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-rw-r--r--wqflask/wqflask/templates/new_index_page.html174
1 files changed, 156 insertions, 18 deletions
diff --git a/wqflask/wqflask/templates/new_index_page.html b/wqflask/wqflask/templates/new_index_page.html
index b415daee..ab9e188b 100644
--- a/wqflask/wqflask/templates/new_index_page.html
+++ b/wqflask/wqflask/templates/new_index_page.html
@@ -13,7 +13,8 @@
<body>
<div class="hero-unit">
<h1>Gene Network</h1>
- <p class="lead">Open Source Bioinformatics Website For Systems Genetics</p>
+ <p class="lead">Open source bioinformatics for systems genetics<br />
+ Brought to you by the University of Tennessee</p>
</div>
@@ -22,18 +23,17 @@
<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>
+ <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="#how_to_section"><i class="icon-chevron-right"></i> How to</a></li>
+ <li><a href="#websites_section"><i class="icon-chevron-right"></i> Affiliates and mirrors</a></li>
</ul>
</div>
<div class="span9">
<section id="search_section">
<div class="page-header">
- <h1>Select and Search</h1>
+ <h1>Select and search</h1>
</div>
<form method="get" action="/search" name="SEARCHFORM">
<fieldset>
@@ -81,11 +81,11 @@
<!-- GET ANY HELP -->
</p>Enter terms, genes, ID numbers in the
- <b>Search</b> field.<br>
+ <b>Search</b> field<br>
Use <b>*</b> or <b>?</b> wildcards (Cyp*a?,
- synap*).<br>
+ synap*)<br>
Use <b>quotes</b> for terms such as <i>"tyrosine
- kinase"</i>.</p>
+ kinase"</i></p>
<!-- SEARCH, MAKE DEFAULT, ADVANCED SEARCH -->
@@ -109,7 +109,7 @@
<section id="getting_started_section">
<div class="page-header">
- <h1>Getting Started</h1>
+ <h1>Getting started</h1>
</div>
<ol style="font-size:12px;font-family:verdana;color:black">
@@ -138,19 +138,21 @@
<li>Optional: Use the <b>Make Default</b> button to save your preferences</li>
</ol>
- <h3>For more information, read our <a href="http://www.genenetwork.org/index4.html" target="_blank">User's Guide</a>.</h3>
+ <h4>For more information, read our
+ <a href="http://www.genenetwork.org/index4.html" target="_blank">
+ user guide</a>.</h4>
</section>
<section id="advanced_section">
<div class="page-header">
- <h1>Advanced Commands</h1>
+ <h1>Advanced commands</h1>
</div>
- <p>You can also do more advanced
- searches. Copy these examples
- into the search field:</p>
+ <p>GeneNetwork supports a variety of advanced searches.</p>
+
+ <p>To try them out copy these examples into the search field:</p>
<ul>
<li><b>POSITION=(chr1 25 30)</b> finds genes, markers, or transcripts on
@@ -172,8 +174,7 @@
<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>
+ 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=
@@ -189,9 +190,146 @@
</ul>
</section>
+ <section id="how_to_section">
+ <div class="page-header">
+ <h1>How to use GeneNetwork</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_section">
+ <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 at <a href="http://ec2.genenetwork.org/" target="_blank">Amazon
+ Cloud (EC2)</a></li>
+
+ <li>GeneNetwork Source Code at <a href=
+ "http://sourceforge.net/projects/genenetwork/" target="_blank">SourceForge</a></li>
+
+ <li>GeneNetwork Source Code at <a href=
+ "https://github.com/genenetwork/genenetwork" target="_blank">GitHub</a></li>
+ </ul>
+ <h3>Mirror and development sites</h3>
+ <ul>
+ <li><a href="http://www.genenetwork.org/" target="_blank">
+ Main GN site</a> at UTHSC</li>
+
+ <li><a href="http://www.genenetwork.waimr.uwa.edu.au/" target="_blank">
+ Australia</a> at the UWA</li>
+
+ <li><a href="http://gn.genetics.ucla.edu/" target="_blank">
+ California</a> at UCLA</li>
+
+ <li><a href="http://genenetwork.helmholtz-hzi.de/" target="_blank">
+ Germany</a> at the HZI</li>
+
+ <li><a href="https://genenetwork.hubrecht.eu/" target="_blank">
+ Netherlands</a> at the Hubrecht
+ (development)</li>
+
+ <li><a href="http://genenetwork.memphis.edu/" target="_blank">
+ Memphis</a> at the U of M</li>
+
+ <li><a href="http://webqtl.bic.nus.edu.sg/" target="_blank">
+ Singapore</a> at the NUS</li>
+
+ <li><a href="http://genenetwork.epfl.ch/" target="_blank">
+ Switzerland</a> at the EPFL</li>
+ </ul>
+ <h3>History and archive</h3>
+
+ <p>The
+ <a href="http://artemis.uthsc.edu" target="_blank">
+ time machine</a>
+ has earlier versions that correspond to specific publication dates.
+ </p>
+
+ <h3>The next generation</h3>
+ <p>Try the <a href=
+ "http://alexandria.uthsc.edu/" target="_blank">
+ development</a> site to explore exerimental data and features.</p>
+ </section>
</div>
</div>
</div>
+
+ <!-- Footer
+ ================================================== -->
+ <footer class="footer">
+ <div class="container">
+ <p class="pull-right"><a href="#">Back to top</a></p>
+
+ <p>Launched in 1994 as <A HREF="http://www.ncbi.nlm.nih.gov/pubmed?term=8043953">The Portable Dictionary of the Mouse Genome</A> and 2001 as WebQTL.</p>
+ <p>Operated by
+ <A HREF="mailto:rwilliams@uthsc.edu">Rob Williams</A>,
+ <A HREF="mailto:lyan6@uthsc.edu">Lei Yan</A>,
+ <A HREF="mailto:zachary.a.sloan@gmail.com">Zachary Sloan</A>, and
+ <A HREF="mailto:acenteno@uthsc.edu" target="_blank">Arthur Centeno</A>.
+ </p>
+ <p>
+ Designed and coded by Sam Ockman, Xiaodong Zhou, Christian Fernandez,
+ Ning Liu, Rudi Alberts, Elissa Chesler, Jintao Wang, Kenneth Manly, Robert W. Williams,
+ and <A HREF="/credit.html">colleagues</A>.
+ </p>
+
+ <p>Built with <a href="http://twitter.github.com/bootstrap/">bootstrap</a>,
+ <a href="http://coffeescript.org/">coffeescript</a>,
+ <a href="http://flask.pocoo.org/">flask</a>,
+ <a href="http://en.wikipedia.org/wiki/Linux">linux</a>,
+ <a href="http://www.python.org/">python</a> and good intentions.
+ </p>
+ <p>Special thanks to CYP1A2 and AHR.</p>
+ <br />
+ <p>GeneNetwork support from:
+ <UL>
+ <LI><a target="_blank" href="http://citg.uthsc.edu">The UT Center for Integrative and Translational Genomics</A>
+ <LI><a target="_blank" href="http://www.iniastress.org">NIAAA</A> Integrative Neuroscience Initiative on Alcoholism (U01 AA016662, U01 AA013499, U24 AA013513, U01 AA014425)
+ <LI><a target="_blank" href="http://www.drugabuse.gov/about/organization/Genetics/geneexpression/index.html">NIDA</A>, <a class="smallsize" target="_blank" href="http://www.nimh.nih.gov/">NIMH</A>, and <a class="smallsize" target="_blank" href="http://www.niaaa.nih.gov/">NIAAA</A> (P20-DA 21131)
+ <LI>NCI <a target="_blank" href="http://emice.nci.nih.gov/">MMHCC</A> (U01CA105417) and
+ <a target="_blank" href="http://www.ncrr.nih.gov/">NCRR</A>
+ <a target="_blank" href="http://www.nbirn.net/TestBeds/Mouse/index.htm">BIRN</A>
+ (U24 RR021760)
+ </li>
+ </UL>
+ </p>
+
+ <ul class="footer-links">
+ <li><a href="http://atlas.uthsc.edu/mailman/listinfo/genenetwork" target="_blank">Join the mailing list</a></li>
+ <!--<li><a href="#">Friend us on facebook</a></li>-->
+ <!--<li><a href="#">Follow us on twitter</a></li>-->
+ </ul>
+ </div>
+ </footer>
<!--<script src="/javascript/selectDatasetMenu.js"-->
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generated by cgit v1.2.3 (git 2.44.0) at 2024-11-24 02:58:50 +0000