db93d1ac9ffd179e8e70e2c98999c98fbb9efd5d markd Wed Apr 17 21:12:30 2024 -0700 added missing or outdated ENCODE files from the rr diff --git src/hg/htdocs/ENCODE/index.html src/hg/htdocs/ENCODE/index.html old mode 100644 new mode 100755 index 3f98673..635bce4 --- src/hg/htdocs/ENCODE/index.html +++ src/hg/htdocs/ENCODE/index.html @@ -1,190 +1,190 @@ <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN" "http://www.w3.org/TR/html4/strict.dtd"> <html> <head> <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"> <title>ENCODE at UCSC</title> <link rel="stylesheet" href="/style/HGStyle.css" type="text/css"> <link rel="stylesheet" href="/style/encodeProject.css" type="text/css"> <style> /* using tables for layout, sorry */ table { border-style: none /* DEBUG */ /* border: 2px solid red; */ } td { border-style: none; vertical-align: top; } /* override visited img links in HGStyle */ .screenshot { display: block; margin: auto !important; margin-top: 15px !important; margin-bottom: 15px !important; border: 1px solid gray !important; width: 300px; height: 200px; } /* left menu */ .leftBlueBar { background-color: #00457c; padding: 10px; } .leftBarSection { color: #f1b521; background-color: #00457c; font-style: italic; font-weight: bold; font-size: 75%; padding-bottom: 6px; } /* override from HGStyle */ .leftbar { background-color: #00457c; } </style> </head> <body> <div class="encodeHeader"> <a href="/ENCODE/index.html"><img src="/images/gbLogoOnly.png" style="height:80%" alt="ENCODE Project at UCSC" title="ENCODE Project at UCSC"></a> <span class="txt">Encyclopedia of DNA Elements at UCSC</span> <span class="encodeHeaderDates">2003 - 2012</span> </div> <div> <table> <tr> <!-- left menu bar --> <td width="12%" class="leftBlueBar"> <div class="leftBarSection">Human Data at UCSC</div> <a class="leftbar" href="downloads.html">Downloads</a> <hr><a class="leftbar" href="/ENCODE/dataMatrix/encodeDataMatrixHuman.html">Experiment Matrix</a> <hr><a class="leftbar" href="search.html">Search</a> <hr><a class="leftbar" href="/cgi-bin/hgTracks?db=hg19">Genome Browser (hg19)</a> <hr><a class="leftbar" href="/ENCODE/dataSummary.html" title="formerly Data Summary">Experiment List</a> <hr><a class="leftbar" href="cellTypes.html">Cell Types</a> <hr> <div class="leftBarSection">Mouse Data at UCSC</div> <a class="leftbar" href="downloadsMouse.html">Downloads</a> <hr><a class="leftbar" href="/ENCODE/dataMatrix/encodeDataMatrixMouse.html">Experiment Matrix</a> <hr><a class="leftbar" href="search.html">Search</a> <hr><a class="leftbar" href="/cgi-bin/hgTracks?db=mm9">Genome Browser (mm9)</a> <hr><a class="leftbar" href="/ENCODE/dataSummaryMouse.html"title="formerly Data Summary">Experiment List</a> <hr><a class="leftbar" href="cellTypesMouse.html">Cell Types</a> <hr> <div class="leftBarSection">Metadata Terms</div> <a class="leftbar" href="otherTerms.html">Registered Variables</a> <hr><a class="leftbar" href="antibodies.html">Antibodies</a> <hr> <div class="leftBarSection">Other Resources</div> <a class="leftbar" href="newsarch.html">News Archive</a> <hr><a class="leftbar" href="contributors.html">First Production (2007-2012)</a> <hr><a class="leftbar" href="pilot.html">Pilot (2003-2007)</a> <hr><a class="leftbar" href="contacts.html">Contacts</a> </td> <!-- main content --> <td> <table> <tr> <td colspan="2"> <div style="margin-top: 0; margin-left: 10px;" class="wrapper"> <div class="bar"><h4 class="title">About</h4></div> <div class="content"> <p>The <a href="http://www.genome.gov/10005107" target="_blank">Encyclopedia of DNA Elements</a> (ENCODE) Consortium is an international collaboration of research groups funded by the National Human Genome Research Institute (<a href="http://www.genome.gov/" target="_blank">NHGRI</a>). The goal of ENCODE is to build a comprehensive parts list of functional elements in the human genome, including elements that act at the protein and RNA levels, and regulatory elements that control cells and circumstances in which a gene is active.</p> <p> <b><em>ENCODE results from 2007 and later are available from the ENCODE Project Portal</em></b>, <a href="https://encodeproject.org" target=_blank>encodeproject.org</a>. This covers data generated during the two production phases 2007-2012 and 2013-present. The ENCODE Project Portal also hosts additional ENCODE access tools, and ENCODE project pages including up-to-date information about data releases, publications, and upcoming tutorials.</b> </p> -<!--#if expr='"$SERVER_NAME" = /hgwdev.*.soe.ucsc.edu/ || "$SERVER_NAME" = "genome-test.soe.ucsc.edu"'--> +<!--#if expr='"$SERVER_NAME" = /hgwdev.*.cse.ucsc.edu/ || "$SERVER_NAME" = "genome-test.cse.ucsc.edu"'--> <p> <b>WARNING: This is a test site.</b> Data and tools here are under construction, have not been quality reviewed, and are subject to change at any time. For high-quality reviewed annotations on the UCSC production server, visit <a HREF="http://genome.ucsc.edu/ENCODE">http://genome.ucsc.edu/ENCODE</a>.</p> <!--#endif --> <p> UCSC coordinated data for the ENCODE Consortium from its inception in 2003 (Pilot phase) to the end of the first 5 year phase of whole-genome data production in 2012. All data produced by ENCODE investigators and the results of ENCODE analysis projects from this period are hosted in the UCSC Genome browser and database. Explore ENCODE data using the image links below or via the left menu bar. <b><em>All ENCODE data at UCSC are freely available for download and analysis</em></b>.</p> </div><!--end content--> </div><!--end wrapper--> </td> </tr> <!-- screenshot launchers 2x2 matrix --> <tr> <td> <div style="margin-left:10px;" class="wrapper"> <!--<div style="height:100%; margin-top:0; margin-left:10px; margin-right:10px" class="wrapper"> --> <div class="bar"><h4 class="title">Explore ENCODE data (2003 - 2012) at UCSC</h4></div> <div class="content"> <a href="dataMatrix/encodeDataMatrixHuman.html"><img class="screenshot" src="../images/encode/dataMatrix.png"></a> </div> </div> <!-- end wrapper --> </td> <td> <div style="margin-left:10px;" class="wrapper"> <!-- <div style="height: 100%; margin-top:0;" class="wrapper"> --> <div class="bar"><h4 class="title">View ENCODE data (2003 - 2012) in the UCSC Genome Browser</h4></div> <a href="../cgi-bin/hgTracks?hgS_doLoadUrl=submit&hgS_loadUrlName=http://genome.ucsc.edu/goldenPath/help/examples/sessions/encodeDemonstration"><img class="screenshot" src="../images/encode/browser.png"></a> </div> </td> </tr> <tr> <td> <div style="margin-left:10px;" class="wrapper"> <!-- <div style="height: 100%; margin-top:10px; margin-left:10px; margin-right:10px" class="wrapper"> --> <div class="bar"><h4 class="title">Search for data (current) at the ENCODE Portal</h4></div> <a href="https://www.encodedcc.org/search/?type=experiment"><img class="screenshot" style="display: block; margin: auto;" src="../images/encode/stanfordSearch.png"></a> </div> </td> <td> <div style="margin-left:10px;" class="wrapper"> <!-- <div style="height: 100%; margin-top:10px" class="wrapper"> --> <div class="bar"><h4 class="title">Search for ENCODE tracks (2003 - 2012) in the UCSC Browser</h4></div> <a href="../cgi-bin/hgTracks?hgt_=1408334670&db=hg19&tsCurTab=advancedTab&hgt_tsDelRow=&hgt_tsAddRow=&hgt_tsPage=&tsSimple=&tsName=&tsDescr=&tsGroup=Any&tsType=Any&hgt_mdbVar1=cell&hgt_mdbVal1=HeLa-S3&hgt_mdbVar2=dataType&hgt_mdbVal2=RnaSeq&hgt_tSearch=search"><img class="screenshot" src="../images/encode/search.png"></a> </div> </td> </tr> <!-- screenshot launchers --> </table> </td> </tr> </table> </body> </html>