grnsight 6.0.4 → 6.0.7

package/_gh_pages/assets/js/main.js

@@ -1,132 +0,0 @@
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-
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-    var SCROLL_START_POINT = 140;
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-
-    var PRIVACY_COOKIE = "_grnsight_privacy_";
-    var checkForPrivacyCookie = function () {
-        // Thank you http://stackoverflow.com/questions/4825683/how-do-i-create-and-read-a-value-from-cookie
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-        if (!getCookie(PRIVACY_COOKIE)) {
-            $("#cookie-notice").removeClass("hidden");
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-            var sidebarShouldScroll = $(window).scrollTop() > SCROLL_START_POINT;
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-
-    var setupDocumentationPanels = function () {
-        var documentationPanelInformation = [ [ ".showSection2", "#section2Content", "#section2" ],
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-
-    var initializePage = function () {
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-        disableSidebarHorizontalMovement("#stickyBar");
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-
-        var pageIsDocumentationPage = (location.pathname === "/GRNsight/documentation.html");
-        if (pageIsDocumentationPage) {
-            setupDocumentationPanels();
-        }
-    };
-
-    initializePage();
-});

package/_gh_pages/beta.html

@@ -1,144 +0,0 @@
-<!doctype html>
-<html>
-
-    <head>
-        <title>GRNsight - Beta</title>
-        <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 v2.6.1 -->
-<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="Beta version of GRNsight, an open source web application and service for visualizing models of small- to medium-scale gene regulatory networks." />
-<meta property="og:description" content="Beta version of 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/beta.html" />
-<meta property="og:url" content="http://localhost:3001/GRNsight/beta.html" />
-<meta property="og:site_name" content="GRNsight" />
-<script type="application/ld+json">
-{"@type":"WebPage","url":"http://localhost:3001/GRNsight/beta.html","description":"Beta version of 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":"Beta","@context":"https://schema.org"}</script>
-<!-- End Jekyll SEO tag -->
-
-    </head>
-
-
-    <body>
-
-        <div id="header">
-            <div id="logo">
-                <a href="http://dondi.github.io/GRNsight"><img id="GRNsightLogo" src="/GRNsight/assets/images/GRNsight_logo_20140710_main_resized.jpg" alt="GRNsight" width="200" height="118"></a></div>
-            <div id="lmu">
-                <a href="http://www.lmu.edu" target="_blank"><img src="/GRNsight/assets/images/LMULogoHQ2.png" alt="LMU logo" width="200" height="118" id="lmuLogo" /></a><br /><br /><br />
-                <p id="subtextLMU">A Joint Project of the<br /> LMU Bioinformatics and Biomathematics Groups</p>
-            </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 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>
-                </button>
-                <a target="_blank" class="cookie-action" href="https://www.google.com/policies/technologies/cookies/">
-                    <strong>Learn More</strong>
-                </a>
-            </div>
-
-        </div>
-
-        <div id="navBar" class=".backBox">
-            <div id="stickyBar" data-spy="affix" data-offset-top="140">
-                <ul class="nav">
-                    <li><a href="/GRNsight/">Home</a></li>
-                    <li><a href="/GRNsight/about.html">About</a></li>
-                    <li><a href="/GRNsight/news.html">News</a></li>
-                    <li><a href="https://github.com/dondi/GRNsight" target="_blank">Developers</a></li>
-                    <li><a href="/GRNsight/documentation.html">Documentation</a></li>
-                    <li><a href="https://github.com/dondi/GRNsight/wiki" target="_blank">Wiki</a></li>
-                    <li><a href="/GRNsight/publications.html">Publications</a></li>
-                    <li><a href="/GRNsight/people.html">People</a></li>
-                    <li><a href="/GRNsight/contact.html">Contact</a></li>
-                    <li><a href="/GRNsight/links.html">Links</a></li>
-                    <li><a href="/GRNsight/beta.html">Beta</a></li>
-                    <li><a href="/GRNsight/about.html#privacy">Privacy</a></li>
-
-                </ul>
-                <p id="modText" class="modNav">
-                    Last modified: 10/05/2020
-                </p>
-            </div>
-
-        </div>
-
-        <div id="mainContent">
-            <p id="pageTitle">Beta <span id="version">v4.0.22</span></p>
-            <div id="graphPageContent">
-                <p><span style="font-weight:bold">Disclaimer: </span>This is the beta version of GRNsight for live testing of new functionality. For the most stable version, please go to the <a href="/GRNsight/">GRNsight home page</a>.</p>
-                <iframe class="embedded-demo" src="https://grnsight.cs.lmu.edu/beta/client"></iframe>
-            </div>
-
-            <div id="footer">
-                <hr id="separate">
-                <ul id="footerNav">
-                                        <li><a href="/GRNsight/">Home</a></li>
-                    <li><a href="/GRNsight/about.html">About</a></li>
-                    <li><a href="/GRNsight/news.html">News</a></li>
-                    <li><a href="https://github.com/dondi/GRNsight" target="_blank">Developers</a></li>
-                    <li><a href="/GRNsight/documentation.html">Documentation</a></li>
-                    <li><a href="https://github.com/dondi/GRNsight/wiki" target="_blank">Wiki</a></li>
-                    <li><a href="/GRNsight/publications.html">Publications</a></li>
-                    <li><a href="/GRNsight/people.html">People</a></li>
-                    <li><a href="/GRNsight/contact.html">Contact</a></li>
-                    <li><a href="/GRNsight/links.html">Links</a></li>
-                    <li><a href="/GRNsight/beta.html">Beta</a></li>
-                    <li><a href="/GRNsight/about.html#privacy">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>.
-
-                    <br>
-
-                    This page has been accessed <span class="ga-report"></span> times.
-
-                    
-                        <span class="ga-upload"></span> files have been uploaded and viewed with GRNsight.
-                    
-                </p>
-
-            </div>
-        </div>
-
-          <script>
-            (function(i,s,o,g,r,a,m){i["GoogleAnalyticsObject"]=r;i[r]=i[r]||function(){
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-            })(window,document,"script","//www.google-analytics.com/analytics.js","ga");
-
-            ga("create", "UA-54882218-1", "auto");
-            ga("send", "pageview");
-        </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>
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-        <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>
-
-</html>

package/_gh_pages/contact.html

@@ -1,178 +0,0 @@
-<!doctype html>
-<html>
-
-    <head>
-        <title>GRNsight - Contact</title>
-        <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 v2.6.1 -->
-<meta name="generator" content="Jekyll v3.9.0" />
-<meta property="og:title" content="Contact" />
-<meta property="og:locale" content="en_US" />
-<meta name="description" content="Contact information for the Principal Investigators of the GRNsight gene regulatory network visualization web application." />
-<meta property="og:description" content="Contact information for the Principal Investigators of the GRNsight gene regulatory network visualization web application." />
-<link rel="canonical" href="http://localhost:3001/GRNsight/contact.html" />
-<meta property="og:url" content="http://localhost:3001/GRNsight/contact.html" />
-<meta property="og:site_name" content="GRNsight" />
-<script type="application/ld+json">
-{"@type":"WebPage","url":"http://localhost:3001/GRNsight/contact.html","description":"Contact information for the Principal Investigators of the GRNsight gene regulatory network visualization web application.","publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"http://localhost:3001/GRNsight/assets/images/GRNsight_logo_20140710_main_resized.jpg"}},"headline":"Contact","@context":"https://schema.org"}</script>
-<!-- End Jekyll SEO tag -->
-
-    </head>
-
-
-    <body>
-
-        <div id="header">
-            <div id="logo">
-                <a href="http://dondi.github.io/GRNsight"><img id="GRNsightLogo" src="/GRNsight/assets/images/GRNsight_logo_20140710_main_resized.jpg" alt="GRNsight" width="200" height="118"></a></div>
-            <div id="lmu">
-                <a href="http://www.lmu.edu" target="_blank"><img src="/GRNsight/assets/images/LMULogoHQ2.png" alt="LMU logo" width="200" height="118" id="lmuLogo" /></a><br /><br /><br />
-                <p id="subtextLMU">A Joint Project of the<br /> LMU Bioinformatics and Biomathematics Groups</p>
-            </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 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>
-                </button>
-                <a target="_blank" class="cookie-action" href="https://www.google.com/policies/technologies/cookies/">
-                    <strong>Learn More</strong>
-                </a>
-            </div>
-
-        </div>
-
-        <div id="navBar" class=".backBox">
-            <div id="stickyBar" data-spy="affix" data-offset-top="140">
-                <ul class="nav">
-                    <li><a href="/GRNsight/">Home</a></li>
-                    <li><a href="/GRNsight/about.html">About</a></li>
-                    <li><a href="/GRNsight/news.html">News</a></li>
-                    <li><a href="https://github.com/dondi/GRNsight" target="_blank">Developers</a></li>
-                    <li><a href="/GRNsight/documentation.html">Documentation</a></li>
-                    <li><a href="https://github.com/dondi/GRNsight/wiki" target="_blank">Wiki</a></li>
-                    <li><a href="/GRNsight/publications.html">Publications</a></li>
-                    <li><a href="/GRNsight/people.html">People</a></li>
-                    <li><a href="/GRNsight/contact.html">Contact</a></li>
-                    <li><a href="/GRNsight/links.html">Links</a></li>
-                    <li><a href="/GRNsight/beta.html">Beta</a></li>
-                    <li><a href="/GRNsight/about.html#privacy">Privacy</a></li>
-
-                </ul>
-                <p id="modText" class="modNav">
-                    Last modified: 6/1/18
-                </p>
-            </div>
-
-        </div>
-
-        <div id="mainContent">
-            <p id="pageTitle">Contact</p>
-            <div id="pageContent">
-                <p style="padding-left:30px">
-                    To request support or features or report bugs, please submit an <a href="https://github.com/dondi/GRNsight/issues">issue</a> to <a href="https://github.com/dondi/GRNsight" target="_blank">GRNsight @ GitHub</a> (requires free GitHub account).
-                    <br><br>
-                    For all other correspondence, please contact the Principal Investigators:
-                </p>
-                <p class="name">Kam D. Dahlquist, Ph.D.</p>
-                <p class="personInfo">
-                    Professor <br>
-                    Department of Biology (Life Sciences Building 289) <br>
-                    <a href="http://kdahlquist.github.io/DahlquistLab/">http://kdahlquist.github.io/DahlquistLab/</a> <br><br>
-                    Loyola Marymount University <br>
-                    1 LMU Drive, MS 8888 <br>
-                    Los Angeles, CA 90045-2659 USA<br>
-                    Tel: 310-338-7697 <br>
-                    Fax: 310-338-5317 <br>
-                    <a href="mailto:kdahlquist@lmu.edu">kdahlquist@lmu.edu</a>
-                </p> <br>
-                <p class="name">John David N. Dionisio, Ph.D.</p>
-                <p class="personInfo">Professor <br>
-                    Department of Electrical Engineering &amp; Computer Science (Doolan 106) <br>
-                    <a href="http://dondi.lmu.build/">http://dondi.lmu.build/</a> <br><br>
-                    Loyola Marymount University <br>
-                    1 LMU Drive, MS 8145 <br>
-                    Los Angeles, CA 90045-2659 USA<br>
-                    Tel: 310-338-5782 <br>
-                    <a href="mailto:dondi@lmu.edu">dondi@lmu.edu</a>
-                </p> <br>
-                <p class="name">Ben G. Fitzpatrick, Ph.D.</p>
-                <p class="personInfo">
-                    Professor <br>
-                    Department of Mathematics (UH 2726) <br><br>
-                    Loyola Marymount University <br>
-                    1 LMU Drive <br>
-                    Los Angeles, CA 90045-2659 USA<br>
-                    Tel: 310-338-7892 <br>
-                    <a href="mailto:bfitzpatrick@lmu.edu">bfitzpatrick@lmu.edu</a>
-                </p> <br>
-                <p class="name">Loyola Marymount University</p>
-                <p class="personInfo">
-                    1 LMU Drive <br>
-                    Los Angeles, CA 90045-2659 USA<br><br>
-                    <a href="http://www.lmu.edu/resources/campusmaps/">Loyola Marymount University Campus Maps</a>
-                </p>
-            </div>
-
-            <div id="footer">
-                <hr id="separate">
-                <ul id="footerNav">
-                                        <li><a href="/GRNsight/">Home</a></li>
-                    <li><a href="/GRNsight/about.html">About</a></li>
-                    <li><a href="/GRNsight/news.html">News</a></li>
-                    <li><a href="https://github.com/dondi/GRNsight" target="_blank">Developers</a></li>
-                    <li><a href="/GRNsight/documentation.html">Documentation</a></li>
-                    <li><a href="https://github.com/dondi/GRNsight/wiki" target="_blank">Wiki</a></li>
-                    <li><a href="/GRNsight/publications.html">Publications</a></li>
-                    <li><a href="/GRNsight/people.html">People</a></li>
-                    <li><a href="/GRNsight/contact.html">Contact</a></li>
-                    <li><a href="/GRNsight/links.html">Links</a></li>
-                    <li><a href="/GRNsight/beta.html">Beta</a></li>
-                    <li><a href="/GRNsight/about.html#privacy">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>.
-
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-                    This page has been accessed <span class="ga-report"></span> times.
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-        <script src="/GRNsight/assets/js/ga-report.js"></script>
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package/_gh_pages/coverage/coverage.json

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