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Diffstat (limited to 'wqflask/wqflask/templates/index_page_orig.html')
| -rwxr-xr-x | wqflask/wqflask/templates/index_page_orig.html | 104 |
1 files changed, 59 insertions, 45 deletions
diff --git a/wqflask/wqflask/templates/index_page_orig.html b/wqflask/wqflask/templates/index_page_orig.html index 30e3f2f6..963531cb 100755 --- a/wqflask/wqflask/templates/index_page_orig.html +++ b/wqflask/wqflask/templates/index_page_orig.html @@ -17,18 +17,18 @@ </header> --> - <div class="container-fluid"> + <div class="container-fluid" style="min-width: 1200px;"> {{ flash_me() }} <div class="row" style="width: 100%;"> - <div class="col-xs-5"> + <div class="col-xs-5" style="min-width: 530px; max-width: 550px;"> <section id="search"> - <div class="page-header"> + <div> <h1>Select and search</h1> </div> - <form method="get" action="/search" name="SEARCHFORM"> + <form method="get" action="/search" target="_blank" name="SEARCHFORM"> <fieldset> <div style="padding: 20px" class="form-horizontal"> @@ -36,10 +36,7 @@ <label for="species" class="col-xs-1 control-label" style="width: 65px !important;">Species:</label> <div class="col-xs-10 controls input-append" style="display: flex; padding-left: 20px;"> <div class="col-8"> - <select name="species" id="species" class="form-control" style="width: 280px !important;"></select> - </div> - <div class="col-4" style="margin-left: 10px;"> - <button type="button" id="make_default" class="btn btn-primary form-control">Make Default</button> + <select name="species" id="species" class="form-control" style="width: 280px !important;"><option>Loading...</option></select> </div> </div> </div> @@ -47,8 +44,8 @@ <div class="form-group"> <label for="group" class="col-xs-1 control-label" style="width: 65px !important;">Group:</label> <div class="col-xs-10 controls input-append" style="padding-left: 20px;"> - <div class="col-8"> - <select name="group" id="group" class="form-control" style="width: 280px !important;"></select> + <div class="col-9"> + <select name="group" id="group" class="form-control" style="width: 340px !important;"><option>Loading...</option></select> <i class="icon-question-sign"></i> </div> </div> @@ -56,23 +53,23 @@ <div class="form-group"> <label for="tissue" class="col-xs-1 control-label" style="width: 65px !important;">Type:</label> - <div class="col-xs-10 controls" style="padding-left: 20px;"> - <div class="col-8"> - <select name="type" id="type" class="form-control" style="width: 280px !important;"></select> + <div class="col-xs-10 controls input-append" style="display: flex; padding-left: 20px;"> + <div class="col-9"> + <select name="type" id="type" class="form-control" style="width: 340px !important;"><option>Loading...</option></select> + </div> + <div class="col-3" style="margin-left: 10px;"> + <button type="button" id="dataset_info" class="btn btn-primary form-control" style="width: 75px !important;">Info</button> </div> </div> </div> <div class="form-group"> <label for="dataset" class="col-xs-1 control-label" style="width: 65px !important;">Dataset:</label> - <div class="col-xs-10 controls input-append" style="display: flex; padding-left: 20px;"> + <div class="col-xs-10 controls" style="display: flex; padding-left: 20px;"> <div class="col-9"> - <select name="dataset" id="dataset" class="form-control" style="width: 340px !important;"></select> + <select name="dataset" id="dataset" class="form-control" style="max-width: 550px; width: 450px !important;"><option>Loading...</option></select> <i class="icon-question-sign"></i> </div> - <div class="col-3" style="margin-left: 10px;"> - <button type="button" id="dataset_info" class="btn btn-primary form-control" style="width: 75px !important;">Info</button> - </div> </div> </div> @@ -115,10 +112,13 @@ <div class="form-group"> <label for="btsearch" class="col-xs-1 control-label" style="width: 65px !important;"></label> - <div class="col-xs-10 controls" style="padding-left: 20px;"> - <div class="col-2 controls" style="width: 100px !important;"> + <div class="col-xs-10 controls" style="display: flex; padding-left: 20px;"> + <div class="col-2 controls"> <input id="btsearch" type="submit" class="btn btn-primary form-control" value="Search"> </div> + <div class="col-2 controls" style="padding-left: 20px;"> + <button type="button" id="make_default" class="btn btn-primary form-control">Make Default</button> + </div> </div> </div> @@ -138,23 +138,37 @@ <h2>Advanced commands</h2> </div> - <p>You can also use advanced commands. Copy these simple examples into the Get Any or Combined search fields:</p> + <p>You can also use advanced commands. Copy these simple examples into the Get Any field for single term searches and Combined for searches with multiple terms:</p> <ul> <li><b>POSITION=(chr1 25 30)</b> finds genes, markers, or transcripts on chromosome 1 between 25 and 30 Mb.</li> - <li><b>MEAN=(15 16) LRS=(23 46)</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">LRS</a> - linkage between 23 and 46.</li> + <li><b>MEAN=(15 16)</b> in the <b>Combined</b> field finds + highly expressed genes (15 to 16 log2 units)</li> <li><b>RANGE=(1.5 2.5)</b> in the <b>Any</b> field finds traits with values with a specified fold-range (minimum = 1). Useful for finding "housekeeping genes" <b>(1.0 1.2)</b> or highly variable molecular assays <b>(10 100)</b>.</li> + <li><b>LRS=(15 1000)</b> or <b>LOD=(2 8)</b> finds all traits with peak LRS or LOD scores between lower and upper limits.</li> + + <li><b>LRS=(9 999 Chr4 122 155)</b> finds all traits on Chr 4 from 122 and 155 Mb with LRS scores between 9 and 999.</li> + + <li><b>cisLRS=(15 1000 5)</b> or <b>cisLOD=(2 8 5)</b> finds all cis eQTLs with peak LRS or LOD scores between lower and upper limits, + with an <b>inclusion</b> zone of 5 Mb around the parent gene.</li> + + <li><b>transLRS=(15 1000 5)</b> or <b>transLOD=(2 8 5)</b> finds all trans eQTLs with peak LRS or LOD scores between lower and upper limits, + with an <b>exclusion</b> zone of 5 Mb around the parent gene. You can also add a fourth term specifying which chromosome you want the transLRS to be on + (for example transLRS=(15 1000 5 7) would find all trans eQTLs with peak LRS on chromosome 7 that is also a trans eQTL with exclusionary zone of 5Mb).</li> + + <li><b>POSITION=(Chr4 122 130) cisLRS=(9 999 10)</b> + finds all traits on Chr 4 from 122 and 155 Mb with cisLRS scores + between 9 and 999 and an inclusion zone of 10 Mb.</li> + <li><b>RIF=mitochondrial</b> searches RNA databases for <a href="https://en.wikipedia.org/wiki/GeneRIF"> GeneRIF</a> links.</li> - <li><b>WIKI=nicotine</b> searches <a href="http://www.genenetwork.org/webqtl/main.py?FormID=geneWiki"> + <li><b>WIKI=nicotine</b> searches <a href="http://gn1.genenetwork.org/webqtl/main.py?FormID=geneWiki"> GeneWiki</a> for genes that you or other users have annotated with the word <i>nicotine</i>.</li> @@ -162,28 +176,26 @@ <a href="http://amigo.geneontology.org/amigo/medial_search?q=GO%3A0045202"> 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="http://www.genenetwork.org/glossary.html#E"> - cis eQTL</a> on Chr 4 from 122 and 155 Mb with LRS scores - between 9 and 999.</li> - <li><b>RIF=diabetes LRS=(9 999 Chr2 100 105) transLRS=(9 999 10)</b> - finds diabetes-associated transcripts with peak <a href="http://www.genenetwork.org/glossary.html#E"> + finds diabetes-associated transcripts with peak <a href="http://gn1.genenetwork.org/glossary.html#E"> trans eQTLs</a> on Chr 2 between 100 and 105 Mb with LRS scores between 9 and 999.</li> </ul> </section> </div> - <div style="padding-left:120px" class="col-xs-4" style="width: 600px !important;"> + <div style="padding-left:80px" class="col-xs-4" style="width: 600px !important;"> <section id="affiliates"> <div class="page-header"> <h1>Affiliates</h1> <ul> - <li><a href="http://ucscbrowser.genenetwork.org/">Genome browser</a> at UTHSC</li> - <li><a href="http://galaxy.genenetwork.org/">Galaxy</a> at UTHSC</li> - <li><a href="https://systems-genetics.org/">Systems Genetics</a> @ EPFL</li> - <li>UTHSC <a href="http://bnw.genenetwork.org/">Bayesian Network Web Server</a></li> + <li><b><a href="http://gn1.genenetwork.org">GeneNetwork 1</a> at UTHSC</b></li> + <li><a href="http://ucscbrowser.genenetwork.org/">Genome Browser</a> at UTHSC</li> + <li><a href="https://systems-genetics.org/">Systems Genetics</a> at EPFL</li> + <li><a href="http://bnw.genenetwork.org/">Bayesian Network Web Server</a> at UTHSC</li> + <li><a href="https://www.geneweaver.org/">GeneWeaver</a></li> + <li><a href="https://phenogen.org/">PhenoGen</a> at University of Colorado</li> + <li><a href="http://www.webgestalt.org/">WebGestalt</a> at Baylor</li> </ul> </div> </section> @@ -195,14 +207,15 @@ <a href="https://twitter.com/GeneNetwork2">more news items...</a> </div> </div> + </section> <section id="websites"> <div class="page-header"> <h1>Github</h1> <ul> <li><a href="https://github.com/genenetwork/genenetwork2">GN2 Source Code</a></li> - <li><a href="https://github.com/genenetwork/gn-docs/wiki">GN2 Document Wiki</a></li> - <li><a href="https://github.com/genenetwork/sysmaintenance">System Maintenance Code</a></li> <li><a href="https://github.com/genenetwork/genenetwork">GN1 Source Code</a></li> + <!--<li><a href="https://github.com/genenetwork/gn-docs/wiki">GN2 Document Wiki</a></li>--> + <li><a href="https://github.com/genenetwork/sysmaintenance">System Maintenance Code</a></li> </ul> </div> </section> @@ -232,9 +245,9 @@ and advice on their use and citation.</p> </section> - --> - </section> + </section> + --> <section id="websites"> <div class="page-header"> <h1>Links</h1> @@ -242,14 +255,15 @@ <h3>GeneNetwork v2:</h3> <ul> <li><a href="http://gn2.genenetwork.org/">Main website</a> at UTHSC</li> - <li><a href="http://test-gn2.genenetwork.org/">Testing website</a> at UTHSC</li> + <!--<li><a href="http://test-gn2.genenetwork.org/">Testing website</a> at UTHSC</li>--> </ul> <h3>GeneNetwork v1:</h3> <ul> - <li><a href="http://www.genenetwork.org/">Main website</a> at UTHSC</li> + <li><a href="http://gn1.genenetwork.org/">Main website</a> at UTHSC</li> <li><a href="http://artemis.uthsc.edu/">Time Machine</a>: Full GN versions from 2009 to 2016 (mm9)</li> Cloud (EC2)</a></li> - </ul> + </ul> + <script type="text/javascript" src="//rf.revolvermaps.com/0/0/8.js?i=526mdlpknyd&m=0&c=ff0000&cr1=ffffff&f=arial&l=33" async="async"></script> </section> <!--<section id="getting-started"> @@ -276,7 +290,7 @@ <li>Select a <b>Dataset</b></li> <li>Enter terms in the search field: words, - genes, ID numbers, probes, advanced search commands</li> + genes, probes, advanced search commands</li> <li>Click the <b>Search</b> button</li> @@ -285,7 +299,7 @@ <h3>User Guide</h3> <h5>Read the - <a href="http://www.genenetwork.org/index4.html"> + <a href="http://gn1.genenetwork.org/index4.html"> user guide</a>.</h5> </section>--> |