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diff --git a/wqflask/wqflask/templates/index_page_orig.html b/wqflask/wqflask/templates/index_page_orig.html deleted file mode 100755 index 87cf1b45..00000000 --- a/wqflask/wqflask/templates/index_page_orig.html +++ /dev/null @@ -1,339 +0,0 @@ -{% extends "base.html" %} -{% block title %}GeneNetwork{% endblock %} -{% block css %} -<style TYPE="text/css"> - p.interact { display: none; } -</style> -{% endblock %} -{% block content %} -<!-- Start of body --> - <div class="container-fluid" style="min-width: 1210px;"> - - {{ flash_me() }} - - <div class="row" style="width: 100%;"> - - <div class="col-xs-4" style="margin-right:50px; min-width: 530px; max-width: 550px;"> - <section id="search"> - <div> - <h1>Select and search</h1> - </div> - <form method="get" action="/search" target="_blank" name="SEARCHFORM"> - <fieldset> - <div style="padding: 20px" class="form-horizontal"> - - <div class="form-group"> - <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;"><option>Loading...</option></select> - </div> - </div> - </div> - - <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="display: flex; padding-left: 20px;"> - <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 class="col-3" style="margin-left: 10px;"> - <button type="button" id="group_info" class="btn btn-primary form-control" style="width: 50px !important;">Info</button> - </div> - </div> - </div> - - <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 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: 50px !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" style="display: flex; padding-left: 20px;"> - <div class="col-9"> - <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> - </div> - - <!-- USER HELP --> - <!--<p >Databases marked with <b>**</b>--> - <!-- suffix are not public yet.<br>--> - <!-- Access requires <a href="/account.html" target=--> - <!-- "_blank" class="fs14">user login</a>.</p>--> - <!-- GET ANY SEARCH --> - - <div class="form-group"> - <label for="or_search" class="col-xs-1 control-label" style="padding-left: 0px; padding-right: 0px; width: 65px !important;">Get Any:</label> - <div class="col-xs-10 controls" style="padding-left: 20px;"> - <div class="col-8"> - <textarea onkeydown="pressed(event)" name="search_terms_or" rows="1" class="form-control search-query" style="resize: vertical; max-width: 550px; width: 450px !important;" id="or_search"></textarea> - </div> - </div> - </div> - - <!-- GET ANY HELP --> - <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-12 controls"> - Enter terms, genes, ID numbers in the <b>Search</b> field.<br> - Use <b>*</b> or <b>?</b> wildcards (Cyp*a?, synap*).<br> - Use <b>quotes</b> for terms such as <i>"tyrosine kinase"</i>. - </div> - </div> - </div> - - <div class="form-group"> - <label for="and_search" class="col-xs-1 control-label" style="padding-left: 0px; padding-right: 0px; width: 65px !important;">Combined:</label> - <div class="col-xs-10 controls" style="padding-left: 20px;"> - <div class="col-8"> - <textarea onkeydown="pressed(event)" name="search_terms_and" rows="1" class="form-control search-query" style="resize: vertical; max-width: 550px; width: 450px !important;" id="and_search"></textarea> - </div> - </div> - </div> - - <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="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> - - <!-- SEARCH, MAKE DEFAULT --> - - <div class="form-group"> - </div> - - <input type="hidden" name="FormID" value="searchResult" class="form-control"> - <!--!<input type="hidden" name="RISet" value="BXD">--> - </div> - </fieldset> - </form> - </section> - <section id="advanced"> - <div class="page-header"> - <h2>Advanced commands</h2> - </div> - - <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)</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://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> - - <li><b>GO:0045202</b> searches for synapse-associated genes listed in the - <a href="http://amigo.geneontology.org/amigo/medial_search?q=GO%3A0045202"> - Gene Ontology</a>.</li> - - <li><b>RIF=diabetes LRS=(9 999 Chr2 100 105) transLRS=(9 999 10)</b> - finds diabetes-associated transcripts with peak <a href="{{ url_for('glossary_blueprint.glossary') }}#E"> - trans eQTLs</a> on Chr 2 between 100 and 105 Mb with LRS - scores between 9 and 999.</li> - </ul> - </section> - </div> - - <div class="col-xs-4" style="width: 600px !important;"> - <section id="affiliates"> - <div class="page-header"> - <h1>Affiliates</h1> - <ul> - <li><b><a href="http://gn1.genenetwork.org">GeneNetwork 1</a> at UTHSC</b></li> - <li><span class="broken_link" href="http://ucscbrowser.genenetwork.org/">Genome Browser</span> 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> - <section id="news-section"> - <div class="page-header"> - <h1>News</h1> - <div id="tweets" style="height: 300px; overflow: scroll; overflow-x: hidden;"></div> - <div align="right"> - <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/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> - <!-- - <section id="tour-info"> - <div class="page-header"> - <h1>Tour and more info</h1> - </div> - - <h3>Thirty minute tour</h3> - <p> - Take the 30 minute - GeneNetwork <a href="http://www.genenetwork.org/tutorial/WebQTLTour/" class="fs14">tour</a> that includes screen shots and - typical steps in the analysis. - </p> - - <h3>Even more info</h3> - <p> - For information about - resources and methods, select the Info buttons next to the Group - and Database fields above. - </p> - - <p>The <a href="/conditionsofUse.html">conditions</a> - and <a href="/statusandContact.html">contact - </a> pages have information on the status of data sets - and advice on their use and citation.</p> - - </section> - - </section> - --> - <section id="websites"> - <div class="page-header"> - <h1>Links</h1> - </div> - <h3>GeneNetwork v2:</h3> - <ul> - <li><a href="http://genenetwork.org/">Main website</a> at UTHSC</li> - <!--<li><a href="http://test-genenetwork.org/">Testing website</a> at UTHSC</li>--> - </ul> - <h3>GeneNetwork v1:</h3> - <ul> - <li><a href="http://gn1.genenetwork.org/">Main website</a> at UTHSC</li> - <li><span class="broken_link" href="http://artemis.uthsc.edu/">Time Machine</span>: Full GN versions from 2009 to 2016 (mm9)</li> - Cloud (EC2)</a></li> - </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"> - <div class="page-header"> - <h1>Getting started</h1> - </div> - - <ol style="font-size:12px;font-family:verdana;color:black"> - <li>Select <b>Species</b> (or All)</li> - - <li>Select <b>Group</b> (a specific sample)</li> - - <li>Select <b>Type</b> of data: - - <ul> - <li>Phenotype (traits)</li> - - <li>Genotype (markers)</li> - - <li>Expression (mRNAs)</li> - </ul> - </li> - - <li>Select a <b>Dataset</b></li> - - <li>Enter terms in the search field: words, - genes, probes, advanced search commands</li> - - <li>Click the <b>Search</b> button</li> - - <li>Optional: Use the <b>Make Default</b> button to save your preferences</li> - </ol> - - <h3>User Guide</h3> - <h5>Read the - <a href="http://gn1.genenetwork.org/index4.html"> - user guide</a>.</h5> - - </section>--> - </div> - </div> - </div> - -{%endblock%} - -{% block js %} - <script src="/static/new/javascript/dataset_select_menu_orig.js"></script> - - <script> - function pressed(e) { - // Has the enter key been pressed? - if ( (window.event ? event.keyCode : e.which) == 13) { - e.preventDefault(); - // If enter key has been pressed and the search fields are non-empty - // manually submit the <form> - if( event.target.value.trim() != "" ) { - document.forms[1].submit(); - } - } - } - </script> - - <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='javascript-twitter-post-fetcher/js/twitterFetcher_min.js') }}"></script> - - <script type="text/javascript"> - var configProfile = { - "profile": {"screenName": 'GeneNetwork2'}, - "domId": 'tweets', - "maxTweets": 5, - "enableLinks": true, - "showUser": false, - "showTime": true, - "showImages": true, - "lang": 'en' - }; - twitterFetcher.fetch(configProfile); - </script> - - -{% endblock %} |