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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"--> <!--type="text/javascript">--> <!--</script>--> |