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authorZachary Sloan2012-10-12 19:10:43 -0500
committerZachary Sloan2012-10-12 19:10:43 -0500
commit3edf991dbb54472f5b594c79f54b7c8e86c84829 (patch)
tree57e1edc9733f3532b94ddaa97d360fb6668a46a3
parentd78728ce6c5290be5905066e674679d5997f2dcc (diff)
downloadgenenetwork2-3edf991dbb54472f5b594c79f54b7c8e86c84829.tar.gz
Continued work on new_index_page
Diffstat
-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"-->
                     <!--type="text/javascript">-->
                     <!--</script>-->

 

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