder="0" marginwidth="0" marginheight="0" scrolling="no" style="border:1px solid #CCC; border-width:1px; margin-bottom:5px; max-width: 100%;" allowfullscreen></iframe>
+                                    <iframe src="//www.slideshare.net/slideshow/embed_code/44236648" width="425" height="355" frameborder="0" marginwidth="0" marginheight="0" scrolling="no" style="border:1px solid #CCC; border-width:1px; margin-bottom:5px; max-width: 100%;" allowfullscreen></iframe>
                                     <figcaption><a href="http://www.slideshare.net/GRNsight/dahlquist-so-calsysbio20140131" title="Dahlquist so calsysbio_20140131" target="_blank">Presentation slides</a> from <a href="//www.slideshare.net/GRNsight" target="_blank">GRNsight</a> on SlideShare</figcaption>
                                 </figure>
@@ -151,7 +179,7 @@
                                 </p>
                                 <figure class="publication">
-                                    <iframe src="http://www.slideshare.net/slideshow/embed_code/35811802" width="427" height="356" allowfullscreen></iframe>
+                                    <iframe src="//www.slideshare.net/slideshow/embed_code/35811802" width="427" height="356" allowfullscreen></iframe>
                                     <figcaption><a href="https://www.slideshare.net/GRNsight/southwick-britain-grnsightcmsi402presentation20140508" title="Southwick britain gr_nsight_cmsi402-presentation_20140508" target="_blank">Presentation slides</a> from <a href="http://www.slideshare.net/GRNsight" target="_blank">GRNsight</a> on SlideShare</figcaption>
                                 </figure>
@@ -167,7 +195,7 @@
                                 </p>
                                 <figure class="publication">
-                                    <iframe src="http://www.slideshare.net/slideshow/embed_code/35811669" width="427" height="356" allowfullscreen></iframe>
+                                    <iframe src="//www.slideshare.net/slideshow/embed_code/35811669" width="427" height="356" allowfullscreen></iframe>
                                     <figcaption><a href="https://www.slideshare.net/GRNsight/southwick-anguiano-lmusymposiumpresentation20140329" title="Southwick anguiano lmu-symposium_presentation_20140329" target="_blank">Presentation slides</a> from <a href="http://www.slideshare.net/GRNsight" target="_blank">GRNsight</a> on SlideShare</figcaption>
                                 </figure>
                             </div>
@@ -185,6 +213,16 @@
                         <div id="posters" class="panel-collapse collapse">
                             <div class="panel-body">
+                                <p class="abstract">
+                                    <b><a href="https://www.open-bio.org/wiki/BOSC_2016">Bioinformatics Open Source Conference (BOSC) 2016</a> and <a href="http://www.iscb.org/ismb2016">Intelligent Systems for Molecular Biology (ISMB) 2016</a>, Orlando, FL</a></b><br><br>
+                                    July 8-12, 2016<br>
+                                    GRNmap and GRNsight: open source software for dynamical systems modeling and visualization of medium-scale gene regulatory networks<br>
+                                    <b>Kam D. Dahlquist</b>, Ben G. Fitzpatrick, John David N. Dionisio, Nicole A. Anguiano, Juan S. Carrillo, Tessa A. Morris, Anindita Varshneya, Natalie E. Williams, K. Grace Johnson, Trixie Anne M. Roque, Kristen M. Horstmann, Mihir Samdarshi, Chukwuemeka E. Azinge, Brandon J. Klein, Margaret J. O’Neil1<br><br>
+                                    Abstract: A gene regulatory network (GRN) consists of genes, transcription factors, and the regulatory connections between them that govern the level of expression of mRNA and proteins from those genes. Our open source MATLAB software package, GRNmap (<a href="http://kdahlquist.github.io/GRNmap/">http://kdahlquist.github.io/GRNmap/</a>), uses ordinary differential equations to model the dynamics of medium-scale GRNs. The program uses a penalized least squares approach (Dahlquist et al. 2015, DOI: 10.1007/s11538-015-0092-6) to estimate production rates, expression thresholds, and regulatory weights for each transcription factor in the network based on gene expression data, and then performs a forward simulation of the dynamics of the network. GRNmap has options for using a sigmoidal or Michaelis-Menten production function.  Parameters for a series of related networks, ranging in size from 15 to 35 genes, were optimized against DNA microarray data measuring the transcriptional response to cold shock in budding yeast, Saccharomyces cerevisiae, for the wild type strain and strains deleted for the transcription factors Cin5, Gln3, Hap4, Hmo1, and Zap1, giving biological insights into this process. GRNsight is an open source web application for visualizing such models of gene regulatory networks (<a href="http://dondi.github.io/GRNsight/index.html">http://dondi.github.io/GRNsight/index.html</a>). GRNsight accepts GRNmap- or user-generated Excel spreadsheets containing an adjacency matrix representation of the GRN and automatically lays out the graph. The application colors the edges and adjusts their thicknesses based on the sign (activation or repression) and the strength (magnitude) of the regulatory relationship, respectively. Users can then modify the graph to define the best visual layout for the network. This work was partially supported by NSF award 0921038.<br><br>
+                                     <a href="http://f1000research.com/posters/5-1618">Click here</a> to view the poster on F1000Research. <a href="//www.slideshare.net/GRNsight/dahlquist-etal-boscismb2016poster-64224013" title="Dahlquist et-al bosc-ismb_2016_poster" target="_blank">Click here</a> to view poster from <a href="//www.slideshare.net/GRNsight" target="_blank">GRNsight</a> on SlideShare.<br><br>
+                                </p>
                                 <p class="abstract">
                                     <b><a href="http://experimentalbiology.org/PDFS/2016/EB-2016-Program-Web-FullProgram.aspx">Experimental Biology 2016, San Diego, CA</a></b><br><br>
                                     April 4, 2016<br>
@@ -199,7 +237,7 @@
                                     <figcaption><a href="//www.slideshare.net/GRNsight/varshneya-samdarshi-lmusymposium2016" title="Varshneya samdarshi lmu_symposium_2016" target="_blank">Poster</a> from <a href="//www.slideshare.net/GRNsight" target="_blank">GRNsight</a> on SlideShare</figcaption>
                                 </figure>
+<br><br>
                                 <p class="abstract">
                                     <b><a href="http://academics.lmu.edu/media/lmuacademics/undergraduateresearchsymposium/documents/ei8ht_Symposium_Long_Program_16_Secured.pdf">Loyola Marymount University 8<sup>th</sup> Annual Undergraduate Research Symposium</a></b><br><br>
                                     March 19, 2016<br>
@@ -225,7 +263,7 @@
                                 </p>
                                 <figure class="publication">
-                                    <iframe src="http://www.slideshare.net/slideshow/embed_code/46240444" width="476" height="400" frameborder="0" marginwidth="0" marginheight="0" scrolling="no"></iframe>
+                                    <iframe src="//www.slideshare.net/slideshow/embed_code/46240444" width="476" height="400" frameborder="0" marginwidth="0" marginheight="0" scrolling="no"></iframe>
                                     <figcaption><a href="http://www.slideshare.net/GRNsight/anguiano-varshneya-lmusymposium2015" title="Anguiano varshneya lmu_symposium_2015" target="_blank">Poster</a> from <a href="http://www.slideshare.net/GRNsight" target="_blank">GRNsight</a> on SlideShare</figcaption>
                                 </figure>
@@ -240,7 +278,7 @@
                                 </p>
                                 <figure class="publication">
-                                    <iframe src="http://www.slideshare.net/slideshow/embed_code/46240444" width="476" height="400" frameborder="0" marginwidth="0" marginheight="0" scrolling="no"></iframe>
+                                    <iframe src="//www.slideshare.net/slideshow/embed_code/46240444" width="476" height="400" frameborder="0" marginwidth="0" marginheight="0" scrolling="no"></iframe>
                                     <figcaption><a href="http://www.slideshare.net/GRNsight/anguiano-varshneya-lmusymposium2015" title="Anguiano varshneya lmu_symposium_2015" target="_blank">Poster</a> from <a href="http://www.slideshare.net/GRNsight" target="_blank">GRNsight</a> on SlideShare</div>
                                 </figure>
@@ -255,7 +293,7 @@
                                 </p>
                                 <figure class="publication">
-                                    <iframe src="http://www.slideshare.net/slideshow/embed_code/42279842" width="476" height="400" frameborder="0" marginwidth="0" marginheight="0" scrolling="no"></iframe>
+                                    <iframe src="//www.slideshare.net/slideshow/embed_code/42279842" width="476" height="400" frameborder="0" marginwidth="0" marginheight="0" scrolling="no"></iframe>
                                     <figcaption><a href="http://www.slideshare.net/GRNsight/anguiano-varshneya-sccurposter20141122" title="Anguiano varshneya sccur-poster_20141122" target="_blank">Poster</a> from <a href="http://www.slideshare.net/GRNsight" target="_blank">GRNsight</a> on SlideShare</figcaption>
                                 </figure>
@@ -270,7 +308,7 @@
                                 </p>
                                 <figure class="publication">
-                                    <iframe src="http://www.slideshare.net/slideshow/embed_code/42279842" width="476" height="400" frameborder="0" marginwidth="0" marginheight="0" scrolling="no"></iframe>
+                                    <iframe src="//www.slideshare.net/slideshow/embed_code/42279842" width="476" height="400" frameborder="0" marginwidth="0" marginheight="0" scrolling="no"></iframe>
                                     <figcaption><a href="http://www.slideshare.net/GRNsight/anguiano-varshneya-sccurposter20141122" title="Anguiano varshneya sccur-poster_20141122" target="_blank">Poster</a> from <a href="http://www.slideshare.net/GRNsight" target="_blank">GRNsight</a> on SlideShare</figcaption>
                                 </figure>
@@ -316,7 +354,7 @@
             </div>
         </div>
-        <script>
+          <script>
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package/_gh_pages/robots.txt ADDED Viewed

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1	+ Sitemap: http://localhost:3001/GRNsight/sitemap.xml