Rename index_page_orig to index_page

3 files changed, 136 insertions, 427 deletions

diff --git a/wqflask/wqflask/templates/index_page.html b/wqflask/wqflask/templates/index_page.html
index 31846f87..87cf1b45 100644..100755
--- a/wqflask/wqflask/templates/index_page.html
+++ b/wqflask/wqflask/templates/index_page.html
@@ -1,78 +1,73 @@
 {% extends "base.html" %}
 {% block title %}GeneNetwork{% endblock %}
+{% block css %}
+<style TYPE="text/css">
+  p.interact { display: none; }
+</style>
+{% endblock %}
 {% block content %}
 <!-- Start of body -->
-
-<!--
-    <header class="jumbotron subhead" id="overview">
-        <div class="container">
-            <h1>GeneNetwork</h1>
-            <p class="lead">Open source bioinformatics for systems genetics</p>
-        </div>
-    </header>
--->
-
-    <div class="container-fluid">
+    <div class="container-fluid" style="min-width: 1210px;">
 
         {{ flash_me() }}
 
-        <div class="row" style="width: 1400px !important;">
+        <div class="row" style="width: 100%;">
 
-            <div class="col-xs-5">
+            <div class="col-xs-4" style="margin-right:50px; min-width: 530px; max-width: 550px;">
                 <section id="search">
-                    <div class="page-header">
+                    <div>
                         <h1>Select and search</h1>
                     </div>
-                    <form method="get" action="/search" name="SEARCHFORM">
+                    <form method="get" action="/search" target="_blank" name="SEARCHFORM">
                         <fieldset>
                             <div style="padding: 20px" class="form-horizontal">
 
                                 <div class="form-group">
                                     <label for="species" class="col-xs-1 control-label" style="width: 65px !important;">Species:</label>
-                                    <div class="col-xs-10 controls input-append" style="padding-right: 0px;">
-                                        <div class="col-xs-8">
-                                          <select name="species" id="species" class="form-control span3" style="width: 280px !important;"></select>
-                                        </div>
-                                        <div class="col-xs-4">
-                                          <button type="button" id="make_default" class="btn btn-primary form-control">Make Default</button>
+                                    <div class="col-xs-10 controls input-append" style="display: flex; padding-left: 20px;">
+                                        <div class="col-8">
+                                          <select name="species" id="species" class="form-control" style="width: 280px !important;"><option>Loading...</option></select>
                                         </div>
                                     </div>
                                 </div>
 
                                 <div class="form-group">
                                     <label for="group" class="col-xs-1 control-label" style="width: 65px !important;">Group:</label>
-                                    <div class="col-xs-10 controls input-append">
-                                        <div class="col-xs-8">
-                                          <select name="group" id="group" class="form-control span3" style="width: 280px !important;"></select>
+                                    <div class="col-xs-10 controls input-append" style="display: flex; padding-left: 20px;">
+                                        <div class="col-9">
+                                          <select name="group" id="group" class="form-control" style="width: 340px !important;"><option>Loading...</option></select>
                                           <i class="icon-question-sign"></i>
                                         </div>
+                                        <div class="col-3" style="margin-left: 10px;">
+                                            <button type="button" id="group_info" class="btn btn-primary form-control" style="width: 50px !important;">Info</button>
+                                        </div>
                                     </div>
                                 </div>
 
                                 <div class="form-group">
                                     <label for="tissue" class="col-xs-1 control-label" style="width: 65px !important;">Type:</label>
-                                    <div class="col-xs-10 controls">
-                                        <div class="col-xs-8">
-                                          <select name="type" id="type" class="form-control span3" style="width: 280px !important;"></select>
+                                    <div class="col-xs-10 controls input-append" style="display: flex; padding-left: 20px;">
+                                        <div class="col-9">
+                                          <select name="type" id="type" class="form-control" style="width: 340px !important;"><option>Loading...</option></select>
+                                        </div>
+                                        <div class="col-3" style="margin-left: 10px;">
+                                            <button type="button" id="dataset_info" class="btn btn-primary form-control" style="width: 50px !important;">Info</button>
                                         </div>
                                     </div>
                                 </div>
 
                                 <div class="form-group">
                                     <label for="dataset" class="col-xs-1 control-label" style="width: 65px !important;">Dataset:</label>
-                                    <div class="col-xs-10 controls input-append">
-                                        <div class="col-xs-10">
-                                          <select name="dataset" id="dataset" class="form-control span5" style="width: 340px !important;"></select>
+                                    <div class="col-xs-10 controls" style="display: flex; padding-left: 20px;">
+                                        <div class="col-9">
+                                          <select name="dataset" id="dataset" class="form-control" style="max-width: 550px; width: 450px !important;"><option>Loading...</option></select>
                                           <i class="icon-question-sign"></i>
                                         </div>
-                                        <div class="col-xs-2">
-                                          <button type="button" id="dataset_info" class="btn btn-primary form-control" style="width: 75px !important;">Info</button>
-                                        </div>
                                     </div>
                                 </div>
 
                                 <!--  USER HELP   -->
-                                <!--<p>Databases marked with <b>**</b>-->
+                                <!--<p >Databases marked with <b>**</b>-->
                                 <!--      suffix are not public yet.<br>-->
                                 <!--     Access requires <a href="/account.html" target=-->
                                 <!--      "_blank" class="fs14">user login</a>.</p>-->
@@ -80,9 +75,9 @@
 
                                 <div class="form-group">
                                     <label for="or_search" class="col-xs-1 control-label" style="padding-left: 0px; padding-right: 0px; width: 65px !important;">Get Any:</label>
-                                    <div class="col-xs-10 controls">
-                                        <div class="col-xs-8">
-                                          <textarea onkeydown="pressed(event)" name="search_terms_or" rows="1" class="form-control search-query" style="max-width: 550px; width: 450px !important;" id="or_search"></textarea>
+                                    <div class="col-xs-10 controls" style="padding-left: 20px;">
+                                        <div class="col-8">
+                                          <textarea onkeydown="pressed(event)" name="search_terms_or" rows="1" class="form-control search-query" style="resize: vertical; max-width: 550px; width: 450px !important;" id="or_search"></textarea>
                                         </div>
                                     </div>
                                 </div>
@@ -90,8 +85,8 @@
                                 <!--  GET ANY HELP   -->
                                 <div class="form-group">
                                     <label for="btsearch" class="col-xs-1 control-label" style="width: 65px !important;"></label>
-                                    <div class="col-xs-10 controls">
-                                        <div class="col-xs-12 controls">
+                                    <div class="col-xs-10 controls" style="padding-left: 20px;">
+                                        <div class="col-12 controls">
                                             Enter terms, genes, ID numbers in the <b>Search</b> field.<br>
                                             Use <b>*</b> or <b>?</b> wildcards (Cyp*a?, synap*).<br>
                                             Use <b>quotes</b> for terms such as <i>"tyrosine kinase"</i>.
@@ -101,19 +96,22 @@
 
                                 <div class="form-group">
                                     <label for="and_search" class="col-xs-1 control-label" style="padding-left: 0px; padding-right: 0px; width: 65px !important;">Combined:</label>
-                                    <div class="col-xs-10 controls">
-                                        <div class="col-xs-8">
-                                          <textarea onkeydown="pressed(event)" name="search_terms_and" rows="1" class="form-control search-query" style="max-width: 550px; width: 450px !important;" id="and_search"></textarea>
+                                    <div class="col-xs-10 controls" style="padding-left: 20px;">
+                                        <div class="col-8">
+                                          <textarea onkeydown="pressed(event)" name="search_terms_and" rows="1" class="form-control search-query" style="resize: vertical; max-width: 550px; width: 450px !important;" id="and_search"></textarea>
                                         </div>
                                     </div>
                                 </div>
 
                                 <div class="form-group">
                                     <label for="btsearch" class="col-xs-1 control-label" style="width: 65px !important;"></label>
-                                    <div class="col-xs-10 controls">
-                                        <div class="col-xs-2 controls" style="width: 100px !important;">
+                                    <div class="col-xs-10 controls" style="display: flex; padding-left: 20px;">
+                                        <div class="col-2 controls">
                                             <input id="btsearch" type="submit" class="btn btn-primary form-control" value="Search">
                                         </div>
+                                        <div class="col-2 controls" style="padding-left: 20px;">
+                                            <button type="button" id="make_default" class="btn btn-primary form-control">Make Default</button>
+                                        </div>
                                     </div>
                                 </div>
 
@@ -133,33 +131,43 @@
                         <h2>Advanced commands</h2>
                     </div>
 
-                    <p>You can also use advanced commands. Copy these simple examples into the Get Any or Combined search fields:</p>
+                    <p>You can also use advanced commands. Copy these simple examples into the Get Any field for single term searches and Combined for searches with multiple terms:</p>
 
                       <ul>
                         <li><b>POSITION=(chr1 25 30)</b> finds genes, markers, or transcripts on
                         chromosome 1 between 25 and 30 Mb.</li>
 
-                        <li><b>MEAN=(15 16) LRS=(23 46)</b> in the <b>Combined</b> field finds
-                        highly expressed genes (15 to 16 log2 units) AND with peak <a href="{{ url_for('glossary_blueprint.glossary') }}#L">LRS</a>
-                        linkage between 23 and 46.</li>
+                        <li><b>MEAN=(15 16)</b> in the <b>Combined</b> field finds
+                        highly expressed genes (15 to 16 log2 units)</li>
 
                         <li><b>RANGE=(1.5 2.5)</b> in the <b>Any</b> field finds traits with values with a specified fold-range (minimum = 1). 
                         Useful for finding "housekeeping genes" <b>(1.0 1.2)</b> or highly variable molecular assays <b>(10 100)</b>.</li>
 
+                        <li><b>LRS=(15 1000)</b> or <b>LOD=(2 8)</b> finds all traits with peak LRS or LOD scores between lower and upper limits.</li>
+
+                        <li><b>LRS=(9 999 Chr4 122 155)</b> finds all traits on Chr 4 from 122 and 155 Mb with LRS scores between 9 and 999.</li>
+
+                        <li><b>cisLRS=(15 1000 5)</b> or <b>cisLOD=(2 8 5)</b> finds all cis eQTLs with peak LRS or LOD scores between lower and upper limits,
+                            with an <b>inclusion</b> zone of 5 Mb around the parent gene.</li>
+
+                        <li><b>transLRS=(15 1000 5)</b> or <b>transLOD=(2 8 5)</b> finds all trans eQTLs with peak LRS or LOD scores between lower and upper limits,
+                            with an <b>exclusion</b> zone of 5 Mb around the parent gene. You can also add a fourth term specifying which chromosome you want the transLRS to be on
+                            (for example transLRS=(15 1000 5 7) would find all trans eQTLs with peak LRS on chromosome 7 that is also a trans eQTL with exclusionary zone of 5Mb).</li>
+
+                        <li><b>POSITION=(Chr4 122 130) cisLRS=(9 999 10)</b>
+                            finds all traits on Chr 4 from 122 and 155 Mb with cisLRS scores
+                            between 9 and 999 and an inclusion zone of 10 Mb.</li>
+
                         <li><b>RIF=mitochondrial</b> searches RNA databases for <a href="https://en.wikipedia.org/wiki/GeneRIF">
                         GeneRIF</a> links.</li>
 
-                        <li><b>WIKI=nicotine</b> searches <a href="http://www.genenetwork.org/webqtl/main.py?FormID=geneWiki">
+                        <li><b>WIKI=nicotine</b> searches <a href="http://gn1.genenetwork.org/webqtl/main.py?FormID=geneWiki">
                         GeneWiki</a> for genes that you or other users have annotated
                         with the word <i>nicotine</i>.</li>
 
                         <li><b>GO:0045202</b> searches for synapse-associated genes listed in the
-                        <a href="http://amigo.geneontology.org/amigo/medial_search?q=GO%3A0045202">Gene Ontology</a>.</li>
-
-                        <li><b>GO:0045202 LRS=(9 99 Chr4 122 155) cisLRS=(9 999 10)</b>
-                        finds synapse-associated genes with <a href="{{ url_for('glossary_blueprint.glossary') }}#E">
-                        cis eQTL</a> on Chr 4 from 122 and 155 Mb with LRS scores
-                        between 9 and 999.</li>
+                        <a href="http://amigo.geneontology.org/amigo/medial_search?q=GO%3A0045202">
+                            Gene Ontology</a>.</li>
 
                         <li><b>RIF=diabetes LRS=(9 999 Chr2 100 105) transLRS=(9 999 10)</b>
                         finds diabetes-associated transcripts with peak <a href="{{ url_for('glossary_blueprint.glossary') }}#E">
@@ -168,8 +176,43 @@
                       </ul>
                 </section>
             </div>
-            <div style="padding-left:120px" class="col-xs-4" style="width: 600px !important;">
-                <!--
+
+            <div class="col-xs-4" style="width: 600px !important;">
+	        <section id="affiliates">
+	            <div class="page-header">
+                        <h1>Affiliates</h1>
+                        <ul>
+                          <li><b><a href="http://gn1.genenetwork.org">GeneNetwork 1</a> at UTHSC</b></li>
+                          <li><span class="broken_link" href="http://ucscbrowser.genenetwork.org/">Genome Browser</span> at UTHSC</li>
+                          <li><a href="https://systems-genetics.org/">Systems Genetics</a> at EPFL</li>
+                          <li><a href="http://bnw.genenetwork.org/">Bayesian Network Web Server</a> at UTHSC</li>
+                          <li><a href="https://www.geneweaver.org/">GeneWeaver</a></li>
+                          <li><a href="https://phenogen.org/">PhenoGen</a> at University of Colorado</li>
+                          <li><a href="http://www.webgestalt.org/">WebGestalt</a> at Baylor</li>
+                        </ul>
+                    </div>
+                </section>
+                <section id="news-section">
+                    <div class="page-header">
+                        <h1>News</h1>
+                        <div id="tweets" style="height: 300px; overflow: scroll; overflow-x: hidden;"></div>
+                        <div align="right">
+                          <a href="https://twitter.com/GeneNetwork2">more news items...</a>
+                        </div>
+                    </div>
+		</section>
+                <section id="websites">
+                    <div class="page-header">
+                        <h1>Github</h1>
+                        <ul>
+                          <li><a href="https://github.com/genenetwork/genenetwork2">GN2 Source Code</a></li>
+                          <li><a href="https://github.com/genenetwork/genenetwork">GN1 Source Code</a></li>
+                          <!--<li><a href="https://github.com/genenetwork/gn-docs/wiki">GN2 Document Wiki</a></li>-->
+                          <li><a href="https://github.com/genenetwork/sysmaintenance">System Maintenance Code</a></li>
+                        </ul>
+                    </div>
+               </section>
+              <!--
                 <section id="tour-info">
                     <div class="page-header">
                         <h1>Tour and more info</h1>
@@ -178,7 +221,7 @@
                     <h3>Thirty minute tour</h3>
                     <p>
                       Take the 30 minute
-                      GeneNetwork <a href="http://www.genenetwork.org/tutorial/WebQTLTour/"  class="fs14">tour</a> that includes screen shots and
+                      GeneNetwork <a href="http://www.genenetwork.org/tutorial/WebQTLTour/" class="fs14">tour</a> that includes screen shots and
                       typical steps in the analysis.
                     </p>
 
@@ -195,34 +238,26 @@
                       and advice on their use and citation.</p>
 
                 </section>
-                -->
 
+                </section>
+                -->
                 <section id="websites">
                     <div class="page-header">
-                        <h1>Affiliates and mirrors</h1>
+                        <h1>Links</h1>
                     </div>
-                    <h3>Websites affiliated with GeneNetwork</h3>
-                    <ul>
-                        <li><span class="broken_link" href="http://ucscbrowser.genenetwork.org/">Genome Browser</span> at UTHSC</li>
-
-                        <li><a href="http://galaxy.genenetwork.org/">Galaxy</a> at
-                        UTHSC</li>
-
-                        <li>GeneNetwork 1 at <span class="broken_link" href="http://ec2.genenetwork.org/">Amazon
-                        Cloud (EC2)</span></li>
-
-                        <li>GeneNetwork 1 Source Code at <a href="http://sourceforge.net/projects/genenetwork/">SourceForge</a></li>
-
-                        <li>GeneNetwork 2 Source Code at <a href="https://github.com/genenetwork/genenetwork2">GitHub</a></li>
-                    </ul>
-                    <h3>GN1 Mirror and development sites</h3>
-
+                    <h3>GeneNetwork v2:</h3>
+                      <ul>
+                        <li><a href="http://genenetwork.org/">Main website</a> at UTHSC</li>
+                        <!--<li><a href="http://test-genenetwork.org/">Testing website</a> at UTHSC</li>-->
+                      </ul>
+                    <h3>GeneNetwork v1:</h3>
                     <ul>
-                        <li><a href="http://gn1.genenetwork.org/">Main GN1 site at UTHSC</a> (main site)</li>
-                        <li><span  class="broken_link" href="http://genenetwork.helmholtz-hzi.de/">Germany at the HZI</span></li>
-                        <li><a href="http://genenetwork.org/">Memphis at the U of M</a></li>
+                        <li><a href="http://gn1.genenetwork.org/">Main website</a> at UTHSC</li>
+                        <li><span class="broken_link" href="http://artemis.uthsc.edu/">Time Machine</span>: Full GN versions from 2009 to 2016 (mm9)</li>
+                            Cloud (EC2)</a></li>
                     </ul>
-                </section>
+                    <script type="text/javascript" src="//rf.revolvermaps.com/0/0/8.js?i=526mdlpknyd&amp;m=0&amp;c=ff0000&amp;cr1=ffffff&amp;f=arial&amp;l=33" async="async"></script>
+               </section>
 
                 <!--<section id="getting-started">
                     <div class="page-header">
@@ -248,7 +283,7 @@
                   <li>Select a <b>Dataset</b></li>
 
                   <li>Enter terms in the search field: words,
-                  genes, ID numbers, probes, advanced search commands</li>
+                  genes, probes, advanced search commands</li>
 
                   <li>Click the <b>Search</b> button</li>
 
@@ -257,7 +292,7 @@
 
                 <h3>User Guide</h3>
                 <h5>Read the
-                <a href="http://www.genenetwork.org/index4.html">
+                <a href="http://gn1.genenetwork.org/index4.html">
                     user guide</a>.</h5>
 
                 </section>-->
@@ -268,11 +303,7 @@
 {%endblock%}
 
 {% block js %}
-
-    <script>
-      gn_server_url = "{{ gn_server_url }}";
-    </script>
-    <script src="/static/new/javascript/dataset_select_menu.js"></script>
+    <script src="/static/new/javascript/dataset_select_menu_orig.js"></script>
 
     <script>
         function pressed(e) {
@@ -288,4 +319,21 @@
         }
     </script>
 
+    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='javascript-twitter-post-fetcher/js/twitterFetcher_min.js') }}"></script>
+
+    <script type="text/javascript">
+      var configProfile = {
+      "profile": {"screenName": 'GeneNetwork2'},
+      "domId": 'tweets',
+      "maxTweets": 5,
+      "enableLinks": true,
+      "showUser": false,
+      "showTime": true,
+      "showImages": true,
+      "lang": 'en'
+      };
+      twitterFetcher.fetch(configProfile);
+    </script>
+
+
 {% endblock %}
diff --git a/wqflask/wqflask/templates/index_page_orig.html b/wqflask/wqflask/templates/index_page_orig.html
deleted file mode 100755
index 87cf1b45..00000000
--- a/wqflask/wqflask/templates/index_page_orig.html
+++ /dev/null
@@ -1,339 +0,0 @@
-{% extends "base.html" %}
-{% block title %}GeneNetwork{% endblock %}
-{% block css %}
-<style TYPE="text/css">
-  p.interact { display: none; }
-</style>
-{% endblock %}
-{% block content %}
-<!-- Start of body -->
-    <div class="container-fluid" style="min-width: 1210px;">
-
-        {{ flash_me() }}
-
-        <div class="row" style="width: 100%;">
-
-            <div class="col-xs-4" style="margin-right:50px; min-width: 530px; max-width: 550px;">
-                <section id="search">
-                    <div>
-                        <h1>Select and search</h1>
-                    </div>
-                    <form method="get" action="/search" target="_blank" name="SEARCHFORM">
-                        <fieldset>
-                            <div style="padding: 20px" class="form-horizontal">
-
-                                <div class="form-group">
-                                    <label for="species" class="col-xs-1 control-label" style="width: 65px !important;">Species:</label>
-                                    <div class="col-xs-10 controls input-append" style="display: flex; padding-left: 20px;">
-                                        <div class="col-8">
-                                          <select name="species" id="species" class="form-control" style="width: 280px !important;"><option>Loading...</option></select>
-                                        </div>
-                                    </div>
-                                </div>
-
-                                <div class="form-group">
-                                    <label for="group" class="col-xs-1 control-label" style="width: 65px !important;">Group:</label>
-                                    <div class="col-xs-10 controls input-append" style="display: flex; padding-left: 20px;">
-                                        <div class="col-9">
-                                          <select name="group" id="group" class="form-control" style="width: 340px !important;"><option>Loading...</option></select>
-                                          <i class="icon-question-sign"></i>
-                                        </div>
-                                        <div class="col-3" style="margin-left: 10px;">
-                                            <button type="button" id="group_info" class="btn btn-primary form-control" style="width: 50px !important;">Info</button>
-                                        </div>
-                                    </div>
-                                </div>
-
-                                <div class="form-group">
-                                    <label for="tissue" class="col-xs-1 control-label" style="width: 65px !important;">Type:</label>
-                                    <div class="col-xs-10 controls input-append" style="display: flex; padding-left: 20px;">
-                                        <div class="col-9">
-                                          <select name="type" id="type" class="form-control" style="width: 340px !important;"><option>Loading...</option></select>
-                                        </div>
-                                        <div class="col-3" style="margin-left: 10px;">
-                                            <button type="button" id="dataset_info" class="btn btn-primary form-control" style="width: 50px !important;">Info</button>
-                                        </div>
-                                    </div>
-                                </div>
-
-                                <div class="form-group">
-                                    <label for="dataset" class="col-xs-1 control-label" style="width: 65px !important;">Dataset:</label>
-                                    <div class="col-xs-10 controls" style="display: flex; padding-left: 20px;">
-                                        <div class="col-9">
-                                          <select name="dataset" id="dataset" class="form-control" style="max-width: 550px; width: 450px !important;"><option>Loading...</option></select>
-                                          <i class="icon-question-sign"></i>
-                                        </div>
-                                    </div>
-                                </div>
-
-                                <!--  USER HELP   -->
-                                <!--<p >Databases marked with <b>**</b>-->
-                                <!--      suffix are not public yet.<br>-->
-                                <!--     Access requires <a href="/account.html" target=-->
-                                <!--      "_blank" class="fs14">user login</a>.</p>-->
-                                <!--  GET ANY  SEARCH -->
-
-                                <div class="form-group">
-                                    <label for="or_search" class="col-xs-1 control-label" style="padding-left: 0px; padding-right: 0px; width: 65px !important;">Get Any:</label>
-                                    <div class="col-xs-10 controls" style="padding-left: 20px;">
-                                        <div class="col-8">
-                                          <textarea onkeydown="pressed(event)" name="search_terms_or" rows="1" class="form-control search-query" style="resize: vertical; max-width: 550px; width: 450px !important;" id="or_search"></textarea>
-                                        </div>
-                                    </div>
-                                </div>
-
-                                <!--  GET ANY HELP   -->
-                                <div class="form-group">
-                                    <label for="btsearch" class="col-xs-1 control-label" style="width: 65px !important;"></label>
-                                    <div class="col-xs-10 controls" style="padding-left: 20px;">
-                                        <div class="col-12 controls">
-                                            Enter terms, genes, ID numbers in the <b>Search</b> field.<br>
-                                            Use <b>*</b> or <b>?</b> wildcards (Cyp*a?, synap*).<br>
-                                            Use <b>quotes</b> for terms such as <i>"tyrosine kinase"</i>.
-                                        </div>
-                                    </div>
-                                </div>
-
-                                <div class="form-group">
-                                    <label for="and_search" class="col-xs-1 control-label" style="padding-left: 0px; padding-right: 0px; width: 65px !important;">Combined:</label>
-                                    <div class="col-xs-10 controls" style="padding-left: 20px;">
-                                        <div class="col-8">
-                                          <textarea onkeydown="pressed(event)" name="search_terms_and" rows="1" class="form-control search-query" style="resize: vertical; max-width: 550px; width: 450px !important;" id="and_search"></textarea>
-                                        </div>
-                                    </div>
-                                </div>
-
-                                <div class="form-group">
-                                    <label for="btsearch" class="col-xs-1 control-label" style="width: 65px !important;"></label>
-                                    <div class="col-xs-10 controls" style="display: flex; padding-left: 20px;">
-                                        <div class="col-2 controls">
-                                            <input id="btsearch" type="submit" class="btn btn-primary form-control" value="Search">
-                                        </div>
-                                        <div class="col-2 controls" style="padding-left: 20px;">
-                                            <button type="button" id="make_default" class="btn btn-primary form-control">Make Default</button>
-                                        </div>
-                                    </div>
-                                </div>
-
-                                <!--  SEARCH, MAKE DEFAULT -->
-
-                                <div class="form-group">
-                                </div>
-
-                                <input type="hidden" name="FormID" value="searchResult" class="form-control">
-                                <!--!<input type="hidden" name="RISet" value="BXD">-->
-                            </div>
-                        </fieldset>
-                    </form>
-                </section>
-                <section id="advanced">
-                    <div class="page-header">
-                        <h2>Advanced commands</h2>
-                    </div>
-
-                    <p>You can also use advanced commands. Copy these simple examples into the Get Any field for single term searches and Combined for searches with multiple terms:</p>
-
-                      <ul>
-                        <li><b>POSITION=(chr1 25 30)</b> finds genes, markers, or transcripts on
-                        chromosome 1 between 25 and 30 Mb.</li>
-
-                        <li><b>MEAN=(15 16)</b> in the <b>Combined</b> field finds
-                        highly expressed genes (15 to 16 log2 units)</li>
-
-                        <li><b>RANGE=(1.5 2.5)</b> in the <b>Any</b> field finds traits with values with a specified fold-range (minimum = 1). 
-                        Useful for finding "housekeeping genes" <b>(1.0 1.2)</b> or highly variable molecular assays <b>(10 100)</b>.</li>
-
-                        <li><b>LRS=(15 1000)</b> or <b>LOD=(2 8)</b> finds all traits with peak LRS or LOD scores between lower and upper limits.</li>
-
-                        <li><b>LRS=(9 999 Chr4 122 155)</b> finds all traits on Chr 4 from 122 and 155 Mb with LRS scores between 9 and 999.</li>
-
-                        <li><b>cisLRS=(15 1000 5)</b> or <b>cisLOD=(2 8 5)</b> finds all cis eQTLs with peak LRS or LOD scores between lower and upper limits,
-                            with an <b>inclusion</b> zone of 5 Mb around the parent gene.</li>
-
-                        <li><b>transLRS=(15 1000 5)</b> or <b>transLOD=(2 8 5)</b> finds all trans eQTLs with peak LRS or LOD scores between lower and upper limits,
-                            with an <b>exclusion</b> zone of 5 Mb around the parent gene. You can also add a fourth term specifying which chromosome you want the transLRS to be on
-                            (for example transLRS=(15 1000 5 7) would find all trans eQTLs with peak LRS on chromosome 7 that is also a trans eQTL with exclusionary zone of 5Mb).</li>
-
-                        <li><b>POSITION=(Chr4 122 130) cisLRS=(9 999 10)</b>
-                            finds all traits on Chr 4 from 122 and 155 Mb with cisLRS scores
-                            between 9 and 999 and an inclusion zone of 10 Mb.</li>
-
-                        <li><b>RIF=mitochondrial</b> searches RNA databases for <a href="https://en.wikipedia.org/wiki/GeneRIF">
-                        GeneRIF</a> links.</li>
-
-                        <li><b>WIKI=nicotine</b> searches <a href="http://gn1.genenetwork.org/webqtl/main.py?FormID=geneWiki">
-                        GeneWiki</a> for genes that you or other users have annotated
-                        with the word <i>nicotine</i>.</li>
-
-                        <li><b>GO:0045202</b> searches for synapse-associated genes listed in the
-                        <a href="http://amigo.geneontology.org/amigo/medial_search?q=GO%3A0045202">
-                            Gene Ontology</a>.</li>
-
-                        <li><b>RIF=diabetes LRS=(9 999 Chr2 100 105) transLRS=(9 999 10)</b>
-                        finds diabetes-associated transcripts with peak <a href="{{ url_for('glossary_blueprint.glossary') }}#E">
-                        trans eQTLs</a> on Chr 2 between 100 and 105 Mb with LRS
-                        scores between 9 and 999.</li>
-                      </ul>
-                </section>
-            </div>
-
-            <div class="col-xs-4" style="width: 600px !important;">
-	        <section id="affiliates">
-	            <div class="page-header">
-                        <h1>Affiliates</h1>
-                        <ul>
-                          <li><b><a href="http://gn1.genenetwork.org">GeneNetwork 1</a> at UTHSC</b></li>
-                          <li><span class="broken_link" href="http://ucscbrowser.genenetwork.org/">Genome Browser</span> at UTHSC</li>
-                          <li><a href="https://systems-genetics.org/">Systems Genetics</a> at EPFL</li>
-                          <li><a href="http://bnw.genenetwork.org/">Bayesian Network Web Server</a> at UTHSC</li>
-                          <li><a href="https://www.geneweaver.org/">GeneWeaver</a></li>
-                          <li><a href="https://phenogen.org/">PhenoGen</a> at University of Colorado</li>
-                          <li><a href="http://www.webgestalt.org/">WebGestalt</a> at Baylor</li>
-                        </ul>
-                    </div>
-                </section>
-                <section id="news-section">
-                    <div class="page-header">
-                        <h1>News</h1>
-                        <div id="tweets" style="height: 300px; overflow: scroll; overflow-x: hidden;"></div>
-                        <div align="right">
-                          <a href="https://twitter.com/GeneNetwork2">more news items...</a>
-                        </div>
-                    </div>
-		</section>
-                <section id="websites">
-                    <div class="page-header">
-                        <h1>Github</h1>
-                        <ul>
-                          <li><a href="https://github.com/genenetwork/genenetwork2">GN2 Source Code</a></li>
-                          <li><a href="https://github.com/genenetwork/genenetwork">GN1 Source Code</a></li>
-                          <!--<li><a href="https://github.com/genenetwork/gn-docs/wiki">GN2 Document Wiki</a></li>-->
-                          <li><a href="https://github.com/genenetwork/sysmaintenance">System Maintenance Code</a></li>
-                        </ul>
-                    </div>
-               </section>
-              <!--
-                <section id="tour-info">
-                    <div class="page-header">
-                        <h1>Tour and more info</h1>
-                    </div>
-
-                    <h3>Thirty minute tour</h3>
-                    <p>
-                      Take the 30 minute
-                      GeneNetwork <a href="http://www.genenetwork.org/tutorial/WebQTLTour/" class="fs14">tour</a> that includes screen shots and
-                      typical steps in the analysis.
-                    </p>
-
-                    <h3>Even more info</h3>
-                    <p>
-                      For information about
-                      resources and methods, select the Info buttons next to the Group
-                      and Database fields above.
-                    </p>
-
-                      <p>The <a href="/conditionsofUse.html">conditions</a>
-                      and <a href="/statusandContact.html">contact
-                      </a> pages have information on the status of data sets
-                      and advice on their use and citation.</p>
-
-                </section>
-
-                </section>
-                -->
-                <section id="websites">
-                    <div class="page-header">
-                        <h1>Links</h1>
-                    </div>
-                    <h3>GeneNetwork v2:</h3>
-                      <ul>
-                        <li><a href="http://genenetwork.org/">Main website</a> at UTHSC</li>
-                        <!--<li><a href="http://test-genenetwork.org/">Testing website</a> at UTHSC</li>-->
-                      </ul>
-                    <h3>GeneNetwork v1:</h3>
-                    <ul>
-                        <li><a href="http://gn1.genenetwork.org/">Main website</a> at UTHSC</li>
-                        <li><span class="broken_link" href="http://artemis.uthsc.edu/">Time Machine</span>: Full GN versions from 2009 to 2016 (mm9)</li>
-                            Cloud (EC2)</a></li>
-                    </ul>
-                    <script type="text/javascript" src="//rf.revolvermaps.com/0/0/8.js?i=526mdlpknyd&amp;m=0&amp;c=ff0000&amp;cr1=ffffff&amp;f=arial&amp;l=33" async="async"></script>
-               </section>
-
-                <!--<section id="getting-started">
-                    <div class="page-header">
-                        <h1>Getting started</h1>
-                    </div>
-
-                <ol style="font-size:12px;font-family:verdana;color:black">
-                  <li>Select <b>Species</b> (or All)</li>
-
-                  <li>Select <b>Group</b> (a specific sample)</li>
-
-                  <li>Select <b>Type</b> of data:
-
-                    <ul>
-                      <li>Phenotype (traits)</li>
-
-                      <li>Genotype (markers)</li>
-
-                      <li>Expression (mRNAs)</li>
-                    </ul>
-                  </li>
-
-                  <li>Select a <b>Dataset</b></li>
-
-                  <li>Enter terms in the search field: words,
-                  genes, probes, advanced search commands</li>
-
-                  <li>Click the <b>Search</b> button</li>
-
-                  <li>Optional: Use the <b>Make Default</b> button to save your preferences</li>
-                </ol>
-
-                <h3>User Guide</h3>
-                <h5>Read the
-                <a href="http://gn1.genenetwork.org/index4.html">
-                    user guide</a>.</h5>
-
-                </section>-->
-            </div>
-        </div>
-    </div>
-
-{%endblock%}
-
-{% block js %}
-    <script src="/static/new/javascript/dataset_select_menu_orig.js"></script>
-
-    <script>
-        function pressed(e) {
-            // Has the enter key been pressed?
-            if ( (window.event ? event.keyCode : e.which) == 13) {
-                e.preventDefault();
-                // If enter key has been pressed and the search fields are non-empty
-                // manually submit the <form>
-                if( event.target.value.trim() != "" ) {
-                    document.forms[1].submit();
-                }
-            }
-        }
-    </script>
-
-    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='javascript-twitter-post-fetcher/js/twitterFetcher_min.js') }}"></script>
-
-    <script type="text/javascript">
-      var configProfile = {
-      "profile": {"screenName": 'GeneNetwork2'},
-      "domId": 'tweets',
-      "maxTweets": 5,
-      "enableLinks": true,
-      "showUser": false,
-      "showTime": true,
-      "showImages": true,
-      "lang": 'en'
-      };
-      twitterFetcher.fetch(configProfile);
-    </script>
-
-
-{% endblock %}
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index c4b510d4..156b4772 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -156,7 +156,7 @@ def index_page():
         import_collections = params['import_collections']
         if import_collections == "true":
             g.user_session.import_traits_to_user(params['anon_id'])
-    return render_template("index_page_orig.html", version=GN_VERSION)
+    return render_template("index_page.html", version=GN_VERSION)
 
 
 @app.route("/tmp/<img_path>")