npm - grnsight - Versions diffs - 3.0.0 → 5.1.0 - Mend

grnsight 3.0.0 → 5.1.0

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 (489) hide show

package/_gh_pages/about.html CHANGED Viewed

@@ -3,27 +3,23 @@
     <head>
         <title>GRNsight - About</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="About" />
-<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/about.html" />
-<meta property="og:url" content="http://dondi.github.io/GRNsight/about.html" />
+<meta property="og:locale" content="en_US" />
+<meta name="description" content="About the GRNsight gene regulatory network visualization web app: availability, compatibility, release notes, funding, privacy statement." />
+<meta property="og:description" content="About the GRNsight gene regulatory network visualization web app: availability, compatibility, release notes, funding, privacy statement." />
+<link rel="canonical" href="http://localhost:3001/GRNsight/about.html" />
+<meta property="og:url" content="http://localhost:3001/GRNsight/about.html" />
 <meta property="og:site_name" content="GRNsight" />
 <script type="application/ld+json">
-  {
-    "@context": "http://schema.org",
-    "@type": "WebPage",
-    "headline": "About",
-    "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/about.html"
-  }
-</script>
+{"@type":"WebPage","url":"http://localhost:3001/GRNsight/about.html","description":"About the GRNsight gene regulatory network visualization web app: availability, compatibility, release notes, funding, privacy statement.","publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"http://localhost:3001/GRNsight/assets/images/GRNsight_logo_20140710_main_resized.jpg"}},"headline":"About","@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>
@@ -68,20 +64,21 @@
                 </ul>
                 <p id="modText" class="modNav">
-                    Last modified: 6/4/16
+                    Last modified: 6/16/19
                 </p>
             </div>
         </div>
         <div id="mainContent">
             <p id="pageTitle">About GRNsight</p>
             <div id="pageContent">
                 <p>
-                    GRNsight is an open source web application for visualizing models of small- to medium-scale gene regulatory networks. GRNsight is a joint project of the <a href="http://www.lmu.edu/" target="_blank">Loyola Marymount University</a> Bioinformatics and Biomathematics Groups, headed by <a href="http://myweb.lmu.edu/kdahlqui/index.htm" target="_blank">Dr. Kam Dahlquist</a>, <a href="http://myweb.lmu.edu/dondi/" target="_blank">Dr. John David N. Dionisio</a>, and <a href="http://myweb.lmu.edu/bfitzpatrick/" target="_blank">Dr. Ben G. Fitzpatrick</a>.  Undergraduate students initiated the development of GRNsight in Spring 2014, including Britain Southwick (Computer Science, ’14) and Nicole Anguiano (Computer Science, ’16), with consultation from Katrina Sherbina (Biomathematics, ’14).  At present, Anindita Varshneya (Biology, ’17), and Mihir Samdarshi (Biology, ’19) are continuing development on the project.
+                    GRNsight is an open source web application for visualizing models of small- to medium-scale gene regulatory networks. GRNsight is a joint project of the <a href="http://www.lmu.edu/" target="_blank">Loyola Marymount University</a> Bioinformatics and Biomathematics Groups, headed by <a href="http://myweb.lmu.edu/kdahlqui/index.htm" target="_blank">Dr. Kam Dahlquist</a>, <a href="http://myweb.lmu.edu/dondi/" target="_blank">Dr. John David N. Dionisio</a>, and <a href="http://myweb.lmu.edu/bfitzpatrick/" target="_blank">Dr. Ben G. Fitzpatrick</a>.  Undergraduate students initiated the development of GRNsight in Spring 2014, including Britain Southwick (Computer Science, ’14) and Nicole Anguiano (Computer Science, ’16), with consultation from Katrina Sherbina (Biomathematics, ’14).  For a list of other former and current developers, see the <a href="http://dondi.github.io/GRNsight/people.html">People page</a>.
                     <br><br>
                     A <a href="http://en.wikipedia.org/wiki/Gene_regulatory_network" target="_blank">gene regulatory network (GRN)</a> consists of genes, transcription factors, and the regulatory connections between them, which govern the level of expression of mRNA and protein from those genes. GRNs can be mathematically modeled and simulated by applications such as <a href = "http://kdahlquist.github.io/GRNmap/index.html" target = "blank">GRNmap</a>, a MATLAB program that estimates the parameters and performs forward simulations of a differential equations model of a GRN. Computer representations of GRNs, such as the models output by GRNmap, are in the form of a tabular spreadsheet (adjacency matrix) that is not easily interpretable. Ideally, GRNs should be displayed as diagrams (graphs) detailing the regulatory relationships (edges) between each gene (node) in the network. To address this need, we developed GRNsight.
                     <br><br>
-                    GRNsight allows users to upload spreadsheets generated by GRNmap and uses the information in these spreadsheets to automatically create and display a graph of the GRN model. The application colors the edges and adjusts their thickness based on the sign (activation or repression) and the strength (magnitude) of the regulatory relationship, respectively. Finally, GRNsight then allows the user to modify the graph in order to define the best visual layout for the network. Most of GRNsight is written in JavaScript. HTTP requests are handled using <a href="http://nodejs.org/" target="_blank">Node.js</a> and the <a href="http://expressjs.com/" target="_blank">Express framework</a>. Graphs are generated through <a href="http://d3js.org/" target="_blank">D3.js</a>, a JavaScript data visualization library.
+                    GRNsight allows users to upload spreadsheets generated by GRNmap and uses the information in these spreadsheets to automatically create and display a graph of the GRN model through a physics-based force simulation or in a grid layout. The application colors the edges and adjusts their thickness based on the sign (activation or repression) and the strength (magnitude) of the regulatory relationship, respectively. Nodes can be colored based on time course gene expression data found in the GRNmap spreadsheet. Finally, GRNsight allows the user to modify the graph in order to define the best visual layout for the network. Most of GRNsight is written in JavaScript. HTTP requests are handled using <a href="http://nodejs.org/" target="_blank">Node.js</a> and the <a href="http://expressjs.com/" target="_blank">Express framework</a>. Graphs are generated through <a href="http://d3js.org/" target="_blank">D3.js</a>, a JavaScript data visualization library.
                     <br><br>
                     Although originally designed for gene regulatory networks, we believe that GRNsight has general applicability for displaying any small, unweighted or weighted network with directed edges for systems biology or other application domains.
                 </p>
@@ -117,26 +114,7 @@
                         <div id="compatibilityContent" class="panel-collapse collapse">
                             <div class="panel-body">
-                                GRNsight has been tested with and confirmed to be working in Chrome version 43.0.2357.65 or higher and Firefox version 38.0.1 or higher on Windows 7 and Mac OS X operating systems. It may not work with other browsers, versions, or operating systems.
-                            </div>
-                        </div>
-                    </div>
-                    <div class="panel panel-default">
-                        <div class="panel-heading">
-                            <p class="panel-title aboutHeaders">
-                                <a href="#privacy" data-toggle="collapse">
-                                    Privacy Statement
-                                </a>
-                            </p>
-                        </div>
-                        <div id="privacy" class="panel-collapse collapse">
-                            <div class="panel-body">
-                                <ul>
-                                    <li>Every user's submitted data are private and not viewable by anyone other than the user. Uploaded data reside as temporary files and are deleted from the GRNsight server during standard operating system file cleanup procedures.</li>
-                                    <li>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 <a href="https://www.google.com/policies/technologies/cookies/">its use of cookies</a>.</li>
-                                </ul>
+                                GRNsight has been tested with and confirmed to be working in Chrome version 75.0.3770.80 or higher and Firefox version 60.0.1 or higher on Windows 7 and Mac OS X operating systems. It may not work with other browsers, versions, or operating systems.
                             </div>
                         </div>
                     </div>
@@ -154,6 +132,276 @@
                             <div class="panel-body">
                                 <div class="panel-group">
+                                    <div class="panel panel-default">
+                                        <div class="panel-heading">
+                                            <p class="panel-title aboutHeaders">
+                                                <a href="#v4_0_0Content" data-toggle="collapse">
+                                                    GRNsight v4.0.0
+                                                </a>
+                                            </p>
+                                        </div>
+                                        <div id="v4_0_0Content" class="panel-collapse collapse">
+                                            <div class="panel-body">
+                                                GRNsight v4.0.0 includes the following new features and bug fixes:
+                                                <ul>
+                                                    <li>GRNsight now follows a strict Model-View-Controller paradigm for its basic architecture. Except for the graphs, all elements displayed in the iframe (the main GRNsight functionality) now follow this architecture. These changes have occurred "under the hood" and will not be noticeable to users, except that it has made GRNsight more robust and has facilitated fixing many bugs caused by the interactions of new features introduced in previous versions </li>
+                                                      <ul>
+                                                        <li>Force Graph Parameter slider values are saved when a graph is uploaded</li>
+                                                        <li>The File -> Reload menu option reloads the graph in the layout configuration it was previously in </li>
+                                                        <li>Reset and Undo Reset Buttons are now grayed out when the Force Graph Parameter sliders are locked </li>
+                                                        <li>Various bugs that arose from the refactor are now fixed.</li>
+                                                      </ul>
+                                                    </li>
+                                                    <li>The Gene Page feature was improved both in its layout and "under the hood" to make database API calls and queries more robust. Changes were made to eventually enable the retrieval of gene information for genes from species other than Saccharomyces cerevisiae</li>
+                                                    <ul>
+                                                      <li>Gene page variables are also now a part of GRNstate in the Model-View-Controller paradigm</li>
+                                                    </ul>
+                                                    <li> Zoom levels remain consistent despite any user-defined parameter changes </li>
+                                                    <li> A bug was fixed in the automatic selection of the edge weight normalization factor. GRNsight now correctly uses the highest magnitude weight value for the default normalization factor, disregarding the sign of the weight </li>
+                                                    <li> Gray edges now only have one thickness </li>
+                                                    <li> GRNsight now returns an error when a file is too large </li>
+                                                    <li> The dropdown menu and sidebar menu viewport sizes now initialize to the same values </li>
+                                                    <li> The Log Fold Change Max Value field will only accept positive values, and the allowable range has been set to 0.01 - 100 </li>
+                                                    <li> GRNsight is now wholly served over HTTPS </li>
+                                                    <li> GRNsight libraries and documentation were updated </li>
+                                                </ul>
+                                            </div>
+                                        </div>
+                                    </div>
+                                    <div class="panel panel-default">
+                                        <div class="panel-heading">
+                                            <p class="panel-title aboutHeaders">
+                                                <a href="#v3_1_0Content" data-toggle="collapse">
+                                                    GRNsight v3.1.0
+                                                </a>
+                                            </p>
+                                        </div>
+                                        <div id="v3_1_0Content" class="panel-collapse collapse">
+                                            <div class="panel-body">
+                                                GRNsight v3.1.0 includes the following new features and bug fixes:
+                                                <ul>
+                                                    <li>Added new gene information page feature
+                                                      <ul>
+                                                        <li>A dynamic gene information webpage now opens when a user right-clicks on a node in the graph. The page sends a series of Asynchronous JavaScript and XML (AJAX) data requests, written using the jQuery JavaScript library, to the JASPAR, NCBI Gene, UniProt, Ensembl, and Saccharomyces Genome Databases. The webpage is then populated with data returned regarding the gene’s description, protein sequence, DNA binding motif frequency matrix and sequence logo, and Gene Ontology terms.</li>
+                                                      </ul>
+                                                    </li>
+                                                    <li>Began a refactor to consolidate state management into a single controller for user selected options
+                                                      <ul>
+                                                        <li>The front end has now started to follow a Model-View-Controller Architecture (MVC), and has a combination of new files to reflect that change</li>
+                                                      </ul>
+                                                    </li>
+                                                    <li>Numbers can now be used as node labels</li>
+                                                    <li>Various bug fixes and UI enhancements
+                                                      <ul>
+                                                        <li>The option to Default to black edges has been reworded to be consistent with node coloring, and the behavior has been changed to reload the graph upon selection</li>
+                                                        <li>The print modal does not load twice when trying to print</li>
+                                                        <li>The viewport "Fit to window" option now functions properly</li>
+                                                        <li>Weight value font now shows up properly</li>
+                                                        <li>The check box for dashed edges has been moved underneath the gray threshold slider</li>
+                                                      </ul>
+                                                    </li>
+                                                </ul>
+                                            </div>
+                                        </div>
+                                    </div>
+                                    <div class="panel panel-default">
+                                        <div class="panel-heading">
+                                            <p class="panel-title aboutHeaders">
+                                                <a href="#v3_0_0Content" data-toggle="collapse">
+                                                    GRNsight v3.0.0
+                                                </a>
+                                            </p>
+                                        </div>
+                                        <div id="v3_0_0Content" class="panel-collapse collapse">
+                                            <div class="panel-body">
+                                                GRNsight v3.0.0 includes the following new features and bug fixes:
+                                                <ul>
+                                                    <li>Node coloring feature was added to visualize gene expression data
+                                                      <ul>
+                                                        <li>Node coloring feature was added to visualize gene expression data</li>
+                                                        <li>GRNsight's Excel spreadsheet controller was expanded to process data from entire GRNmap input or output workbook, including expression and meta data</li>
+                                                        <li>Node coloring feature was implemented</li>
+                                                        <li>Demo Files #1 and #2 were updated to be in the correct format for node coloring</li>
+                                                      </ul>
+                                                    </li>
+                                                    <li>Grid Layout option was added</li>
+                                                    <li>Gray edges options were improved
+                                                      <ul>
+                                                        <li>Gray edge threshold value was changed to percent scale (0 - 100%)</li>
+                                                        <li>Option to show gray edges as dashed was added to increase accessibility for color-blind users</li>
+                                                      </ul>
+                                                    </li>
+                                                    <li>User Interface was updated with new features
+                                                      <ul>
+                                                        <li>Dropdown menu options were expanded to duplicate all functions available in the sidebar menu</li>
+                                                        <li>State variables for user selected options were consolidated</li>
+                                                        <li>New features were added to the client-side testing document</li>
+                                                      </ul>
+                                                    </li>
+                                                    <li>Security Vulnerability with "qs" package was resolved</li>
+                                                    <li>Webpack module bundler added to GRNsight</li>
+                                                </ul>
+                                            </div>
+                                        </div>
+                                    </div>
+                                    <div class="panel panel-default">
+                                        <div class="panel-heading">
+                                            <p class="panel-title aboutHeaders">
+                                                <a href="#v2_3_0Content" data-toggle="collapse">
+                                                    GRNsight v2.3.0
+                                                </a>
+                                            </p>
+                                        </div>
+                                        <div id="v2_3_0Content" class="panel-collapse collapse">
+                                            <div class="panel-body">
+                                                GRNsight v2.3.0 includes the following new features and bug fixes:
+                                                <ul>
+                                                    <li>d3 visualization library was updated to v4.
+                                                        <ul>
+                                                            <li>It was determined that the move from v3 to v4 was feasible.</li>
+                                                            <li>Transitioned GRNsight to d3 v4.</li>
+                                                            <li>Removed sliders for "Charge Distance" and "Gravity" since the combination of "Link Distance" and "Charge" sliders accomplishes the same functionality.</li>
+                                                        </ul>
+                                                    </li>
+                                                    <li>ESLint correctly applied to code base.
+                                                        <ul>
+                                                            <li>Found that ESLint was inconsistent between Mac and Windows developers.</li>
+                                                            <li>Linting errors were fixed.</li>
+                                                        </ul>
+                                                    </li>
+                                                    <li>Bug relating to edge weights were fixed.
+                                                        <ul>
+                                                            <li>Minimum weights have been normalize to zero instead of the smallest weight in the worksheet.</li>
+                                                            <li>Edges that have the same weight value now render as thickest instead of thinnest edge thickness.</li>
+                                                        </ul>
+                                                    </li>
+                                                    <li>Syntactic tests for malformed GraphML XML (.graphml) files were completed which return errors to the user if an incorrectly formatted GraphML XML file is imported into GRNsight.</li>
+                                                    <li>Developer-related issues were resolved.
+                                                        <ul>
+                                                            <li>npm start procedure was fixed for Windows users.</li>
+                                                        </ul>
+                                                    </li>
+                                                </ul>
+                                            </div>
+                                        </div>
+                                    </div>
+                                  <div class="panel panel-default">
+                                      <div class="panel-heading">
+                                          <p class="panel-title aboutHeaders">
+                                              <a href="#v2_1_11Content" data-toggle="collapse">
+                                                  GRNsight v2.1.11
+                                              </a>
+                                          </p>
+                                      </div>
+                                      <div id="v2_1_11Content" class="panel-collapse collapse">
+                                          <div class="panel-body">
+                                              GRNsight v2.1.11 includes the following new features and bug fixes:
+                                              <ul>
+                                                  <li>Improvements were made to the zoom functionality, including:</li>
+                                                    <ul>
+                                                      <li>Zoom now originates from the center of the graph</li>
+                                                      <li>Zoom factor is now annotated on zoom slider</li>
+                                                      <li>A vertical bar on the zoom slider indicates where the 100% zoom level is</li>
+                                                      <li>Mousewheel zoom was disabled</li>
+                                                      <li>Various bugs were fixed</li>
+                                                    </ul>
+                                                  <li>The user can now customize the normalization factor which controls how the thicknesses of the edges are determined based on the weight values or reset it back to the default value for that graph</li>
+                                                    <ul>
+                                                      <li>The user can also set the threshold upon which a weighted edge is colored gray using a slider</li>
+                                                    </ul>
+                                                  <li>Additional tests were added:</li>
+                                                    <ul>
+                                                      <li>Syntactic tests for malformed Simple Interaction Format (.sif) files were completed which return errors to the user if an incorrectly formatted SIF file is imported into GRNsight</li>
+                                                      <li>The routine that checks for syntactic errors in SIF and GraphML files was integrated with the semantic checker routine that looks for error common to all file formats that GRNsight supports</li>
+                                                      <li>Tests for incorrectly named Excel worksheets were added</li>
+                                                      <li>GRNsight now returns an error if a blank Excel, SIF , or GraphML file is uploaded</li>
+                                                    </ul>
+                                                  <li>An automatic client-side test generator was created that generates a document that can be followed by a user to systematically test specific combinations of user interface functions</li>
+                                                  <li>Additional bugs were fixed</li>
+                                                  <li>Code quality was improved by the use of ESLint</li>
+                                              </ul>
+                                          </div>
+                                      </div>
+                                  </div>
+                                    <div class="panel panel-default">
+                                        <div class="panel-heading">
+                                            <p class="panel-title aboutHeaders">
+                                                <a href="#v2_0_20Content" data-toggle="collapse">
+                                                    GRNsight v2.0.20
+                                                </a>
+                                            </p>
+                                        </div>
+                                        <div id="v2_0_20Content" class="panel-collapse collapse">
+                                            <div class="panel-body">
+                                                GRNsight v2.0.20 includes the following new features and bug fixes:
+                                                <ul>
+                                                    <li>When a weighted graph is loaded, the user now has the options to show weights upon mouseover of an edge, always show weights, or never show weights</li>
+                                                    <li>The bounding box and viewport for the graph have been separated allowing for the following new features:</li>
+                                                        <ul>
+                                                            <li>The bounding box can now be fixed to the size of the viewport or adapted to the size of the graph</li>
+                                                            <li>The viewport size can be selected from among small, medium, and large options</li>
+                                                            <li>The best viewport size is automatically detected from the browser</li>
+                                                            <li>The viewport can be fit to the size of the browser window</li>
+                                                            <li>Zooming and scrolling have been enabled and refined</li>
+                                                        </ul>
+                                                    <li>Improvements to visuals have been made, including:</li>
+                                                        <ul>
+                                                            <li>Reducing the white space on either side of a node label for long labels</li>
+                                                            <li>Setting the minimum size of a node</li>
+                                                            <li>Making the pointed arrowhead larger for the thinnest edges</li>
+                                                            <li>Minor adjustments to the placement and centering of edge end-markers</li>
+                                                        </ul>
+                                                    <li>The use of special characters (except for "-" and "_") in node labels are no longer supported due to integration of cytoscape.js code into GRNsight for future implementation of graph statistics feature</li>
+                                                    <li>"Under the hood":</li>
+                                                        <ul>
+                                                            <li>The versions of package dependencies have been standardized and documented in the package.json file</li>
+                                                            <li>Code has been ported to version v0.7.2 of Node-xlsx</li>
+                                                            <li>Testing suite has been refactored into semantic and syntactic tests</li>
+                                                            <li>Additional syntactic tests have been written for SIF format</li>
+                                                            <li>A catch-all syntactic error has been implemented for ill-formed GraphML files so that the server doesn't crash upon loading</li>
+                                                            <li>A cap has been placed on the number of errors returned according to a tunable strictness parameter</li>
+                                                        </ul>
+                                                    <li>Numerous bugs have been fixed</li>
+                                                </ul>
+                                            </div>
+                                        </div>
+                                    </div>
+                                    <div class="panel panel-default">
+                                        <div class="panel-heading">
+                                            <p class="panel-title aboutHeaders">
+                                                <a href="#v1_18Content" data-toggle="collapse">
+                                                    GRNsight v1.18
+                                                </a>
+                                            </p>
+                                        </div>
+                                        <div id="v1_18Content" class="panel-collapse collapse">
+                                            <div class="panel-body">
+                                                GRNsight v1.18 includes the following new features and bug fixes:
+                                                <ul>
+                                                    <li>Implemented import of weighted and unweighted network data from Simple Interaction Format (SIF, *.sif) format.</li>
+                                                    <li>Implemented export of weighted and unweighted network data to Simple Interaction Format (SIF, *.sif) format.</li>
+                                                    <li>Implemented import of weighted and unweighted network data from GraphML (*.graphml) format.</li>
+                                                    <li>Implemented export of weighted and unweighted network data to GraphML (*.graphml) format.</li>
+                                                    <li>Menu items for features that are not yet implemented are hidden.</li>
+                                                    <li>The true filenames of the demo files now display in the menu bar.</li>
+                                                    <li>Fixed bug where weights were not displaying upon edge mouseover by new implementation of the feature.</li>
+                                                </ul>
+                                            </div>
+                                        </div>
+                                    </div>
                                     <div class="panel panel-default">
                                         <div class="panel-heading">
                                             <p class="panel-title aboutHeaders">
@@ -313,7 +561,7 @@
                                                     </li>
                                                     <li>
                                                         Printing was enabled in the File menu. Mac users can utilize native print to PDF function available from their operating system to print the graph to a PDF file. Windows users will need to have the full version of Adobe Acrobat (or other "print to PDF" utility) to print graphs to a PDF file. There is a known bug with the print function printing an extra blank page that is currently being investigated for a fix in a later release.
-                                                    </li>
+                                                    </li>
                                                     <li>Various bug fixes were implemented regarding the loading of the Demo GRNs and unusual behavior of the first node created from a spreadsheet.</li>
                                                 </ul>
                                             </div>
@@ -371,7 +619,7 @@
                                                             <li>The web client receives data from the server and generates the graph visualization.</li>
                                                         </ul>
                                                     </li>
-                                                    <li>GRNsight uses the <a href="http://d3js.org/" target="_blank">Data-Driven Documents (D3)</a> JavaScript library to generate a graph derived from input network data.
+                                                    <li>GRNsight uses the <a href="http://d3js.org/" target="_blank">Data-Driven Documents (D3)</a> JavaScript library to generate a graph derived from input network data.
                                                         <ul>
                                                             <li>D3 dynamically manipulates HTML and Scalable Vector Graphics (SVG) to form the elements of the graph.</li>
                                                             <li>GRNsight implements D3’s force layout, which applies a physics-based simulation to the graph.</li>
@@ -418,6 +666,33 @@
                         </div>
                     </div>
+                    <div class="panel panel-default">
+                        <div class="panel-heading">
+                            <p class="panel-title aboutHeaders">
+                                <a data-toggle="collapse" href="#citingContent">
+                                    How to Cite GRNsight
+                                </a>
+                            </p>
+                        </div>
+                        <div id="citingContent" class="panel-collapse collapse">
+                            <div class="panel-body">
+                              <div>
+                                If you use GRNsight in your work, please cite:
+                              </div>
+                              <div style="margin-left: 30px; padding-top: 10px; padding-bottom: 10px;">
+                                Dahlquist, K.D., Dionisio, J.D.N., Fitzpatrick, B.G., Anguiano, N.A., Varshneya, A., Southwick, B.J., Samdarshi, M. (2016) GRNsight: a web application and service for visualizing models of small- to medium-scale gene regulatory networks. PeerJ Computer Science 2:e85. <a href="https://doi.org/10.7717/peerj-cs.85" target="_blank">DOI: 10.7717/peerj-cs.85</a>.
+                              </div>
+                              <div>
+                                This publication references GRNsight v1.18.1. The <a href="https://zenodo.org/" target="_blank">Zenodo</a>-generated DOI for the latest software release is:
+                              </div>
+                              <div style="margin-left: 30px; padding-top: 10px; padding-bottom: 10px;">
+                                <a href="https://zenodo.org/badge/latestdoi/16195791"><img src="https://zenodo.org/badge/16195791.svg" alt="DOI"></a>
+                              </div>
+                            </div>
+                        </div>
+                    </div>
                     <div class="panel panel-default">
                         <div class="panel-heading">
                             <p class="panel-title aboutHeaders">
@@ -429,10 +704,46 @@
                         <div id="fundingContent" class="panel-collapse collapse">
                             <div class="panel-body">
-                                This work is partially supported by <a href="http://www.nsf.gov/awardsearch/showAward?AWD_ID=0921038" target="_blank">NSF award 0921038</a> (Kam D. Dahlquist, Ben G. Fitzpatrick, and Katrina Sherbina), the Loyola Marymount University Rains Research Assistant Program (Nicole Anguiano), and the Loyola Marymount University Summer Undergraduate Research Program (Anindita Varshneya).
+                                This work is partially supported by <a href="http://www.nsf.gov/awardsearch/showAward?AWD_ID=0921038" target="_blank">NSF award 0921038</a> (Kam D. Dahlquist, Ben G. Fitzpatrick, and Katrina Sherbina), a Kadner-Pitts Research Grant (Kam D. Dahlquist), the Loyola Marymount University Rains Research Assistant Program (Nicole A. Anguiano, Eileen J. Choe, Mihir Samdarshi), and the Loyola Marymount University Summer Undergraduate Research Program (Anindita Varshneya, John L. Lopez).
                             </div>
                         </div>
                     </div>
+                    <div class="panel panel-default">
+                        <div class="panel-heading">
+                            <p class="panel-title aboutHeaders">
+                                <a href="#privacy" data-toggle="collapse">
+                                    Privacy Statement
+                                </a>
+                            </p>
+                        </div>
+                        <div id="privacy" class="panel-collapse collapse">
+                            <div class="panel-body">
+                                <ul>
+                                    <li>Every user's submitted data are private and not viewable by anyone other than the user. Uploaded data reside as temporary files and are deleted from the GRNsight server during standard operating system file cleanup procedures.</li>
+                                    <li>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 <a href="https://www.google.com/policies/technologies/cookies/">its use of cookies</a>.</li>
+                                </ul>
+                            </div>
+                        </div>
+                    </div>
+                    <div class="panel panel-default">
+                        <div class="panel-heading">
+                            <p class="panel-title aboutHeaders">
+                                <a href="#codeOfConduct" data-toggle="collapse">
+                                    Code of Conduct
+                                </a>
+                            </p>
+                        </div>
+                        <div id="codeOfConduct" class="panel-collapse collapse">
+                            <div class="panel-body">
+                                This project has been released with a Contributor Code of Conduct. Participants in this project have agreed to abide by its terms. The full Code of Conduct can be read <a href="https://github.com/dondi/GRNsight/blob/master/CODE_OF_CONDUCT.md">here</a>.
+                            </div>
+                        </div>
+                    </div>
                 </div>
             </div>
@@ -472,7 +783,7 @@
             </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)
@@ -481,10 +792,14 @@
             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/assets/css/footer.css ADDED Viewed

@@ -0,0 +1,3 @@
+body {
+  margin-left: -160px;
+}

package/_gh_pages/assets/css/main.css CHANGED Viewed

@@ -12,10 +12,10 @@ body {
 iframe.embedded-demo {
 	padding:0;
 	margin:0;
-	height:770px;
-	width:1350px;
-    overflow:scroll;
-    border:0;
+  min-height: 750px;
+	width:100%;
+  overflow: visible;
+  border:0;
 }
 #header {
@@ -93,6 +93,9 @@ iframe.embedded-demo {
 	list-style-type: none;
 	line-height: 2;
 	font-size: 15px;
+	flex-direction: column;
+	margin: 15px 0;
+	padding-left: 40px;
 	border-right: 1px solid #828282;
 	width:159px;
 }
@@ -128,25 +131,25 @@ a:active {
 	padding: 5px 5px 5px 5px;
 }
-.fixWidthforImage {
-	min-width: 1525px;
+.people-columns {
+  display: flex;
+  flex-wrap: wrap;
+  margin: -5px;
 }
-.fixWidthforImage > div.pull-left {
-	margin-bottom: 1em;
-}
-.fixWidthforImage > div.pull-right {
-	max-width: 720px; margin-right:200px;
+.people-columns > section {
+  flex-grow: 1;
+  margin: 5px;
 }
 #pageTitle {
 	font-size: 25px;
 	color: #141414;
+	margin: 25px 0;
 }
 #pageContent {
-	color:#141414;
+    color: #141414;
 	font-size: 14px;
 	padding: 0px 5px 5px 10px;
     margin-right: 8em;
@@ -162,6 +165,13 @@ a:active {
 	width: 95%;
 }
+#graphPageContent {
+    color: #141414,inherit;
+    font-size: 14px;
+    padding: 0;
+    margin: 0 auto;
+}
 p.panel-title.aboutHeaders {
 	font-size: 16px;
 	font-weight: bold;
@@ -253,10 +263,13 @@ figure.publication > figcaption > a {
 }
 #separate {
+	margin-bottom: 20px;
+	margin-top: 20px;
 	width:90%;
 }
 #footerNav {
+	margin: 12px 0;
 	padding-top:20px;
 	list-style-type: none;
 	font-size: 12px;
@@ -271,6 +284,7 @@ figure.publication > figcaption > a {
 #CCLicense {
 	font-size: 12px;
+	margin: 12px 0;
 	text-align: center;
 }
@@ -325,6 +339,7 @@ html {
     right: 2ex;
     text-shadow: none;
     top: 1ex;
+    z-index: 999;
 }
 .cookie-action {
@@ -346,4 +361,3 @@ html {
 	color: #125432;
     text-decoration: underline;
 }