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-rwxr-xr-xgn2/wqflask/templates/index_page.html893
1 files changed, 447 insertions, 446 deletions
diff --git a/gn2/wqflask/templates/index_page.html b/gn2/wqflask/templates/index_page.html
index f2294e60..d3af519b 100755
--- a/gn2/wqflask/templates/index_page.html
+++ b/gn2/wqflask/templates/index_page.html
@@ -1,518 +1,519 @@
{% extends "base.html" %}
-{% block title %}GeneNetwork{% endblock %}
+{% block title %} GeneNetwork {% endblock %}
+
+<link rel="stylesheet"
+ type="text/css"
+ href="{{ url_for('css', filename='uikit/css/uikit.min.css') }}" />
+
+
{% 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" />
- <!-- 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; }
+<link rel="stylesheet" href="/static/new/css/index_page.css" />
+<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 {
+ .media {
+ padding-bottom:10px;
+ border-bottom: 1px solid #c8ccc9;
+ }
- width: 95%;
- height: 100%;
- border-radius: 5px;
- /*transform: scale(1.1); image small?*/
- border:1px solid #c8ccc9;
- }
+ .media img {
- .toots {
- margin:0 auto;
- max-width: 500px;
- height: 160px;
- position: relative;
- border-radius:10px;
- background-color: #F9F9F9;
+ 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;
- }
+ h2 {
+ margin-bottom: 0px;
+ }
- .toot {
- padding-top:8px;
- background:#f9f9f9;
- color:#000;
-
- }
- </style>
+ ul {
+ margin-top: 0px;
+ }
+
+ .toot {
+ padding-top:8px;
+ background:#f9f9f9;
+ color:#000;
+
+ }
+
+</style>
{% endblock %}
{% block search %}
- {% include "gsearch.html" %}
+{% include "gsearch.html" %}
{% 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 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>
- <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>
+ <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>
- </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>
+ <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 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 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 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 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 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 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>
- <!-- 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>
+ <!-- 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>
- <!-- 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/xapian-search-queries"
- target="_blank">see more hints</a>
- </strong>
- </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/xapian-search-queries"
+ target="_blank">see more hints</a>
+ </strong>
</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 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 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 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>
- <!-- 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>
+ <!-- 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("gn_docs_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>
- <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>
+ <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>
- <b>POSITION=(chr1 25 30)</b> finds genes, markers, or transcripts on
- chromosome 1 between 25 and 30 Mb.
+ <a href="https://github.com/genenetwork/genenetwork2">GN2 Source Code</a>
</li>
<li>
- <b>MEAN=(15 16)</b> in the <b>Combined</b> field finds
- highly expressed genes (15 to 16 log2 units)
+ <a href="https://github.com/genenetwork/genenetwork3">GN3 Source Code</a>
</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>
+ <a href="https://github.com/genenetwork/genenetwork">GN1 Source Code</a>
</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.
+ <a href="https://github.com/genenetwork/sysmaintenance">System Maintenance Code</a>
</li>
+ </ul>
+ </ul>
+ <ul>
+ <li>GeneNetwork v2</li>
+ <ul>
<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.
+ <a href="https://genenetwork.org/">Main website</a> at UTHSC
</li>
+ </ul>
+ </ul>
+ <ul>
+ <li>GeneNetwork v1</li>
+ <ul>
<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.
+ <a href="http://gn1.genenetwork.org/">Main website</a> at UTHSC
</li>
+ </ul>
+ </ul>
+ <ul>
+ <li>Affiliates</li>
+ <ul>
<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).
+ <b><a href="http://gn1.genenetwork.org">GeneNetwork 1</a> at UTHSC</b>
</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.
+ <a href="https://systems-genetics.org/">Systems Genetics</a> at EPFL
</li>
<li>
- <b>RIF=mitochondrial</b> searches RNA databases for <a href="https://en.wikipedia.org/wiki/GeneRIF">GeneRIF</a> links.
+ <a href="http://bnw.genenetwork.org/">Bayesian Network Web Server</a> at UTHSC
</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>.
+ <a href="https://www.geneweaver.org/">GeneWeaver</a>
</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>.
+ <a href="https://phenogen.org/">PhenoGen</a> at University of Colorado
</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("gn_docs_blueprint.glossary") }}#E">trans eQTLs</a> on Chr 2 between 100 and 105 Mb with LRS
- scores between 9 and 999.
+ <a href="http://www.webgestalt.org/">WebGestalt</a> at Baylor
</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>
+ <ul>
+ <li>GeneNetwork hosted portals</li>
<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>
+ <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>
- </section>
- </div>
+ </ul>
+ </section>
</div>
</div>
+</div>
+
{% endblock %}
+<script language="javascript"
+ type="text/javascript"
+ src="{{ url_for('js', filename='uikit/js/uikit-icons.min.js') }}"></script>
+<script src="{{ url_for('js', filename='jquery/jquery.min.js') }}"
+ type="text/javascript"></script>
+<script src="{{ url_for('js', filename='bootstrap/js/bootstrap.min.js') }}"
+ type="text/javascript"></script>
{% block js %}
- <script src="/static/new/javascript/dataset_select_menu_orig.js"></script>
- <script src="{{ url_for('js', filename='jquery/jquery.min.js') }}"
- type="text/javascript"></script>
- <script src="{{ url_for('js', filename='bootstrap/js/bootstrap.min.js') }}"
- type="text/javascript"></script>
- <script type="text/javascript">
-$(document).on('submit', '#searchform', function(event){
+<!--Note this is locally built emfed package see source file:https://github.com/sampsyo/emfed -->
+<script type="module" src="static/new/javascript/emfed.bundle.js"></script>
+<script src="/static/new/javascript/dataset_select_menu_orig.js"></script>
+<script>
+
+ $(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);
- }
- });
+ 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();
+ 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>
+ });
+ 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>
+ if( event.target.value.trim() != "" ) {
+ saveBeforeSubmit(event.target.value.trim())
+ $("#searchform").prop("action", "/search")
+ $("#searchform")[0].submit();
+ }
+
+ }
+ }
+
+
+</script>
{% endblock %}
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-25 14:04:27 +0000