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index.html
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---
---
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<title>Home :: Biodalliance</title>
<!-- meta name="viewport" content="width=device-width, initial-scale=1.0" -->
<meta name="description" content="">
<meta name="author" content="">
<!-- Le styles -->
<link href="bootstrap/css/bootstrap.css" rel="stylesheet">
<style type="text/css">
body {
padding-top: 80px;
padding-bottom: 40px;
}
</style>
<link href="../assets/css/bootstrap-responsive.css" rel="stylesheet">
<script language="javascript" src="{{site.uiprefix}}/dalliance-compiled.js"></script>
<script language="javascript">
var b = new Browser({
chr: '22',
viewStart: 29890000,
viewEnd: 30050000,
cookieKey: 'human-grc_h37-fp',
coordSystem: {
speciesName: 'Human',
taxon: 9606,
auth: 'GRCh',
version: '37',
ucscName: 'hg19',
},
chains: {
hg18ToHg19: {
uri: '//www.biodalliance.org/datasets/hg18ToHg19.bb',
type: 'bigbed',
coords: {
speciesName: 'Human',
taxon: 9606,
auth: 'NBCI',
version: 36,
ucscName: 'hg17'
}
}
},
sources: [{name: 'Genome',
twoBitURI: '//www.biodalliance.org/datasets/hg19.2bit',
tier_type: 'sequence'},
{name: 'Genes',
desc: 'Gene structures from GENCODE 19',
bwgURI: '//www.biodalliance.org/datasets/gencode.bb',
stylesheet_uri: '//www.biodalliance.org/stylesheets/gencode.xml',
collapseSuperGroups: true,
trixURI: '//www.biodalliance.org/datasets/geneIndex.ix'},
{name: 'DNase I', desc: 'GM12878 DNaseI signals from UW',
pennant: '//genome.ucsc.edu/images/encodeThumbnail.jpg',
bwgURI: '//www.biodalliance.org/datasets/encode/wgEncodeUwDnaseGm12878Aln_2Reps.norm5.rawsignal.bw',
style: [{type: 'default', style: {glyph: 'HISTOGRAM', BGCOLOR: 'rgb(8,104,172)', HEIGHT: 30, id: 'style1'}}],
noDownsample: true},
{name: 'H3K4me1', desc: 'GM12878 H3K4me1 signal from Broad',
pennant: '//genome.ucsc.edu/images/encodeThumbnail.jpg',
bwgURI: '//www.biodalliance.org/datasets/encode/wgEncodeBroadHistoneGm12878H3k4me1StdAln_2Reps.norm5.rawsignal.bw',
style: [{type: 'default', style: {glyph: 'HISTOGRAM', BGCOLOR: 'rgb(166,71,71)', HEIGHT: 30, id: 'style1'}}],
noDownsample: true},
{name: 'H3K4me2', desc: 'GM12878 H3K4me2 signal from Broad',
pennant: '//genome.ucsc.edu/images/encodeThumbnail.jpg',
bwgURI: '//www.biodalliance.org/datasets/encode/wgEncodeBroadHistoneGm12878H3k4me2StdAln_2Reps.norm5.rawsignal.bw',
style: [{type: 'default', style: {glyph: 'HISTOGRAM', BGCOLOR: 'rgb(166,71,71)', HEIGHT: 30, id: 'style1'}}],
noDownsample: true},
{name: 'H3K4me3', desc: 'GM12878 H3K4me3 signal from UW',
pennant: '//genome.ucsc.edu/images/encodeThumbnail.jpg',
bwgURI: '//www.biodalliance.org/datasets/encode/wgEncodeUwHistoneGm12878H3k4me3StdAln_2Reps.norm5.rawsignal.bw',
style: [{type: 'default', style: {glyph: 'HISTOGRAM', BGCOLOR: 'rgb(166,71,71)', HEIGHT: 30, id: 'style1'}}],
noDownsample: true},
{name: 'GM12878 ChromHMM', desc: 'GM12878 ChromHMM Genome Segmentation',
pennant: '//genome.ucsc.edu/images/encodeThumbnail.jpg',
bwgURI: '//www.biodalliance.org/datasets/encode/gm12878.ChromHMM.bb',
style: [{type: 'bigbed', style: {glyph: 'BOX', FGCOLOR: 'black', BGCOLOR: 'blue', HEIGHT: 8, BUMP: false, LABEL: false, ZINDEX: 20, BGITEM: true, id: 'style1'}},
{type: 'bb-translation', style: {glyph: 'BOX', FGCOLOR: 'black', BGITEM: true, BGCOLOR: 'red', HEIGHT: 10, BUMP: true, ZINDEX: 20, id: 'style2'}},
{type: 'bb-transcript', style: {glyph: 'BOX', FGCOLOR: 'black', BGCOLOR: 'white', HEIGHT: 10, ZINDEX: 10, BUMP: true, LABEL: true, id: 'style3'}}]}
],
uiPrefix: '{{site.uiprefix}}/',
setDocumentTitle: false,
disablePoweredBy: true,
noTitle: true,
hubs: ['http://ngs.sanger.ac.uk/production/ensembl/regulation/hub.txt', 'http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/hub.txt']
});
</script>
<!-- Fav and touch icons -->
<!-- <link rel="apple-touch-icon-precomposed" sizes="144x144" href="../assets/ico/apple-touch-icon-144-precomposed.png">
<link rel="apple-touch-icon-precomposed" sizes="114x114" href="../assets/ico/apple-touch-icon-114-precomposed.png">
<link rel="apple-touch-icon-precomposed" sizes="72x72" href="../assets/ico/apple-touch-icon-72-precomposed.png">
<link rel="apple-touch-icon-precomposed" href="../assets/ico/apple-touch-icon-57-precomposed.png">
<link rel="shortcut icon" href="../assets/ico/favicon.png" -->
</head>
<body>
{% include topbar.html %}
<div class="container">
<div class="hero-unit" style='padding: 35px'>
<h3 style='margin-top: 0px'>Fast, embeddable genome visualization</h3>
<div id="svgHolder" style="background: white; padding: 5px; margin-top: 20px"></div>
</div>
<!-- Example row of columns -->
<div class="row">
<div class="span6">
<h2>Introduction</h2>
<p>
Biodalliance is a fast, interactive, genome visualization tool that's easy to <a href='embed.html'>embed</a> in web pages and applications.
It supports integration of data from a wide variety of sources, and can load data directly from popular genomics file formats including
bigWig, BAM, and VCF. This means you can build a fully-featured genome browser, such as the example on this page, using only a standard
web server and a directory full of files — no databases or server-side support code are needed.
</p>
</div>
<div class="span6">
<h2>News</h2>
<p><strong>3 Feb 2015</strong> Dalliance 0.13 is released with BAM and gene rendering improvements</p>
<p><strong>July 2014</strong> Discuss Dalliance at <a href="http://www.open-bio.org/wiki/BOSC_2014">BOSC 2014</a></p>
<p><strong>8 May</strong> Dalliance 0.12 is released with support for plain BED, WIG, and VCF files, and substantial performance improvements.</p>
<p><a href="oldnews.html">Older news...</a>
</div>
</div>
<hr>
<footer>
<p>Last update {{ site.time | date_to_long_string }}</p>
</footer>
</div> <!-- /container -->
<!-- Le javascript
================================================== -->
<!-- Placed at the end of the document so the pages load faster -->
<script src="bootstrap-without-jquery.js"></script>
</body>
</html>