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{% extends "base.html" %}
{% block title %}GeneNetwork{% endblock %}
{% block css %}
<!-- UIkit CSS -->
<link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='uikit/css/uikit.min.css') }}"/>
<link rel="stylesheet" href="/static/new/css/index_page.css" />
<link rel="stylesheet" href="/static/new/css/autocomplete.css"/>
<!-- UIkit JS -->
<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='uikit/js/uikit.min.js') }}"></script>
<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='uikit/js/uikit-icons.min.js') }}"></script>
<!--locally built emfed package see source file:https://github.com/sampsyo/emfed -->
<script type="module" src="static/new/javascript/emfed.bundle.js"></script>
<link rel="stylesheet" type="text/css"
href="static/new/css/toots.css">
<style TYPE="text/css">
p.interact { display: none; }
.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;
}
.toots {
margin:0 auto;
max-width: 500px;
height: 160px;
position: relative;
border-radius:10px;
background-color: #F9F9F9;
}
h2 {
margin-bottom: 0px;
}
ul {
margin-top: 0px;
}
.toot {
padding-top:8px;
background:#f9f9f9;
color:#000;
}
</style>
{% endblock %}
{% block content %}
<!-- Start of body -->
<div class="container-fluid" style="min-width: 1210px;">
{{ flash_me() }}
{%if anon_collections | length > 0%}
<div class="panel panel-warning">
<div class="panel-heading">
<h3 class="panel-title">Import Anonymous Collections</h3>
</div>
<div class="panel-body">
<p>
There {%if anon_collections | length > 1%}are{%else%}is{%endif%}
{{anon_collections | length}} anonymous
collection{%if anon_collections | length > 1%}s{%endif%}
associated with your current session. What do you wish to do?
</p>
<p class="text-danger" style="font-weight: bold;">
<small>
If you choose to ignore this, the anonymous collections will be
eventually deleted and lost.
</small>
</p>
<form action="{{url_for('handle_anonymous_collections')}}"
method="POST">
<div class="form-group">
<input type="radio" id="rdo-import" value="import"
name="anon_choice" />
<label for="rdo-import">Import</label>
<input type="radio" id="rdo-delete" value="delete"
name="anon_choice" />
<label for="rdo-delete">Delete</label>
</div>
<input type="submit" class="btn btn-warning" value="Submit" />
</form>
</div>
</div>
{%endif%}
<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 class="page-header">
<h2>Select and Search</h2>
</div>
<form method="get" action="/search" target="_blank" id="searchform" name="SEARCHFORM",
data-gn_server_url="{{gn_server_url}}">
<fieldset>
<div style="padding-left: 20px; padding-right: 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-9">
<select name="species" id="species" class="form-control" style="width: 340px !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 form-control info-button"><span class="glyphicon glyphicon-flag"></span> 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 form-control info-button"><span class="glyphicon glyphicon-flag"></span> 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>
<!-- 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 autocomplete">
<textarea id="myInput" onkeyup="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><strong><a style="text-decoration: none;" href="https://issues.genenetwork.org/topics/xapian-search-queries" target=”_blank” >see more hints</a></strong></div>
</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 autocomplete">
<textarea id="myInput" onkeyup="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">
<button id="btsearch" class="btn btn-primary form-control"><span class="glyphicon glyphicon-search"></span> Search</button>
</div>
<div class="col-2 align-self-end controls" style="padding-left: 20px;">
<button type="button" id="make_default" class="btn form-control info-button"><span class="glyphicon glyphicon-pushpin"></span> Lock Menu</button>
</div>
</div>
</div>
<!-- SEARCH, MAKE DEFAULT -->
<div class="form-group">
</div>
<input type="hidden" name="accession_id" value="None" class="form-control">
<input type="hidden" name="FormID" value="searchResult" class="form-control">
</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="tutorials">
<div class="page-header">
<h2>Tutorials</h2>
</div>
<div class="uk-grid-match uk-child-width-1-3@m" uk-grid>
<div>
<strong><a class="uk-link-text" href="/tutorials">Webinars & Courses</a></strong><br>
In-person courses, live webinars and webinar recordings<br>
<a href="/tutorials" class="uk-icon-link" uk-icon="laptop" ratio="2"></a>
</div>
<div>
<strong><a class="uk-link-text" href="/tutorials">Tutorials</a></strong><br>
Tutorials: Training materials in HTML, PDF and video formats<br>
<a href="/tutorials" class="uk-icon-link" uk-icon="file-text" ratio="2"></a>
</div>
<div>
<strong><a class="uk-link-text" href="/tutorials">Documentation</a></strong><br>
Online manuals, handbooks, fact sheets and FAQs<br>
<a href="/tutorials" class="uk-icon-link" uk-icon="album" ratio="2"></a>
</div>
</div>
</section>
<section id="news-section">
<div class="page-header">
<h2>News</h2>
</div>
<div id="mastadon" style="height: 405px; overflow: scroll; overflow-x: hidden;">
<a class="mastodon-feed" target="_blank"
href="https://genomic.social/@genenetwork"
data-toot-limit="5"
>Genenetwork mastadon</a>
</div>
<div align="right">
<a href="https://genomic.social/@genenetwork">more news items...</a>
</div>
</section>
<section id="websites">
<div class="page-header">
<h2>Links</h2>
</div>
<ul>
<li>Github</li>
<ul>
<li><a href="https://github.com/genenetwork/genenetwork2">GN2 Source Code</a></li>
<li><a href="https://github.com/genenetwork/genenetwork3">GN3 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>
</ul>
<ul>
<li>GeneNetwork v2</li>
<ul>
<li><a href="https://genenetwork.org/">Main website</a> at UTHSC</li>
</ul>
</ul>
<ul>
<li>GeneNetwork v1</li>
<ul>
<li><a href="http://gn1.genenetwork.org/">Main website</a> at UTHSC</li>
</ul>
</ul>
<ul>
<li>Affiliates</li>
<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>
</ul>
<ul>
<li>GeneNetwork hosted portals</li>
<ul>
<li><a href="https://www.opar.io/">Omics Portal For Addiction Research</a></li>
<li><a href="https://msk.genenetwork.org/">GN4MSK musculoskeletal</a></li>
<li><a href="https://genecup.org/">GeneCup: Mining PubMed for Gene Relationships using Custom Ontologies</a></li>
</ul>
</ul>
</section>
</div>
</div>
</div>
{%endblock%}
{% block js %}
<script src="/static/new/javascript/dataset_select_menu_orig.js"></script>
<script type="text/javascript">
$(document).on('submit', '#searchform', function(event){
event.preventDefault()
let user_searches = [];
$(".search-query").each(function() {
this_search = $(this).val().trim();
if (this_search != ""){
user_searches.push(this_search);
}
});
for (i=0; i<user_searches.length; ++i){
saveBeforeSubmit(user_searches[i])
}
$( "#searchform" )[0].submit();
});
</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() != "" ) {
saveBeforeSubmit(event.target.value.trim())
$("#searchform").prop("action", "/search")
$("#searchform")[0].submit();
}
}
}
</script>
{% endblock %}
|
