diff options
| author | BonfaceKilz | 2021-04-23 17:27:31 +0300 |
|---|---|---|
| committer | BonfaceKilz | 2021-04-23 17:42:26 +0300 |
| commit | 2114ad9e84ad7778e048b52cf865b5f031ceab88 (patch) | |
| tree | ec11082fd60181879189de8575473086ddf495a4 | |
| parent | d2e2046a3ce1af0ca97ea1b6d9ccb3a4c9aecf7c (diff) | |
| download | genenetwork2-2114ad9e84ad7778e048b52cf865b5f031ceab88.tar.gz | |
Rename index_page_orig to index_page
| -rwxr-xr-x[-rw-r--r--] | wqflask/wqflask/templates/index_page.html | 222 | ||||
| -rwxr-xr-x | wqflask/wqflask/templates/index_page_orig.html | 339 | ||||
| -rw-r--r-- | wqflask/wqflask/views.py | 2 |
3 files changed, 136 insertions, 427 deletions
diff --git a/wqflask/wqflask/templates/index_page.html b/wqflask/wqflask/templates/index_page.html index 31846f87..87cf1b45 100644..100755 --- a/wqflask/wqflask/templates/index_page.html +++ b/wqflask/wqflask/templates/index_page.html @@ -1,78 +1,73 @@ {% extends "base.html" %} {% block title %}GeneNetwork{% endblock %} +{% block css %} +<style TYPE="text/css"> + p.interact { display: none; } +</style> +{% endblock %} {% block content %} <!-- Start of body --> - -<!-- - <header class="jumbotron subhead" id="overview"> - <div class="container"> - <h1>GeneNetwork</h1> - <p class="lead">Open source bioinformatics for systems genetics</p> - </div> - </header> ---> - - <div class="container-fluid"> + <div class="container-fluid" style="min-width: 1210px;"> {{ flash_me() }} - <div class="row" style="width: 1400px !important;"> + <div class="row" style="width: 100%;"> - <div class="col-xs-5"> + <div class="col-xs-4" style="margin-right:50px; 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"> <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="padding-right: 0px;"> - <div class="col-xs-8"> - <select name="species" id="species" class="form-control span3" style="width: 280px !important;"></select> - </div> - <div class="col-xs-4"> - <button type="button" id="make_default" class="btn btn-primary form-control">Make Default</button> + <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"> - <div class="col-xs-8"> - <select name="group" id="group" class="form-control span3" 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="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"> - <div class="col-xs-8"> - <select name="type" id="type" class="form-control span3" 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: 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 input-append"> - <div class="col-xs-10"> - <select name="dataset" id="dataset" class="form-control span5" style="width: 340px !important;"></select> + <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 class="col-xs-2"> - <button type="button" id="dataset_info" class="btn btn-primary form-control" style="width: 75px !important;">Info</button> - </div> </div> </div> <!-- USER HELP --> - <!--<p>Databases marked with <b>**</b>--> + <!--<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>--> @@ -80,9 +75,9 @@ <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"> - <div class="col-xs-8"> - <textarea onkeydown="pressed(event)" name="search_terms_or" rows="1" class="form-control search-query" style="max-width: 550px; width: 450px !important;" id="or_search"></textarea> + <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> @@ -90,8 +85,8 @@ <!-- 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"> - <div class="col-xs-12 controls"> + <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>. @@ -101,19 +96,22 @@ <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"> - <div class="col-xs-8"> - <textarea onkeydown="pressed(event)" name="search_terms_and" rows="1" class="form-control search-query" style="max-width: 550px; width: 450px !important;" id="and_search"></textarea> + <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"> - <div class="col-xs-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> @@ -133,33 +131,43 @@ <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="{{ url_for('glossary_blueprint.glossary') }}#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> <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>GO:0045202 LRS=(9 99 Chr4 122 155) cisLRS=(9 999 10)</b> - finds synapse-associated genes with <a href="{{ url_for('glossary_blueprint.glossary') }}#E"> - cis eQTL</a> on Chr 4 from 122 and 155 Mb with LRS scores - between 9 and 999.</li> + <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"> @@ -168,8 +176,43 @@ </ul> </section> </div> - <div style="padding-left:120px" class="col-xs-4" style="width: 600px !important;"> - <!-- + + <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> @@ -178,7 +221,7 @@ <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 + GeneNetwork <a href="http://www.genenetwork.org/tutorial/WebQTLTour/" class="fs14">tour</a> that includes screen shots and typical steps in the analysis. </p> @@ -195,34 +238,26 @@ and advice on their use and citation.</p> </section> - --> + </section> + --> <section id="websites"> <div class="page-header"> - <h1>Affiliates and mirrors</h1> + <h1>Links</h1> </div> - <h3>Websites affiliated with GeneNetwork</h3> - <ul> - <li><span class="broken_link" href="http://ucscbrowser.genenetwork.org/">Genome Browser</span> at UTHSC</li> - - <li><a href="http://galaxy.genenetwork.org/">Galaxy</a> at - UTHSC</li> - - <li>GeneNetwork 1 at <span class="broken_link" href="http://ec2.genenetwork.org/">Amazon - Cloud (EC2)</span></li> - - <li>GeneNetwork 1 Source Code at <a href="http://sourceforge.net/projects/genenetwork/">SourceForge</a></li> - - <li>GeneNetwork 2 Source Code at <a href="https://github.com/genenetwork/genenetwork2">GitHub</a></li> - </ul> - <h3>GN1 Mirror and development sites</h3> - + <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 GN1 site at UTHSC</a> (main site)</li> - <li><span class="broken_link" href="http://genenetwork.helmholtz-hzi.de/">Germany at the HZI</span></li> - <li><a href="http://genenetwork.org/">Memphis at the U of M</a></li> + <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> - </section> + <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"> @@ -248,7 +283,7 @@ <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> @@ -257,7 +292,7 @@ <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>--> @@ -268,11 +303,7 @@ {%endblock%} {% block js %} - - <script> - gn_server_url = "{{ gn_server_url }}"; - </script> - <script src="/static/new/javascript/dataset_select_menu.js"></script> + <script src="/static/new/javascript/dataset_select_menu_orig.js"></script> <script> function pressed(e) { @@ -288,4 +319,21 @@ } </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 %} 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 %} diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index c4b510d4..156b4772 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -156,7 +156,7 @@ def index_page(): import_collections = params['import_collections'] if import_collections == "true": g.user_session.import_traits_to_user(params['anon_id']) - return render_template("index_page_orig.html", version=GN_VERSION) + return render_template("index_page.html", version=GN_VERSION) @app.route("/tmp/<img_path>") |