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authorBonfaceKilz2021-04-23 17:27:31 +0300
committerBonfaceKilz2021-04-23 17:42:26 +0300
commit2114ad9e84ad7778e048b52cf865b5f031ceab88 (patch)
treeec11082fd60181879189de8575473086ddf495a4
parentd2e2046a3ce1af0ca97ea1b6d9ccb3a4c9aecf7c (diff)
downloadgenenetwork2-2114ad9e84ad7778e048b52cf865b5f031ceab88.tar.gz
Rename index_page_orig to index_page
-rwxr-xr-x[-rw-r--r--]wqflask/wqflask/templates/index_page.html222
-rwxr-xr-xwqflask/wqflask/templates/index_page_orig.html339
-rw-r--r--wqflask/wqflask/views.py2
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>")