about summary refs log tree commit diff
path: root/web/index.html.20110408
diff options
context:
space:
mode:
authorzsloan2015-03-27 20:28:51 +0000
committerzsloan2015-03-27 20:28:51 +0000
commitd0911a04958a04042da02a334ccc528dae79cc17 (patch)
tree3c48e2e937c1dbeaf00a5697c87ed251afa5c8f1 /web/index.html.20110408
parenta840ad18e1fe3db98a359a159e9b9b72367a2839 (diff)
downloadgenenetwork2-d0911a04958a04042da02a334ccc528dae79cc17.tar.gz
Removed everything from 'web' directory except genofiles and renamed the directory to 'genotype_files'
Diffstat (limited to 'web/index.html.20110408')
-rwxr-xr-xweb/index.html.20110408367
1 files changed, 0 insertions, 367 deletions
diff --git a/web/index.html.20110408 b/web/index.html.20110408
deleted file mode 100755
index bcae525b..00000000
--- a/web/index.html.20110408
+++ /dev/null
@@ -1,367 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
-<HTML><HEAD>
-<TITLE>GeneNetwork Search</TITLE>
-<META http-equiv=Content-Type CONTENT ="text/html; charset=iso-8859-1">
-<META NAME="keywords" CONTENT="genetics, bioinformatics, genome, phenome, gene expression, complex trait analysis, gene mapping, SNP, quantitative trait locus QTL, expression eQTL, WebQTL, Traitnet, Traitnetwork, personalized medicine">
-<META NAME="description" CONTENT ="GeneNetwork is a free scientific web resource used to study relationships between differences in genes, environmental factors, phenotypes, and disease risk." >
-<META NAME="author" CONTENT ="GeneNetwork developers" >
-<META NAME="title" CONTENT ="GeneNetwork Search" >
-<META NAME="pages" CONTENT ="">
-<META NAME="collection" CONTENT ="" >
-<META NAME="geo.placename" CONTENT ="Memphis, TN" >
-<META NAME="geo.region" CONTENT="US-TN">
-<LINK REL="apple-touch-icon" href="/images/ipad_icon3.png" />
-<LINK REL="stylesheet" TYPE="text/css" HREF='css/general.css'>
-<LINK REL="stylesheet" TYPE="text/css" HREF='css/menu.css'>
-<SCRIPT SRC="javascript/webqtl.js"></SCRIPT>
-<SCRIPT SRC="javascript/dhtml.js"></SCRIPT>
-<SCRIPT SRC="javascript/searchtip.js"></SCRIPT>
-</HEAD>
-
-
-<BODY  bottommargin="2" leftmargin="1" rightmargin="1" topmargin="4" text=#000000 bgColor=#ffffff onload="javascript:initialDatasetSelection();">
-
-<TABLE cellSpacing=5 cellPadding=5 width="100%" border=0>
-	<TBODY>
-		<!--  TOP BANNER   -->
-		<TR>
-			<script language="JavaScript" src="/javascript/header.js"></script> 
-		</TR>
-<!--  SINGLE LARGE TABLE CELL FOR THE "SELECT RESOURCE AND SEARCH" PANEL -->
-
-		<TR>
-			<TD bgColor=#eeeeee class="solidBorder">
-				<Table width= "100%" cellPadding=12 cellSpacing=5>
-					<TR>		
-						<TD vAlign=top width="40%" align="left" height=10 bgColor=#eeeeee>
-							<p style="font-size:18px;font-family:verdana;color:black"><B> Select and Search</B>
-							<Form METHOD="POST" ACTION="webqtl/main.py" ENCTYPE="multipart/form-data" NAME="SEARCHFORM">
-								<TABLE width="100%">
-					
-					<!--  SPECIES  SELECTION -->				
-									<TR>
-										<TD align=right height="35" style="font-size:14px;font-family:verdana;color:black" width="16%">
-											<B>Species:</B>
-										</TD>
-
-										<TD width="3%">
-										</TD>
-
-										<TD NOWRAP width="85%" align="left">
-											<DIV Id="menu0">
-												<Select NAME="species" size=1 id="species" onchange="fillOptions('species');">
-												</Select>
-											</DIV>
-										</TD>
-									</TR>
-				
-					<!--  GROUP  SELECTION -->	
-			
-									<TR>
-										<TD align="right" height="35" style="font-size:14px;font-family:verdana;color:black">
-											<B>Group:</B>
-										</TD>
-
-										<TD width="3%">
-										</TD>
-
-										<TD NOWRAP width="85%" align="left">
-											<DIV Id="menu1">
-												<Select NAME="cross" size=1 id="cross" onchange="fillOptions('cross');">
-												</Select>
-											<input type="button" class="button" value=" Info " onCLick="javascript:crossinfo();">
-											</DIV>
-										</TD>
-									</TR>
-
-
-					<!--  TYPE  SELECTION -->		
-		
-									<TR>
-										<TD align=right height=35 style="font-size:14px;font-family:verdana;color:black">
-											<B>Type:</B>
-										</TD>
-
-										<TD width="3%">
-										</TD>
-										<TD NOWRAP width="85%" align="left">
-											<DIV Id="menu2">
-												<Select NAME="tissue" size=1 id="tissue" onchange="fillOptions('tissue');">
-												</Select>
-											</DIV>
-										</TD>
-									</TR>
-		
-
-					<!--  DATABASE  SELECTION -->		
-									<TR>
-										<TD align=right height=35 style="font-size:14px;font-family:verdana;color:black">
-											<B>Database:</B>
-										</TD>
-
-										<TD width="3%">
-										</TD>
-
-										<TD NOWRAP width="85%" align="left">
-											<DIV Id="menu3">
-												<Select NAME="database" size=1 id="database"> 
-												</Select>
-												<input type="button" class="button" value=" Info " onCLick="javascript:databaseinfo();">
-											</DIV>
-										</TD>
-									</TR>
-
-					<!--  USER HELP   -->				
-									<TR>
-										<TD align=right height=20 width="10%">
-										</TD>
-										<TD width="3%">
-										</TD>
-
-										<TD align="left" width="85%">
-											<P class="fs12">&nbsp;&nbsp;&nbsp;&nbsp;Databases marked with <B>**</B> suffix are not public yet. 
-											<BR>&nbsp;&nbsp;&nbsp;&nbsp;Access requires <A HREF="http://www.genenetwork.org/account.html" target="_blank" class="fs14"><small>user login</small></A>.</P>
-										</TD>
-									</TR>
-
-
-<!--  GET ANY  SEARCH -->			
-									<TR>
-										<TD align=right height=35 NOWRAP="on" style="font-size:14px;font-family:verdana;color:black" width="10%">
-											<B>Get Any:</B>
-										</TD>
-
-										<TD width="3%">
-										</TD>
-
-										<TD NOWRAP width="85%" align="left">
-											<input id="tfor" name="ORkeyword" style="width:420px; background-color:white; font-family:verdana; font-size:14px" type="text" maxlength="500">
-										</TD>
-									</TR>
-
-
-
-<!--  GET ANY HELP   -->
-									<TR>
-										<TD align=right height=20 width="10%">
-										</TD>
-										<TD width="3%">
-										</TD>
-										<TD width="85%" align="left">
-											<P class="fs12">&nbsp;&nbsp;&nbsp;&nbsp;Enter terms, genes, ID numbers in the <B>Get Any</B> field.  
-											<BR>&nbsp;&nbsp;&nbsp;&nbsp;Use <B>*</B> or <B>?</B> wildcards (Cyp*a?, synap*).
-											<BR>&nbsp;&nbsp;&nbsp;&nbsp;Use <B>Combined</B> for terms such as <I>tyrosine kinase</I>.</P>
-										</TD>
-									</TR>
-
-
-
-<!--  COMBINED SEARCH  -->
-
-									<TR>
-										<TD align=right height=35 NOWRAP="on" STYLE="font-size:14px;font-family:verdana;color:black" width="10%">
-											<B>Combined:</B>
-										</TD>
-										<TD width="3%">
-										</TD>
-
-										<TD NOWRAP width="85%" align="left">
-											<input id="tfand" NAME="ANDkeyword"  STYLE="width:420px; background-color:white; font-family:verdana; font-size:14px" type="text" maxlength="500">
-											<input name="matchwhole" type="hidden" value="ON"> 
-										</TD>
-									</TR>
-
-
-
-<!--  SEARCH, MAKE DEFAULT, ADVANCED SEARCH -->
-
-									<TR ALIGN="center">
-										<TD width="3%">
-										</TD>
-										<TD width="3%">
-										</TD>										
-										<TD ALIGN="left" HEIGHT="40" COLSPAN=3>
-											<INPUT id="btsearch" TYPE="Submit" CLASS="button" STYLE="font-size:12px" VALUE="  Search  ">&nbsp;&nbsp;&nbsp;&nbsp;
-										       <INPUT TYPE="button" CLASS="button" STYLE="font-size:12px" VALUE="  Make Default  " onClick = "setDefault(this.form);">&nbsp;&nbsp;&nbsp;&nbsp;	
-											<INPUT TYPE="button" CLASS="button" STYLE="font-size:12px" VALUE="  Advanced Search  " onClick="javascript:window.open('index3.html', '_self');">
-										</TD>
-									</TR>
-								</TABLE>
-								<INPUT TYPE="hidden" NAME="FormID" VALUE="searchResult">
-								<INPUT TYPE="hidden" NAME="RISet" VALUE="BXD">
-								<SCRIPT SRC="/javascript/selectDatasetMenu.js"></SCRIPT>
-							</FORM>
-							</CENTER>
-
-
-
-
-
-<!--  QUICK HELP  -->
-
-<P><LEFT>&nbsp;______________________________________________________
-
-<P STYLE="font-size:13px;font-family:verdana;color:black"><B>&nbsp;
-
-Quick HELP Examples and </B>
-<A HREF="http://www.genenetwork.org/index4.html" target="_blank"  class="fs14"><B>
- User's Guide</B></A></P>
-
-
-</CENTER style="font-size:12px;font-family:verdana;color:black">
-&nbsp;&nbsp;You can also use advanced commands. Copy these simple examples 
-<BR>&nbsp;&nbsp;into the <B>Get Any</B> or <B>Combined</B> search fields:
-<UL style="font-size:12px;font-family:verdana;color:black">
-
-<LI><B><I>POSITION=(chr1 25 30)</I></B> finds genes, markers, or transcripts on chromosome 1 between 25 and 30 Mb.
-
-<LI><B><I>MEAN=(15 16) LRS=(23 46)</I></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"  class="fs14"><small>LRS</small></A> linkage between 23 and 46.
-
-<LI><B><I>RIF=mitochondrial</I></B> searches RNA databases for <A HREF="http://www.ncbi.nlm.nih.gov/projects/GeneRIF/GeneRIFhelp.html" target="_blank"  class="fs14"><small>GeneRIF</small></A> links.
-
-<LI><B><I>WIKI=nicotine</I></B> searches <A HREF="http://www.genenetwork.org/webqtl/main.py?FormID=geneWiki" target="_blank"  class="fs14"><small>GeneWiki</small></A> for genes that you or other users have annotated with the word <I>nicotine</I>.
-
-<LI><B><I>GO:0045202</I></B> searches for synapse-associated genes listed in the <A HREF="http://www.godatabase.org/cgi-bin/amigo/go.cgi" target="_blank"  class="fs14"><small>Gene Ontology</small></A>.
-
-<LI><B><I>GO:0045202 LRS=(9 99 Chr4 122 155) cisLRS=(9 999 10)</I> </B><BR> in <B>Combined</B> finds synapse-associated genes with <A HREF="http://www.genenetwork.org/glossary.html#E" target="_blank"  class="fs14"><small>cis eQTL</small></A> on Chr 4 from 122 and 155 Mb with LRS scores between 9 and 999.
-
-<LI><B><I>RIF=diabetes LRS=(9 999 Chr2 100 105) transLRS=(9 999 10)</I> </B><BR> in <B>Combined</B> finds diabetes-associated transcripts with peak <A HREF="http://www.genenetwork.org/glossary.html#E" target="_blank"  class="fs14"><small>trans eQTLs</small></A> on Chr 2 between 100 and 105 Mb with LRS scores between 9 and 999.
-
-</UL> 
-</DIR>
-					</TD>				
-						<!-- END OF FIND SELECTOR PULL-DOWN PANEL (LEFT SIDE)  -->
-
-
-
-
-
-<!-- START OF TOP RIGHT PANEL  -->
-
-
-<TD vAlign=top width="40%" bgColor=#FFFFFF>
-							<p style="font-size:15px;font-family:verdana;color:black"><B>Top New Features</B> &nbsp;&nbsp; </p>
-							<BLOCKQUOTE>
-								<p style="font-size:12px;font-family:verdana;color:black"> <A HREF="http://ucscbrowser.genenetwork.org/" target="_blank" class="fs14"><small>RNA-seq and Whole-Genome Sequencing</small></A> data for mouse BXD strains and DBA/2J.</P>
-							</BLOCKQUOTE>		
-
-							<BLOCKQUOTE>
-								<p style="font-size:12px;font-family:verdana;color:black"> <A HREF="http://galaxy.genenetwork.org/" target="_blank" class="fs14"><small>CITG Open Galaxy Service</small></A>: 200-core cluster at UTHSC for next-gen sequence analysis.</P>
-							</BLOCKQUOTE>
-
-
-							<P>____________________________
-
-
-
-						
-							<p style="font-size:15px;font-family:verdana;color:black"><B>Getting Started</B> &nbsp;&nbsp; </p>
-							<OL style="font-size:12px;font-family:verdana;color:black">
-								<LI>Select <B>Species</B> (or select All) 
-								<LI>Select <B>Group</B> (a specific sample)
-								<LI>Select <B>Type</B> of data:  
-								<UL>
-									<LI>Phenotype (traits)
-									<LI>Genotype (markers)
-									<LI>Expression (mRNAs)
-								</UL>
-								<LI>Select a <B>Database</B> 
-								<LI>Enter search terms in the <B>Get Any</B> or <B>Combined</B> field: words, genes, ID numbers, probes, advanced search commands 
-								<LI>Click on the <B>Search</B> button
-								<LI>Optional: Use the <B>Make Default</B> button to save your preferences
-							
-							</OL>
-							<P>____________________________
-
-<p style="font-size:14px;font-family:verdana;color:black"><B>How to Use GeneNetwork</B>
-
-							<BLOCKQUOTE>
-								<p style="font-size:12px;font-family:verdana;color:black">Take a 20-40 minute GeneNetwork <A HREF="http://www.genenetwork.org/tutorial/WebQTLTour/" target="_blank" class="fs14"><small>Tour</small></A> that includes screen shots and typical steps in the analysis.</P>
-							</BLOCKQUOTE>							
-							<BLOCKQUOTE>
-								<p style="font-size:12px;font-family:verdana;color:black">For information about resources and methods, select the <img src="http://www.genenetwork.org/images/upload/Info.png" alt="INFO" border= 0 valign="middle"> buttons.</P>
-													
-														
-<p style="font-size:12px;font-family:verdana;color:black">Try the <A HREF="http://proust.uthsc.edu" target="_blank" class="fs14"><small>Test</small></A> site to explore data and features that are being implemented.</P>
-
-
-<p style="font-size:12px;font-family:verdana;color:black">Review the <A HREF="conditionsofUse.html" target="_blank" class="fs14"><small>Conditions</small></A> and <A HREF="statusandContact.html" target="_blank" class="fs14"><small>Contacts</small></A> pages for information on the status of data sets and advice on their use and citation.</P> 
-
-
-							</BLOCKQUOTE>
-							
-
-							<p style="font-size:14px;font-family:verdana;color:black"><B>Mirror and Development Sites</B></P>
-
-							<UL>
-								<LI><A HREF="http://www.genenetwork.org/" target="_blank" style="font-size:12px;font-family:verdana;color:blue">Main GN site at UTHSC</A> (main site)
-								<LI><A HREF="http://www.genenetwork.waimr.uwa.edu.au/" target="_blank" style="font-size:12px;font-family:verdana;color:blue">Australia at the UWA</A>
-								<LI><A HREF="http://www.sysgen.org.au/bottom.html" target="_blank" style="font-size:12px;font-family:verdana;color:blue">Genome-Centered Systems Genetics at UWA</A> (Morahan and colleagues)			
-								<LI><A HREF="http://gn.genetics.ucla.edu/" target="_blank" style="font-size:12px;font-family:verdana;color:blue">California at UCLA</A>
-								<LI><A HREF="http://genenetwork.helmholtz-hzi.de/" target="_blank" style="font-size:12px;font-family:verdana;color:blue">Germany at the HZI</A> (QTLminer site, Development)
-								<LI><A HREF="https://genenetwork.hubrecht.eu/" target="_blank" style="font-size:12px;font-family:verdana;color:blue">Netherlands at the Hubrecht</A> (Development)
-								<LI><A HREF="http://xzhou3.memphis.edu/" target="_blank" style="font-size:12px;font-family:verdana;color:blue">Memphis at the U of M</A>
-								<LI><A HREF="http://gnat.versailles.inra.fr/" target="_blank" style="font-size:12px;font-family:verdana;color:blue">France at INRA, Versailles</A> (Development)
-								<LI><A HREF="http://webqtl.bic.nus.edu.sg/" target="_blank" style="font-size:12px;font-family:verdana;color:blue">Singapore at the NUS</A>
- 								<LI><A HREF="http://genenetwork.epfl.ch/" target="_blank" style="font-size:12px;font-family:verdana;color:blue">Switzerland at the EPFL</A>
-								<LI><A HREF="http://biopubinfo.zju.edu.cn/" target="_blank" style="font-size:12px;font-family:verdana;color:blue">China at ZJU</A> (no update)</li>
-							</UL>
-
-
-							<p style="font-size:14px;font-family:verdana;color:black"><B>History and Archive</B>
-
-							<BLOCKQUOTE>
-								<p style="font-size:12px;font-family:verdana;color:black">GeneNetwork's <A HREF="http://artemis.uthsc.edu" target="_blank" class="fs14"><small>Time Machine</small></A> links to earlier versions that correspond to specific publication dates.</P>
-							</BLOCKQUOTE> 
-
-						<!--  EDITOR'S  BUTTON  -->
-							<A HREF="/webqtl/main.py?FormID=editHtml"><img src="/images/modify.gif" alt="modify this page" border= 0 align="right"></A></P>
-						</TD>
-
-<!-- End of "getting started" table row -->		
-					</TR>
-				</TABLE>
-			</TD>
-		</TR>
-		
-		<TR>
-			<TD align=center bgColor=#ddddff class="solidBorder">
-			<!--   START OF FOOTER   -->
-				<TABLE width="100%">
-					<script language='JavaScript' src='/javascript/footer.js'></script> 
-				</TABLE>
-		<!--End of footer-->
-		</TD>
-	</TR>
-</TABLE>
-<!-- /Footer -->
-<!-- menu script itself. you should not modify this file -->
-<script language="JavaScript" src="javascript/menu_new.js"></script>
-<!-- items structure. menu hierarchy and links are stored there -->
-<script language="JavaScript" src="javascript/menu_items.js"></script>
-<!-- files with geometry and styles structures -->
-<script language="JavaScript" src="javascript/menu_tpl.js"></script>
-<script language="JavaScript">
-	<!--//
-	// Note where menu initialization block is located in HTML document.
-	// Don't try to position menu locating menu initialization block in
-	// some table cell or other HTML element. Always put it before </body>
-	// each menu gets two parameters (see demo files)
-	// 1. items structure
-	// 2. geometry structure
-	new menu (MENU_ITEMS, MENU_POS);
-	// make sure files containing definitions for these variables are linked to the document
-	// if you got some javascript error like "MENU_POS is not defined", then you've made syntax
-	// error in menu_tpl.js file or that file isn't linked properly.
-	
-	// also take a look at stylesheets loaded in header in order to set styles
-	//-->
-</script>
-<script src="http://www.google-analytics.com/urchin.js" type="text/javascript">
-</script>
-<script type="text/javascript">
-_uacct = "UA-3782271-1";
-urchinTracker();
-</script>
-</BODY>
-</HTML>