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<!DOCTYPE html>
<html lang="en-US">
<head>
<meta charset="UTF-8">
<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
<title>dms-view</title>
<script src="https://d3js.org/d3.v5.min.js"></script>
<script src="https://d3js.org/d3-array.v2.min.js"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/underscore.js/1.9.1/underscore-min.js"></script>
<script src="https://cdn.jsdelivr.net/npm/opentype.js@1.1.0/dist/opentype.min.js"></script>
<script src="https://cdn.jsdelivr.net/npm/marked@0.8.2/marked.min.js"></script>
<link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/4.3.1/css/bootstrap.min.css" integrity="sha384-ggOyR0iXCbMQv3Xipma34MD+dH/1fQ784/j6cY/iJTQUOhcWr7x9JvoRxT2MZw1T" crossorigin="anonymous">
<link rel="stylesheet" href="styles.css" />
<!-- Global site tag (gtag.js) - Google Analytics -->
<script async src="https://www.googletagmanager.com/gtag/js?id=UA-169775293-1"></script>
<script>
window.dataLayer = window.dataLayer || [];
function gtag(){dataLayer.push(arguments);}
gtag('js', new Date());
gtag('config', 'UA-169775293-1');
</script>
</head>
<body>
<div class="container">
<div class="row mt-3">
<div class="col-12">
<h1>dms-view</h1>
dms-view is an interactive visualization tool for deep mutational scanning.
Please see the <a href="https://dms-view.github.io/docs">documentation (dms-view.github.io/docs)</a> for detailed instructions on <a href="https://dms-view.github.io/docs/tutorial/">using the tool</a> or <a href="https://dms-view.github.io/docs/dataupload/">uploading your own data</a>.
For more information on the tool itself, checkout the <a href="https://www.biorxiv.org/content/10.1101/2020.05.14.096842v1">preprint</a>
<h4>Instructions:</h4>
Select points of interest by <span style="font-weight:bold">clicking</span> or <span style="font-weight:bold">brushing</span> (click, hold and swipe).
Deselect points by <span style="font-weight:bold">clicking</span> again or <span style="font-weight:bold">brushing</span> while holding down the <span style="font-style:italic">shift key</span> or after changing the radio button from <span style="font-style:italic">select</span> to <span style="font-style:italic">deselect</span>.
Change between different <span style="font-style:italic">conditions</span>, different <span style="font-style:italic">site-level metrics</span>, different <span style="font-style:italic">mutation-level metrics</span> and different <span style="font-style:italic">protein-representations</span> using the dropdown menus.
</div>
</div>
<div class="row mb-5 border-top border-bottom pt-3 pb-3">
<div class="col-8">
<div class="alert alert-danger" role="alert" id="dataFormFieldAlert" hidden>
<strong>Error reading the data URL!</strong>
Please review the URL below or check the contents of the datafile by reviewing the
<a href="https://dms-view.github.io/docs/dataupload/" target="_blank">documentation</a>.
</div>
<p><input id="data-url" text="text" class="form-control" placeholder="Data URL (relative or absolute paths allowed)" /></p>
<p>
<input type='radio' id="select" name="mode" value="select" checked /> select
<input type='radio' id="deselect" name="mode" value="deselect" /> deselect
<input id="selected_sites" text="text" class="form-control" style="display: inline; width: 50%" placeholder="Selected sites (e.g., '144' or '144,160')" />
<button id="clearButton" class="button">clear selections</button>
</p>
<div id="line_plot" class="row"></div>
<div id="logo_plot" class="row"></div>
</div>
<div class="col-4">
<div class="alert alert-danger" role="alert" id="proteinFormFieldAlert" hidden>
<strong>Error reading the protein structure URL!</strong>
Please review the URL below or check the contents of the protein structure by reviewing the
<a href="https://dms-view.github.io/docs/dataupload/" target="_blank">documentation</a>.
</div>
<p><input id="pdb-url" text="text" class="form-control" placeholder="PDB URL" /></p>
<select name="polymerSelect">
<option value="cartoon">cartoon</option>
<option value="spacefill">spacefill</option>
<option value="licorice">sticks</option>
<option value="surface">surface</option>
</select>
<div id="protein" style="width: 400px; height: 550px;"></div>
</div>
</div>
<div id="description" class="row mt-3">
<div class="col-12">
<div class="alert alert-danger" role="alert" id="markdownFormFieldAlert" hidden>
<strong>Error reading the description URL!</strong>
Please review the URL below or check the contents of the description markdown by reviewing the
<a href="https://dms-view.github.io/docs/dataupload/" target="_blank">documentation</a>.
</div>
<p><input id="markdown-url" text="text" class="form-control" placeholder="markdown URL" /></p>
<div id="markdown-output"></div>
</div>
</div>
<footer class="footer-copyright bg-light text-center pl-3 mt-4 mb-4">
<div class="row p-3 mb-0">
<span>Copyright 2020 by Sarah Hilton and John Huddleston.
<a href="https://thenounproject.com/search/?q=eraser&creator=1997209&i=1144641">Eraser icon</a> by Setyo Ari Wibowo from <a href="https://thenounproject.com/">The Noun Project</a></span>
</div>
</footer>
</div>
<script src="main.js"></script>
<script src="line_plot_zoom.js" type="text/javascript"></script>
<script src="ngl.js"></script>
<script src="prot_struct.js" type="text/javascript"></script>
<script src="logoplot.js" type="text/javascript"></script>
</body>
</html>