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-rw-r--r--wqflask/wqflask/templates/new_index_page.html226
1 files changed, 167 insertions, 59 deletions
diff --git a/wqflask/wqflask/templates/new_index_page.html b/wqflask/wqflask/templates/new_index_page.html
index 85c63b3f..b415daee 100644
--- a/wqflask/wqflask/templates/new_index_page.html
+++ b/wqflask/wqflask/templates/new_index_page.html
@@ -1,91 +1,199 @@
+<!DOCTYPE html>
+<html lang="en">
<head>
<title>GeneNetwork</title>
<link REL="stylesheet" TYPE="text/css" href="/static/packages/bootstrap/css/bootstrap.min.css" />
+ <link REL="stylesheet" TYPE="text/css" href="/static/packages/bootstrap/css/bootstrap-responsive.min.css" />
+ <link REL="stylesheet" TYPE="text/css" href="/static/packages/bootstrap/css/docs.css" />
<script src="https://ajax.googleapis.com/ajax/libs/jquery/1.8.2/jquery.min.js"></script>
<script src="/static/packages/bootstrap/js/bootstrap.min.js"></script>
</head>
<body>
- <div class="container">
+ <div class="hero-unit">
+ <h1>Gene Network</h1>
+ <p class="lead">Open Source Bioinformatics Website For Systems Genetics</p>
+ </div>
- <div class="hero-unit">
- <h1>Gene Network</h1>
- </div>
- <div>
- <form method="get" action="/search" name="SEARCHFORM">
- <fieldset>
- <legend>Select and Search</legend>
- <label for="species">Species:</label>
- <select name="species" size="1" id="species" onchange="fillOptions('species');">
- </select>
-
- <div class="input-append">
- <label for="cross">Group: </label>
- <select name="cross" id="cross" onchange="fillOptions('cross');">
- </select>
- <i class="icon-question-sign"></i>
- <!--<input type="button" class="btn" value="Info" onclick=-->
- <!-- "javascript:crossinfo();" />-->
+
+ <div class="container">
+ <div class="row">
+ <div class="span3 bs-docs-sidebar">
+ <ul class="nav nav-list bs-docs-sidenav">
+ <li><a href="#search_section"><i class="icon-chevron-right"></i> Search</a></li>
+ <li><a href="#getting_started_section"><i class="icon-chevron-right"></i> Getting Started</a></li>
+ <li><a href="#advanced_section"><i class="icon-chevron-right"></i> Advanced Commands</a></li>
+ <li><a href="#html-template"><i class="icon-chevron-right"></i> How To Use</a></li>
+ <li><a href="#examples"><i class="icon-chevron-right"></i> History</a></li>
+ <li><a href="#what-next"><i class="icon-chevron-right"></i> Mirrors and Other Sites</a></li>
+ </ul>
+ </div>
+
+ <div class="span9">
+ <section id="search_section">
+ <div class="page-header">
+ <h1>Select and Search</h1>
</div>
+ <form method="get" action="/search" name="SEARCHFORM">
+ <fieldset>
+ <!--<legend>Select and Search</legend>-->
+ <label for="species">Species:</label>
+ <select name="species" size="1" id="species" onchange="fillOptions('species');">
+ </select>
+
+ <div class="input-append">
+ <label for="cross">Group: </label>
+ <select name="cross" id="cross" onchange="fillOptions('cross');">
+ </select>
+ <!--<i class="icon-question-sign"></i>-->
+ <input type="button" class="btn" value="Info" onclick=
+ "javascript:crossinfo();" />
+ </div>
+
+
+ <label for="type">Type:</label>
+ <select name="tissue" id="tissue" onchange=
+ "fillOptions('tissue');"></select>
+
+
+ <div class="input-append">
+ <label for="database">Database:</label>
+ <select name="database" id="database">
+ </select> <input type="button" class="btn" value="Info" name="info_database" />
+ </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 -->
- <label for="type">Type:</label>
- <select name="tissue" id="tissue" onchange=
- "fillOptions('tissue');"></select>
+ <label for="tfor">Search:</label>
+ <input class="search-query"
+ id="tfor" name="ORkeyword"
+ type="text" maxlength="500">
- <div class="input-append">
- <label for="database">Database:</label>
- <select name="database" id="database">
- </select> <input type="button" class="btn" value="Info" name="info_database" />
+ <!-- GET ANY HELP -->
+
+ </p>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>.</p>
+
+ <!-- SEARCH, MAKE DEFAULT, ADVANCED SEARCH -->
+
+
+ <input id="btsearch" type="submit"
+ class="btn btn-primary" value="Search">
+
+ <input type=
+ "button" class="btn" value="Make Default" onclick=
+ "setDefault(this.form);">
+
+ <input type="button" class=
+ "btn" value="Advanced Search" onclick=
+ "javascript:window.open('/index3.html', '_self');">
+
+ <input type="hidden" name="FormID" value="searchResult"> <input type=
+ "hidden" name="RISet" value="BXD">
+ </fieldset>
+ </form>
+ </section>
+
+ <section id="getting_started_section">
+ <div class="page-header">
+ <h1>Getting Started</h1>
</div>
- <!-- USER HELP -->
+ <ol style="font-size:12px;font-family:verdana;color:black">
+ <li>Select <b>Species</b> (or select All)</li>
+
+ <li>Select <b>Group</b> (a specific sample)</li>
- <!--<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>-->
+ <li>Select <b>Type</b> of data:
- <!-- GET ANY SEARCH -->
+ <ul>
+ <li>Phenotype (traits)</li>
- <label for="tfor">Search:</label>
+ <li>Genotype (markers)</li>
- <input class="search-query"
- id="tfor" name="ORkeyword"
- type="text" maxlength="500">
+ <li>Expression (mRNAs)</li>
+ </ul>
+ </li>
- <!-- GET ANY HELP -->
+ <li>Select a <b>Database</b></li>
- </p>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>.</p>
+ <li>Enter terms in the search field: words,
+ genes, ID numbers, probes, advanced search commands</li>
- <!-- SEARCH, MAKE DEFAULT, ADVANCED SEARCH -->
+ <li>Click on the <b>Search</b> button</li>
+ <li>Optional: Use the <b>Make Default</b> button to save your preferences</li>
+ </ol>
- <input id="btsearch" type="submit"
- class="btn btn-primary" value="Search">
+ <h3>For more information, read our <a href="http://www.genenetwork.org/index4.html" target="_blank">User's Guide</a>.</h3>
- <input type=
- "button" class="btn" value="Make Default" onclick=
- "setDefault(this.form);">
+ </section>
- <input type="button" class=
- "btn" value="Advanced Search" onclick=
- "javascript:window.open('/index3.html', '_self');">
- <input type="hidden" name="FormID" value="searchResult"> <input type=
- "hidden" name="RISet" value="BXD">
- </fieldset>
- </form>
+ <section id="advanced_section">
+ <div class="page-header">
+ <h1>Advanced Commands</h1>
+ </div>
+
+ <p>You can also do more advanced
+ searches. Copy these examples
+ into the search field:</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=
+ "http://www.ncbi.nlm.nih.gov/projects/GeneRIF/GeneRIFhelp.html" 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>
</div>
- <!--<script src="/javascript/selectDatasetMenu.js"-->
- <!--type="text/javascript">-->
- <!--</script>-->
+ <!--<script src="/javascript/selectDatasetMenu.js"-->
+ <!--type="text/javascript">-->
+ <!--</script>-->
</body>
+</html>
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-27 09:03:22 +0000