wqflask/base/indexBody.py


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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">&nbsp;&nbsp;&nbsp;&nbsp;Databases marked with <B>**</B> suffix are not public yet.
                                                                                        <BR>&nbsp;&nbsp;&nbsp;&nbsp;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">&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>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> &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://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>
"""