Merge branch 'testing' into feature/integrate-correlation-api

13 files changed, 413 insertions, 552 deletions

diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html
index ccb2ac5a..ddb1d272 100644
--- a/wqflask/wqflask/templates/base.html
+++ b/wqflask/wqflask/templates/base.html
@@ -69,6 +69,7 @@
                             <ul class="dropdown-menu">
                               <li><a href="{{ url_for('references_blueprint.references') }}">References</a></li>
                               <li><a href="/tutorials">Tutorials/Primers</a></li>
+                              <li><a href="{{ url_for('blogs_blueprint.blogs_list') }}">Blogs</a></li>
                               <li><a href="{{ url_for('glossary_blueprint.glossary') }}">Glossary of Term</a></li>
                               <li><a href="http://gn1.genenetwork.org/faq.html">FAQ</a></li>
                               <li><a href="{{ url_for('policies_blueprint.policies') }}">Policies</a></li>
@@ -191,7 +192,7 @@
                     Translational Systems Genetics of Mitochondria, Metabolism, and Aging (R01AG043930, 2013-2018)
                 </li>
                 <li>
-                    <a href="http://www.iniastress.org/">NIAAA</a>
+                    <a href="https://www.ohsu.edu/iniastress-consortium">NIAAA</a>
                     Integrative Neuroscience Initiative on Alcoholism (U01 AA016662, U01 AA013499, U24 AA013513, U01 AA014425, 2006-2017)
                 </li>
                 <li>
@@ -257,7 +258,6 @@
     <script src="{{ url_for('js', filename='jquery-ui/jquery-ui.min.js') }}" type="text/javascript"></script>
 
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='colorbox/jquery.colorbox-min.js') }}"></script>
-    <!--<script type="text/javascript" src="/static/new/javascript/login.js"></script>-->
 
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/parsley.min.js') }}"></script>
 
diff --git a/wqflask/wqflask/templates/blogs.html b/wqflask/wqflask/templates/blogs.html
new file mode 100644
index 00000000..314eb733
--- /dev/null
+++ b/wqflask/wqflask/templates/blogs.html
@@ -0,0 +1,12 @@
+{% extends "base.html" %}
+{% block title %}Blogs {% endblock %}
+{% block css %}
+<link rel="stylesheet" type="text/css" href="/static/new/css/markdown.css" />
+{% endblock %}
+{% block content %}
+<div class="github-btn-container">
+</div>
+<div id="markdown" class="container">
+    {{ rendered_markdown|safe }}
+</div>
+{% endblock %}
\ No newline at end of file
diff --git a/wqflask/wqflask/templates/blogs_list.html b/wqflask/wqflask/templates/blogs_list.html
new file mode 100644
index 00000000..6bad4628
--- /dev/null
+++ b/wqflask/wqflask/templates/blogs_list.html
@@ -0,0 +1,52 @@
+{% extends "base.html" %}
+{% block title %}Blogs {% endblock %}
+{% block css %}
+<style type="text/css">
+.container {
+    height: 100vh;
+}
+
+.blog_year {
+    font-weight: bold;
+    font-size: 48px;
+    padding: 12px 10px;
+}
+
+.blog_title {
+    padding: 10px 15px;
+
+}
+
+
+
+.blog_title a {
+    font-size: 1.3em;
+    padding-left: 10px;
+    letter-spacing: 0.07em;
+    text-decoration: underline;
+}
+</style>
+<link rel="stylesheet" type="text/css" href="/static/new/css/markdown.css" />
+{% endblock %}
+{% block content %}
+<div id="markdown" class="container">
+    <div>
+        {% for year, year_blogs in blogs.items() %}
+        <div class="blog_year">
+            <h3>{{year}}</h3>
+        </div>
+        {%for blog in year_blogs%}
+        <div>
+            <div class="blog_title">
+                <ul>
+                    <li>
+                        <a href="{{ url_for('blogs_blueprint.display_blog',blog_path = blog.full_path)}}">{{blog['subtitle']}}</a>
+                    </li>
+                </ul>
+            </div>
+        </div>
+        {% endfor %}
+        {%endfor%}
+    </div>
+</div>
+{% endblock %}
\ No newline at end of file
diff --git a/wqflask/wqflask/templates/collections/add.html b/wqflask/wqflask/templates/collections/add.html
index b4e5385b..0398c6e4 100644
--- a/wqflask/wqflask/templates/collections/add.html
+++ b/wqflask/wqflask/templates/collections/add.html
@@ -49,8 +49,20 @@
 </div>
 
 <script>
-    $('#add_form').parsley();
-    $('#add_form').on('submit', function(){
-      parent.jQuery.colorbox.close();
-    });
+  $('#add_form').parsley();
+  $('#add_form').on('submit', function(){
+    parent.jQuery.colorbox.close();
+  });
+
+  apply_default = function() {
+    let default_collection_id = $.cookie('default_collection');
+    if (default_collection_id) {
+      let the_option = $('[name=existing_collection] option').filter(function() {
+        return ($(this).val().split(":")[0] == default_collection_id);
+      })
+      the_option.prop('selected', true);
+    }
+  }
+
+  apply_default();
 </script>
diff --git a/wqflask/wqflask/templates/collections/view.html b/wqflask/wqflask/templates/collections/view.html
index 8d5e3616..9ec98ab1 100644
--- a/wqflask/wqflask/templates/collections/view.html
+++ b/wqflask/wqflask/templates/collections/view.html
@@ -14,6 +14,7 @@
             <span id="collection_name">{{ uc.name }}</span>
             <input type="text" name="new_collection_name" style="font-size: 20px; display: none; width: 500px;" class="form-control" placeholder="{{ uc.name }}"> 
             <button class="btn btn-default" style="display: inline;" id="change_collection_name">Change Collection Name</button>
+            <button class="btn btn-default" style="display: inline;" id="make_default">Make Default</button>
         </h1>
         <h3>This collection has {{ '{}'.format(numify(trait_obs|count, "record", "records")) }}</h3>
 
@@ -231,6 +232,21 @@
                     $('#collection_name').css('display', 'inline');
                 }
             });
+
+            make_default = function() {
+                alert("The current collection is now your default collection.")
+                let uc_id = $('#uc_id').val();
+                $.cookie('default_collection', uc_id, {
+                    expires: 365,
+                    path: '/'
+                });
+
+                let default_collection_id = $.cookie('default_collection');
+            };
+
+            $("#make_default").on("click", function(){
+                make_default();
+            });
         });
     </script>
 
diff --git a/wqflask/wqflask/templates/edit_trait.html b/wqflask/wqflask/templates/edit_trait.html
new file mode 100644
index 00000000..b9a31fc6
--- /dev/null
+++ b/wqflask/wqflask/templates/edit_trait.html
@@ -0,0 +1,86 @@
+{% extends "base.html" %}
+{% block title %}Trait Submission{% endblock %}
+{% block content %}
+<!-- Start of body -->
+  <form method="post" action="/show_temp_trait">
+    <div class="container-fluid">
+
+        {{ flash_me() }}
+
+        <div class="row" style="width: 1400px !important;">
+            <div class="col-xs-3">
+                <section id="description">
+                    <div>
+                        <h2 style="color: #5a5a5a;">Introduction</h2>
+                        <hr>
+                        <p>The trait values that you enter are statistically compared with verified genotypes collected at a set of microsatellite markers in each RI set. The markers are drawn from a set of over 750, but for each set redundant markers have been removed, preferentially retaining those that are most informative.</p>
+                        <p>These error-checked RI mapping data match theoretical expectations for RI strain sets. The cumulative adjusted length of the RI maps are approximately 1400 cM, a value that matches those of both MIT maps and Chromosome Committee Report maps. See our <a target="_blank" href="http://www.nervenet.org/papers/BXN.html">full description</a> of the genetic data collected as part of the WebQTL project.</p>
+                    </div>
+                </section>
+                <br>
+                <section id="description">
+                    <div>
+                        <h2 style="color: #5a5a5a;">About Your Data</h2>
+                        <hr>
+                        <p>You can open a separate window giving the number of strains for each data set and sample data.</p>
+                        <p>None of your submitted data is copied or stored by this system except during the actual processing of your submission. By the time the reply page displays in your browser, your submission has been cleared from this system.</p>
+                    </div>
+                </section>
+            </div>
+            <div style="padding-left:20px" class="col-xs-6" style="width: 600px !important;">
+                <section id="submission_form">
+                    <div class="form-group">
+                        <h2 style="color: #5a5a5a;">Edit Trait Form</h2>
+                        <hr>
+                        <div style="margin-bottom: 150px;" class="form-horizontal">
+                          <h3>Choose Dataset to Edit:</h3>
+                          <br>
+                          <div class="col-xs-10">
+                            <!-- Species -->
+                            <div class="form-group">
+                              <label for="species" class="col-xs-2 control-label">Species: </label>
+                              <div class="col-xs-4 controls">
+                                <select name="species" id="species" class="form-control span3" style="width: 280px !important;"></select>
+                              </div>
+                            </div>
+                            <!-- Group -->
+                            <div class="form-group">
+                              <label for="group" class="col-xs-2 control-label">Group: </label>
+                              <div class="col-xs-4 controls">
+                                <select name="group" id="group" class="form-control span3" style="width: 280px !important;"></select>
+                              </div>
+                            </div>
+                            <!-- Type -->
+                            <div class="form-group">
+                                <label for="group" class="col-xs-2 control-label">Type: </label>
+                                <div class="col-xs-4 controls">
+                                    <select name="type" id="type" class="form-control span3" style="width: 280px !important;"></select>
+                                </div>
+                            </div>
+                            <!-- Dataset -->
+                            <div class="form-group">
+                                <label for="group" class="col-xs-2 control-label">DataSet: </label>
+                                <div class="col-xs-4 controls">
+                                    <select name="dataset" id="dataset" class="form-control span3" style="width: 280px !important;"></select>
+                                </div>
+                            </div>
+                          </div>
+                          <div class="controls" style="display:block; margin-left: 40%; margin-right: 20%;">
+                              <input type="submit" style="width: 110px; margin-right: 25px;" class="btn btn-primary form-control col-xs-2" value="Submit Trait">
+                              <input type="reset" style="width: 110px;" class="btn btn-primary form-control col-xs-2" value="Reset">
+                          </div>
+                        </div>
+                </section>
+            </div>
+        </div>
+    </div>
+  </form>
+
+{%endblock%}
+
+  {% block js %}
+  <script src="/static/new/javascript/dataset_select_menu_edit_trait.js"></script>
+    <script>
+      gn_server_url = "{{ gn_server_url }}";
+    </script>
+{% endblock %}
diff --git a/wqflask/wqflask/templates/index_page.html b/wqflask/wqflask/templates/index_page.html
index 31846f87..7b103305 100644..100755
--- a/wqflask/wqflask/templates/index_page.html
+++ b/wqflask/wqflask/templates/index_page.html
@@ -1,88 +1,102 @@
 {% extends "base.html" %}
 {% block title %}GeneNetwork{% endblock %}
-{% block content %}
-<!-- Start of body -->
+{% block css %}
+<style TYPE="text/css">
+  p.interact { display: none; }
 
-<!--
-    <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">
+  
+
+  .tweet  {
+
+   padding:5px;
+   color:#000;
+
+  }
+
+  .media {
+    padding-bottom:10px;
+    border-bottom: 1px solid #c8ccc9;
+  }
+
+  .media img {
+
+    width: 95%;
+    height: 100%;
+    border-radius: 5px;
+    /*transform: scale(1.1); image small?*/
+    border:1px solid #c8ccc9;
+
+  }
+</style>
+{% endblock %}
+{% block content %}
+<!-- Start of body -->
+    <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>-->
-                                <!--      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">
-                                        <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 +104,8 @@
                                 <!--  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>.
@@ -101,29 +115,30 @@
 
                                 <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>
 
                                 <!--  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>
@@ -133,33 +148,43 @@
                         <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">
@@ -168,99 +193,56 @@
                       </ul>
                 </section>
             </div>
-            <div style="padding-left:120px" class="col-xs-4" style="width: 600px !important;">
-                <!--
-                <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>
 
+            <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><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>Affiliates and mirrors</h1>
+                        <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/sysmaintenance">System Maintenance Code</a></li>
+                        </ul>
                     </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>
-
-                    <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>
-                    </ul>
-                </section>
-
-                <!--<section id="getting-started">
+               </section>
+                <section id="websites">
                     <div class="page-header">
-                        <h1>Getting started</h1>
+                        <h1>Links</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:
-
+                    <h3>GeneNetwork v2:</h3>
+                      <ul>
+                        <li><a href="http://genenetwork.org/">Main website</a> at UTHSC</li>
+                      </ul>
+                    <h3>GeneNetwork v1:</h3>
                     <ul>
-                      <li>Phenotype (traits)</li>
-
-                      <li>Genotype (markers)</li>
-
-                      <li>Expression (mRNAs)</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>
-                  </li>
-
-                  <li>Select a <b>Dataset</b></li>
-
-                  <li>Enter terms in the search field: words,
-                  genes, ID numbers, 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://www.genenetwork.org/index4.html">
-                    user guide</a>.</h5>
-
-                </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>
             </div>
         </div>
     </div>
@@ -268,11 +250,7 @@
 {%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 +266,21 @@
         }
     </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 7f82b35c..00000000
--- a/wqflask/wqflask/templates/index_page_orig.html
+++ /dev/null
@@ -1,349 +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 -->
-
-<!--
-    <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" 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/templates/loading.html b/wqflask/wqflask/templates/loading.html
index 926f258d..1adeb2bd 100644
--- a/wqflask/wqflask/templates/loading.html
+++ b/wqflask/wqflask/templates/loading.html
@@ -7,34 +7,62 @@
   {% endfor %}
   <div class="container">
     <div>
-      <div style="min-height: 80vh; display: flex; align-items: center; text-align: center;">
-        <div style="margin-bottom: 5px; left: 50%; margin-right: -50%; margin-top: 10%; transform: translate(-50%, -50%); position: absolute;">
-        {% if start_vars.tool_used == "Mapping" %}
-        <h1>Computing the Maps</h1>
-        <br>
-        <i>n</i> = {{ start_vars.n_samples }}
-        <br>
-        Method = {% if start_vars.method == "gemma" %}GEMMA{% else %}{{ start_vars.method }}{% endif %}
-        <br>
-        {% if start_vars.transform != "" %}
-        transform = {{ start_vars.transform }}
-        <br>
-        {% endif %}
-        MAF >= {{ start_vars.maf }}
-        {% else %}
-        <h1>Loading&nbsp;{{ start_vars.tool_used }}&nbsp;Results...</h1>
-        {% endif %}
-        <br><br>
-        <img align="center" src="/static/gif/89.gif">
-        </div>
-        <!--<div style="margin-left: auto; margin-right: auto; display: block; width: 50%; top:50%;">
+      <div style="min-height: 80vh; display: flex; align-items: center; text-align: left;">
+        <div style="margin-bottom: 5px; left: 50%; margin-right: -50%; top: 50%; transform: translate(-50%, -50%); position: absolute;">
+          {% if start_vars.tool_used == "Mapping" %}
+          <h1>Computing the Maps</h1>
+          <br>
+          <b>Trait Metadata</b>
+          <br>
+          species = <b><i>{{ start_vars.species[0] | upper }}{{ start_vars.species[1:] }}</i></b>
+          <br>
+          group = <b><i>{{ start_vars.group[0] | upper }}{{ start_vars.group[1:] }}</i></b>
+          <br>
+          trait identifier = <b><i>{{ start_vars.trait_id }}</i></b>
+          <br>
+          n of sample = <b><i>{{ start_vars.n_samples }}</i></b>
+          {% if start_vars.transform != "" %}
+          <br>
+          transformation = <b><i>{{ start_vars.transform }}</i></b>
+          {% endif %}
+          <br><br>
+          <b>Mapping Metadata</b>
+          <br>
+          mapping method = <b><i>{% if start_vars.method == "gemma" %}GEMMA {% if start_vars.use_loco == "True" %}using LOCO {% endif %}{% else %}{{ start_vars.method }}{% endif %}</i></b>
+          {% if start_vars.maf != "" and start_vars.method != "reaper" %}
+          <br>
+          minor allele frequency lower limit = <b><i>{{ start_vars.maf }}</i></b>
+          {% endif %}
+          {% if start_vars.covariates != "" and start_vars.method != "reaper" %}
+          <br>
+          {% set covariate_list = start_vars.covariates.split(",") %}
+          cofactors = <b><i>{% for covariate in covariate_list %}{% set this_covariate = covariate.split(":")[0] %}{{ this_covariate }}{% if not loop.last %}, {% endif %}{% endfor %}</i></b>
+          {% endif %}
+          {% if start_vars.control_marker != "" and start_vars.do_control == "true" and start_vars.method != "gemma" %}
+          <br>
+          marker covariate = <b><i>{{ start_vars.control_marker }}</i></b>
+          {% endif %}
+          {% set genofile_desc = start_vars.genofile.split(":")[1] %}
+          <br>
+          Genotype File = <b><i>{{ genofile_desc }}</i></b>
+          {% if start_vars.num_perm | int > 0 and start_vars.method != "gemma" %}
+          <br>
+          n of permutations = <b><i>{{ start_vars.num_perm }}</i></b>
+          {% endif %}
+          {% if num_bootstrap in start_vars %}
+          {% if start_vars.num_bootstrap | int > 0 and start_vars.method == "reaper" %}
+          <br>
+          n of bootstrap = <b><i>{{ start_vars.num_bootstrap }}</i></b>
+          {% endif %}
+          {% endif %}
+          {% else %}
+          <h1>Loading&nbsp;{{ start_vars.tool_used }}&nbsp;Results...</h1>
+          {% endif %}
+          <br><br>
+          <div style="text-align: center;">
             <img align="center" src="/static/gif/89.gif">
-        </div>-->
-        <!--
-        <div class="progress center-block" style="margin-left: 25%; margin-right: 25%; position: absolute; height:50px; width:50%; top:50%;">
-          <div class="progress-bar progress-bar-striped active" role="progressbar" aria-valuenow="100" aria-valuemin="0" aria-valuemax="100" style="width:100%;"></div>
+          </div>
         </div>
-        -->
       </div>
     </div>
   </div>
diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html
index c08b21ef..73d7501b 100644
--- a/wqflask/wqflask/templates/mapping_results.html
+++ b/wqflask/wqflask/templates/mapping_results.html
@@ -17,8 +17,9 @@
         <input type="hidden" name="temp_uuid" value="{{ temp_uuid }}">
         {% if temp_trait is defined %}
         <input type="hidden" name="temp_trait" value="{{ temp_trait }}">
-        <input type="hidden" name="group" value="{{ group }}">
         {% endif %}
+        <input type="hidden" name="group" value="{{ dataset.group.name }}">
+        <input type="hidden" name="species" value="{{ dataset.group.species }}">
         <input type="hidden" name="trait_id" value="{{ this_trait.name }}">
         <input type="hidden" name="dataset" value="{{ dataset.name }}">
         <input type="hidden" name="genofile" value="{{ genofile_string }}">
@@ -71,7 +72,7 @@
               {% endif %}
               <br>
               <br>
-              <a id="export_mapping_results" href="#" target="_blank" >Download Full Results</a>
+              <a class="export_mapping_results" href="#" target="_blank" >Download Full Results</a>
           </div>
           <div id="gn1_map_options" class="col-xs-5" style="outline: 3px double #AAAAAA; padding: 10px; margin: 10px;">
             <div class="col-xs-8" style="padding: 0px;">
@@ -247,6 +248,7 @@
         <button class="btn btn-default" id="deselect_all"><span class="glyphicon glyphicon-remove"></span> Deselect All</button>
         <button class="btn btn-default" id="invert"><span class="glyphicon glyphicon-resize-vertical"></span> Invert</button>
         {% if geno_db_exists == "True" %}<button class="btn btn-success" id="add" disabled><span class="glyphicon glyphicon-plus-sign"></span> Add</button>{% endif %}
+        <button class="btn btn-default export_mapping_results" >Download <span class="glyphicon glyphicon-download"></span></button>
         <br />
         <br />
           <div id="table_container" style="width:{% if 'additive' in trimmed_markers[0] %}600{% else %}550{% endif %}px;">
@@ -480,7 +482,7 @@
 
         var mapping_input_list = ['temp_uuid', 'trait_id', 'dataset', 'tool_used', 'form_url', 'method', 'transform', 'trimmed_markers', 'selected_chr', 'chromosomes', 'mapping_scale', 'sample_vals',
                             'score_type', 'suggestive', 'significant', 'num_perm', 'permCheck', 'perm_output', 'perm_strata', 'categorical_vars', 'num_bootstrap', 'bootCheck', 'bootstrap_results',
-                            'LRSCheck', 'covariates', 'maf', 'use_loco', 'manhattan_plot', 'color_scheme', 'manhattan_single_color', 'control_marker', 'control_marker_db', 'do_control', 'genofile',
+                            'LRSCheck', 'covariates', 'maf', 'use_loco', 'manhattan_plot', 'color_scheme', 'manhattan_single_color', 'control_marker', 'do_control', 'genofile',
                             'pair_scan', 'startMb', 'endMb', 'graphWidth', 'lrsMax', 'additiveCheck', 'showSNP', 'showGenes', 'viewLegend', 'haplotypeAnalystCheck', 
                             'mapmethod_rqtl_geno', 'mapmodel_rqtl_geno', 'temp_trait', 'group', 'species', 'reaper_version', 'primary_samples', 'n_samples']
 
@@ -612,7 +614,7 @@
             return $('#marker_regression_form').submit();
         }
 
-        $('#export_mapping_results').click(export_mapping_results);
+        $('.export_mapping_results').click(export_mapping_results);
 
         $('#browser_tab').click(function() {
           $('#gn1_map_options').css("display", "none")
diff --git a/wqflask/wqflask/templates/show_trait_transform_and_filter.html b/wqflask/wqflask/templates/show_trait_transform_and_filter.html
index b70ca590..e3f5ef81 100644
--- a/wqflask/wqflask/templates/show_trait_transform_and_filter.html
+++ b/wqflask/wqflask/templates/show_trait_transform_and_filter.html
@@ -20,7 +20,7 @@
     <div id="remove_samples_invalid" class="alert alert-error" style="display:none;">
           Please check that your input is formatted correctly, e.g. <strong>3, 5-10, 12</strong>
     </div>
-    {% if sample_groups[0].attributes %}
+    {% if categorical_attr_exists == "true" %}
     <div class="input-append block-div-2">
         <label for="exclude_column">Block samples by group:</label>
         <select id="exclude_column" size=1>
diff --git a/wqflask/wqflask/templates/submit_trait.html b/wqflask/wqflask/templates/submit_trait.html
index 68b06f55..3572b0a9 100644
--- a/wqflask/wqflask/templates/submit_trait.html
+++ b/wqflask/wqflask/templates/submit_trait.html
@@ -14,7 +14,7 @@
                         <h2 style="color: #5a5a5a;">Introduction</h2>
                         <hr>
                         <p>The trait values that you enter are statistically compared with verified genotypes collected at a set of microsatellite markers in each RI set. The markers are drawn from a set of over 750, but for each set redundant markers have been removed, preferentially retaining those that are most informative.</p>
-                        <p>These error-checked RI mapping data match theoretical expectations for RI strain sets. The cumulative adjusted length of the RI maps are approximately 1400 cM, a value that matches those of both MIT maps and Chromosome Committee Report maps. See our full description of the genetic data collected as part of the WebQTL project.</p>
+                        <p>These error-checked RI mapping data match theoretical expectations for RI strain sets. The cumulative adjusted length of the RI maps are approximately 1400 cM, a value that matches those of both MIT maps and Chromosome Committee Report maps. See our <a target="_blank" href="http://www.nervenet.org/papers/BXN.html">full description</a> of the genetic data collected as part of the WebQTL project.</p>
                     </div>
                 </section>
                 <br>
@@ -53,7 +53,7 @@
                             </div>
                           </div>
                         </div>
-                        <div style="padding-bottom: 50px;" class="form-horizontal">
+                        <div style="padding-bottom: 50px; margin-bottom:400px" class="form-horizontal">
                           <h3>2. Enter Trait Data:</h3>
                           <h4 style="color:red;">File uploading isn't enabled yet, but is coming soon.</h4>
                           <br>
@@ -61,18 +61,6 @@
                             <img src="/static/new/images/step2.gif">
                           </div>
                           <div class="col-xs-10">
-                            <!--
-                            <div class="form-group" style="padding-left: 15px;">
-                              <p>
-                                 <b>From a File:</b> You can enter data by entering a file name here. The file should contain a series of numbers representing trait values. 
-                                 The values can be on one line separated by spaces or tabs, or they can be on separate lines. Include one value for each progeny individual
-	                         or recombinant inbred line. Represent missing values with a non-numeric character such as "x". If you have chosen a recombinant inbred set,
-                                 when you submit your data will be displayed in a form where you can confirm and/or edit them. If you enter a file name here, any data that
-                                 you paste into the next section will be ignored.
-                              </p>
-                              <input type="file" name="trait_file" style="border-width: 1px; border-style: solid; border-color: #999999;">
-                            </div>
-                            -->
                             <div class="form-group" style="padding-left: 15px;">
                               <p>
                                  <b>Paste or Type Multiple Values:</b> You can enter data by pasting a series of numbers representing trait values into this area. 
@@ -89,6 +77,24 @@
                             <input type="reset" style="width: 110px;" class="btn btn-primary form-control col-xs-2" value="Reset">
                           </div>
                         </div>
+                        <div style="padding-bottom: 50px;" class="form-horizontal">
+                            <h3>3. Enable Use of Trait Variance:</h3>
+                            <div class="col-xs-2" style=""display: flex; align-items: center;">
+                                <img src="/static/new/images/step3.gif">
+                            </div>
+                                                      <div class="col-xs-10">
+                            <div class="form-group" style="padding-left: 15px;">
+                              <p>
+                                  <b>Name Your Trait:</b> <span style="color:red;">(optional)</span>
+                              </p>
+                              <textarea name="trait_name" rows="1" cols="30"></textarea>
+                            </div>
+                          </div>
+                          <div class="controls" style="display:block; margin-left: 40%; margin-right: 20%;">
+                              <input type="submit" style="width: 110px; margin-right: 25px;" class="btn btn-primary form-control col-xs-2" value="Submit Trait">
+                              <input type="reset" style="width: 110px;" class="btn btn-primary form-control col-xs-2" value="Reset">
+                          </div>
+                        </div>
                 </section>
             </div>
         </div>
diff --git a/wqflask/wqflask/templates/tutorials.html b/wqflask/wqflask/templates/tutorials.html
index f9d12ba5..ce5d0e3d 100644
--- a/wqflask/wqflask/templates/tutorials.html
+++ b/wqflask/wqflask/templates/tutorials.html
@@ -8,7 +8,8 @@
 	<P class="title"><H2>Tutorials/Primers</H2></P>
 	<UL>
 		<LI><A HREF="http://www.nervenet.org/tutorials/HS_Rat_Using_GeneNetwork_21Apr2020v7.pptx">Statistical and genetic functions, 
-and initial mapping results for Rat GWAS P50 as implemented in GeneNetwork.org</A><P></P>
+			and initial mapping results for Rat GWAS P50 as implemented in GeneNetwork.org</A></LI>
+		<LI><A HREF="https://opar.io/training/osga-webinar-series-2020.html">Webinar Series - Quantitative Genetics Tools for Mapping Trait Variation to Mechanisms, Therapeutics, and Interventions</A></LI>
 	</UL>
 	<P></P>
 </TD>