aboutsummaryrefslogtreecommitdiff
path: root/wqflask/wqflask/templates/index_page_orig.html
diff options
context:
space:
mode:
Diffstat (limited to 'wqflask/wqflask/templates/index_page_orig.html')
-rwxr-xr-xwqflask/wqflask/templates/index_page_orig.html285
1 files changed, 285 insertions, 0 deletions
diff --git a/wqflask/wqflask/templates/index_page_orig.html b/wqflask/wqflask/templates/index_page_orig.html
new file mode 100755
index 00000000..9fba0e31
--- /dev/null
+++ b/wqflask/wqflask/templates/index_page_orig.html
@@ -0,0 +1,285 @@
+{% extends "base.html" %}
+{% block title %}GeneNetwork{% 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">
+
+ {{ flash_me() }}
+
+ <div class="row" style="width: 1400px !important;">
+
+ <div class="col-xs-5">
+ <section id="search">
+ <div class="page-header">
+ <h1>Select and search</h1>
+ </div>
+ <form method="get" action="/search" 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>
+ </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>
+ <i class="icon-question-sign"></i>
+ </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>
+ </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>
+ <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>
+ </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">
+ <div class="col-xs-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">
+ <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>
+ </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;">
+ <input id="btsearch" type="submit" class="btn btn-primary form-control" value="Search">
+ </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 or Combined search fields:</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="http://www.genenetwork.org/glossary.html#L" target="_blank">LRS</a>
+ linkage between 23 and 46.</li>
+
+ <li><b>RIF=mitochondrial</b> searches RNA databases for <a href="https://en.wikipedia.org/wiki/GeneRIF" target="_blank">
+ GeneRIF</a> links.</li>
+
+ <li><b>WIKI=nicotine</b> searches <a href="http://www.genenetwork.org/webqtl/main.py?FormID=geneWiki" target="_blank">
+ 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://www.godatabase.org/cgi-bin/amigo/go.cgi" target="_blank">
+ 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="http://www.genenetwork.org/glossary.html#E" target="_blank">
+ cis eQTL</a> on Chr 4 from 122 and 155 Mb with LRS scores
+ between 9 and 999.</li>
+
+ <li><b>RIF=diabetes LRS=(9 999 Chr2 100 105) transLRS=(9 999 10)</b>
+ finds diabetes-associated transcripts with peak <a href="http://www.genenetwork.org/glossary.html#E" target="_blank">
+ trans eQTLs</a> on Chr 2 between 100 and 105 Mb with LRS
+ scores between 9 and 999.</li>
+ </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/" target="_blank" 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" target="_blank">conditions</a>
+ and <a href="/statusandContact.html" target="_blank">contact
+ </a> pages have information on the status of data sets
+ and advice on their use and citation.</p>
+
+ </section>
+ -->
+
+ <section id="websites">
+ <div class="page-header">
+ <h1>Affiliates and mirrors</h1>
+ </div>
+ <h3>Websites affiliated with GeneNetwork</h3>
+ <ul>
+ <li><a href="http://ucscbrowser.genenetwork.org/" target="_blank">Genome
+ browser</a> at UTHSC</li>
+
+ <li><a href="http://galaxy.genenetwork.org/" target="_blank">Galaxy</a> at
+ UTHSC</li>
+
+ <li>GeneNetwork 1 at <a href="http://ec2.genenetwork.org/" target="_blank">Amazon
+ Cloud (EC2)</a></li>
+
+ <li>GeneNetwork 1 Source Code at <a href="http://sourceforge.net/projects/genenetwork/" target="_blank">SourceForge</a></li>
+
+ <li>GeneNetwork 2 Source Code at <a href="https://github.com/genenetwork/genenetwork2" target="_blank">GitHub</a></li>
+ </ul>
+ <h3>GN1 Mirror and development sites</h3>
+
+ <ul>
+ <li><a href="http://www.genenetwork.org/" target="_blank">Main GN1 site at UTHSC</a> (main site)</li>
+ <li><a href="http://genenetwork.helmholtz-hzi.de/" target="_blank">Germany at the HZI</a></li>
+ <li><a href="http://genenetwork.memphis.edu/" target="_blank">Memphis at the U of M</a></li>
+ </ul>
+ </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, 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" target="_blank">
+ 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) {
+ // 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>
+
+{% endblock %}
generated by cgit v1.2.3 (git 2.44.0) at 2024-12-13 14:51:03 +0000