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Diffstat (limited to 'web/webqtl/base/indexBody.py')
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diff --git a/web/webqtl/base/indexBody.py b/web/webqtl/base/indexBody.py new file mode 100755 index 00000000..aa67dffa --- /dev/null +++ b/web/webqtl/base/indexBody.py @@ -0,0 +1,290 @@ +index_body_string = """ +<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"> Databases marked with <B>**</B> suffix are not public yet. + <BR> Access requires <A HREF="/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"> Enter terms, genes, ID numbers in the <B>Get Any</B> field. + <BR> Use <B>*</B> or <B>?</B> wildcards (Cyp*a?, synap*). + <BR> 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 "> + <INPUT TYPE="button" CLASS="button" STYLE="font-size:12px" VALUE=" Make Default " onClick = "setDefault(this.form);"> + <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> ______________________________________________________ + +<P STYLE="font-size:13px;font-family:verdana;color:black"><B> + +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"> + You can also use advanced commands. Copy these simple examples +<BR> 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>Websites Affiliated with GeneNetwork</B></p> + <p style="font-size:12px;font-family:verdana;color:black"> + <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 Codes at <a href="http://sourceforge.net/projects/genenetwork/" target="_blank">SourceForge</a></li> + </ul> + </p> + <P>____________________________ + + <p style="font-size:15px;font-family:verdana;color:black"><B>Getting Started</B> </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://alexandria.uthsc.edu/" target="_blank" class="fs14"><small>Workstation</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://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> + <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://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> + </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> + + +</P> + </TD> +""" |