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index.html
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<!DOCTYPE html>
<html>
<head>
<title>DiVil</title>
<meta http-equiv="Content-Security-Policy" content="
default-src 'self'
'sha256-mQyxHEuwZJqpxCw3SLmc4YOySNKXunyu2Oiz1r3/wAE='
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script-src 'self'
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img-src 'self' https://* data: w3.org/svg/2000;
child-src 'none';
connect-src 'self' https://www.ebi.ac.uk/biomodels/">
<meta charset="UTF-8">
<meta name="viewport" content="width=device-width, initial-scale=1, maximum-scale=1">
<script type="text/javascript" src="thirdParty/d3.v5.js"></script>
<script type="text/javascript" src="thirdParty/jquery-2.1.4.min.js"></script>
<script type="text/javascript" src="javascriptAndCss/sboTermMapping.js"></script>
<script type="text/javascript" src="javascriptAndCss/showSbgn.js"></script>
<script type="text/javascript" src="javascriptAndCss/customSymbol.js"></script>
<script type="text/javascript" src="bives/bivesTool.js"></script>
<script type="text/javascript" src="javascriptAndCss/localFiles.js"></script>
<script type="text/javascript" src="javascriptAndCss/downloadSBGNML.js"></script>
<script type="text/javascript" src="javascriptAndCss/downloadSVG.js"></script>
<script type="text/javascript" src="javascriptAndCss/downloadPNG.js"></script>
<script type="text/javascript" src="thirdParty/FileSaver.js"></script>
<script type="text/javascript" src="javascriptAndCss/appendDefs.js"></script>
<script type="text/javascript" src="javascriptAndCss/sbmlParser.js"></script>
<script type="text/javascript" src="javascriptAndCss/xmlDiffParser.js"></script>
<script type="text/javascript" src="javascriptAndCss/arrowsOnNodes.js"></script>
<script type="text/javascript" src="javascriptAndCss/xmlParser.js"></script>
<script type="text/javascript" src="javascriptAndCss/parseUrl.js"></script>
<script type="text/javascript" src="thirdParty/ctop.js"></script>
<script src="thirdParty/xmlBeautify.js"></script>
<!-- Mathjax-->
<script>
MathJax = {
startup: {
typeset: false
}
// your configuration here, if needed
};
</script>
<script type="text/javascript" id="MathJax-script" async src="thirdParty/mml-chtml.js">
</script>
<link href="javascriptAndCss/bootstrap.min.css" rel="stylesheet">
<link href="javascriptAndCss/bootstrap-dashboard.css" rel="stylesheet">
<link rel="stylesheet" href="javascriptAndCss/style.css">
</head>
<body>
<div class="modal fade" id="errorModal" tabindex="-1" role="dialog" aria-labelledby="errorModelLabel"
aria-hidden="true">
<div class="modal-dialog">
<div class="modal-content">
<div class="modal-header">
<h5 class="modal-title" id="errorModelLabel">Failed to load ressources from BioModels</h5>
</div>
<div class="modal-body" id="errorModalBody">
...
</div>
<div class="modal-footer">
<button type="button" class="btn btn-secondary" data-bs-dismiss="modal">
Close
</button>
</div>
</div>
</div>
</div>
<header class="navbar sticky-top flex-md-nowrap p-0 shadow">
<div class=" col-2 justify-content-center d-none d-md-flex p-1 row">
<img class="me-0 px-2" id="logo" src="img/divil_logo.svg">
</div>
<div class=" col-1 justify-content-center d-md-none d-lg-none d-xl-none row">
<img class="me-0 px-1" id="logo" src="img/divil_icon.svg">
</div>
<div class="col-10 col-md-9 col-lg-9 col-xl-9 row">
<form id="local-files-form" class="row">
<div class="col-9 p-1">
<div class="form-group">
<div class="custom-file">
<input class="form-control form-control-sm mb-1" id="formFile1" type="file">
<input class="form-control form-control-sm" id="formFile2" type="file">
</div>
</div>
</div>
<div class="col-3 justify-content-center p-1 btn-group-vertical">
<button id="compareModels" type="button" class="btn btn-primary menuBtn">compare</button>
<div class="dropdown btn-group menuBtn d-flex justify-content-end">
<button class="btn btn-secondary dropdown-toggle disabled" type="button" id="downloadBtn"
data-bs-toggle="dropdown" aria-expanded="false">
Download
</button>
<ul class="dropdown-menu" aria-labelledby="downloadBtn">
<li><a class="dropdown-item" id="sbgnMlDownload" href="#">SBGN-ML</a></li>
<li><a class="dropdown-item" id="svgDownload" href="#">SVG</a></li>
<li><a class="dropdown-item" id="pngDownload" href="#">PNG</a></li>
</ul>
</div>
</div>
</form>
</div>
<div class="col-1 row">
<a class="row justify-content-center" href="https://github.com/Gebbi8/DiVil"><img class="icon"
id="github-logo" src="img/GitHub-Mark.svg"></a>
<a class="row justify-content-center">
<img class="icon" id="info" data-bs-toggle="offcanvas" href="#offcanvasExample" role="button"
aria-controls="offcanvasExample" src="img/info-icon.svg">
</a>
</div>
</div>
</div>
</header>
<div class="container-fluid">
<div class="row">
<!-- <div class="progress">
<div id="progressM1" class="progress-bar progress-bar-striped progress-bar-animated" role="progressbar"
style="width: 25%" aria-valuenow="10" aria-valuemin="0" aria-valuemax="100"></div>
<div id="progressM2" class="progress-bar progress-bar-striped bg-success progress-bar-animated"
role="progressbar" style="width: 25%" aria-valuenow="25" aria-valuemin="0" aria-valuemax="100">
</div>
<div id="progressDiff" class="progress-bar progress-bar-striped bg-info progress-bar-animated"
role="progressbar" style="width: 25%" aria-valuenow="50" aria-valuemin="0" aria-valuemax="100">
</div>
<div id="progressDivil" class="progress-bar progress-bar-striped bg-warning progress-bar-animated"
role="progressbar" style="width: 25%" aria-valuenow="75" aria-valuemin="0" aria-valuemax="100">
</div>
</div> -->
<!--<div class="col-2 " id="forceControls">
<div class="force alpha">
<p><label>alpha</label> Simulation activity</p>
<div class="alpha_bar" onclick="updateAll();">
<div id="alpha_value"></div>
</div>
</div>
<div class="force">
<p><label>center</label> Shifts the view, so the graph is centered at this location.</p>
<label>
x
<output id="center_XSliderOutput">.5</output>
<input type="range" min="0" max="1" value=".5" step="0.01"
oninput="d3.select('#center_XSliderOutput').text(value); forceProperties.center.x=value; updateAll();">
</label>
<label>
y
<output id="center_YSliderOutput">.5</output>
<input type="range" min="0" max="1" value=".5" step="0.01"
oninput="d3.select('#center_YSliderOutput').text(value); forceProperties.center.y=value; updateAll();">
</label>
</div>
<hr>
<div class="force">
<p><label><input type="checkbox" checked
onchange="forceProperties.charge.enabled = this.checked; updateAll();"> charge</label>
Attracts
(+) or repels (-) nodes to/from each other.</p>
<label title="Negative strength repels nodes. Positive strength attracts nodes.">
strength
<output id="charge_StrengthSliderOutput">-30</output>
<input type="range" min="-200" max="50" value="-30" step=".1"
oninput="d3.select('#charge_StrengthSliderOutput').text(value); forceProperties.charge.strength=value; updateAll();">
</label>
<label title="Minimum distance where force is applied">
distanceMin
<output id="charge_distanceMinSliderOutput">1</output>
<input type="range" min="0" max="50" value="1" step=".1"
oninput="d3.select('#charge_distanceMinSliderOutput').text(value); forceProperties.charge.distanceMin=value; updateAll();">
</label>
<label title="Maximum distance where force is applied">
distanceMax
<output id="charge_distanceMaxSliderOutput">2000</output>
<input type="range" min="0" max="2000" value="2000" step=".1"
oninput="d3.select('#charge_distanceMaxSliderOutput').text(value); forceProperties.charge.distanceMax=value; updateAll();">
</label>
</div>
<hr>
<div class="force">
<p><label><input type="checkbox" checked
onchange="forceProperties.collide.enabled = this.checked; updateAll();"> collide</label>
Prevents nodes from overlapping</p>
<label>
strength
<output id="collide_StrengthSliderOutput">.7</output>
<input type="range" min="0" max="2" value=".7" step=".1"
oninput="d3.select('#collide_StrengthSliderOutput').text(value); forceProperties.collide.strength=value; updateAll();">
</label>
<label title="Size of nodes">
radius
<output id="collide_radiusSliderOutput">70</output>
<input type="range" min="0" max="100" value="70" step="1"
oninput="d3.select('#collide_radiusSliderOutput').text(value); forceProperties.collide.radius=value; updateAll();">
</label>
<label
title="Higher values increase rigidity of the nodes (WARNING: high values are computationally expensive)">
iterations
<output id="collide_iterationsSliderOutput">1</output>
<input type="range" min="1" max="10" value="1" step="1"
oninput="d3.select('#collide_iterationsSliderOutput').text(value); forceProperties.collide.iterations=value; updateAll();">
</label>
</div>
<hr>
<div class="force">
<p><label><input type="checkbox"
onchange="forceProperties.forceX.enabled = this.checked; updateAll();">
forceX</label> Acts like gravity. Pulls all points towards an X location.</p>
<label>
strength
<output id="forceX_StrengthSliderOutput">.1</output>
<input type="range" min="0" max="1" value=".1" step="0.01"
oninput="d3.select('#forceX_StrengthSliderOutput').text(value); forceProperties.forceX.strength=value; updateAll();">
</label>
<label
title="The X location that the force will push the nodes to (NOTE: This demo multiplies by the svg width)">
x
<output id="forceX_XSliderOutput">.5</output>
<input type="range" min="0" max="1" value=".5" step="0.01"
oninput="d3.select('#forceX_XSliderOutput').text(value); forceProperties.forceX.x=value; updateAll();">
</label>
</div>
<hr>
<div class="force">
<p><label><input type="checkbox"
onchange="forceProperties.forceY.enabled = this.checked; updateAll();">
forceY</label> Acts like gravity. Pulls all points towards a Y location.</p>
<label>
strength
<output id="forceY_StrengthSliderOutput">.1</output>
<input type="range" min="0" max="1" value=".1" step="0.01"
oninput="d3.select('#forceY_StrengthSliderOutput').text(value); forceProperties.forceY.strength=value; updateAll();">
</label>
<label
title="The Y location that the force will push the nodes to (NOTE: This demo multiplies by the svg height)">
y
<output id="forceY_YSliderOutput">.5</output>
<input type="range" min="0" max="1" value=".5" step="0.01"
oninput="d3.select('#forceY_YSliderOutput').text(value); forceProperties.forceY.y=value; updateAll();">
</label>
</div>
<hr>
<div class="force">
<p><label><input type="checkbox" checked
onchange="forceProperties.link.enabled = this.checked; updateAll();"> link</label> Sets
link
length</p>
<label title="The force will push/pull nodes to make links this long">
distance
<output id="link_DistanceSliderOutput">30</output>
<input type="range" min="0" max="100" value="30" step="1"
oninput="d3.select('#link_DistanceSliderOutput').text(value); forceProperties.link.distance=value; updateAll();">
</label>
<label
title="Higher values increase rigidity of the links (WARNING: high values are computationally expensive)">
iterations
<output id="link_IterationsSliderOutput">1</output>
<input type="range" min="1" max="10" value="1" step="1"
oninput="d3.select('#link_IterationsSliderOutput').text(value); forceProperties.link.iterations=value; updateAll();">
</label>
</div>
</div>
<main id="bivesGraph" class="col-10 ms-sm-auto px-md-4">
<div id="container" class="svg-container"></div>
</main> -->
<main id="bivesGraph" class="ms-sm-auto px-md-4">
<div id="container" class="svg-container"></div>
</main>
<div id="infoPopup" class="alert alert-primary alert-dismissible fade show" role="alert">
<button type="button" class="btn-close" data-bs-hide="alert" aria-label="Close"></button>
</div>
</div>
<!-- <div class="row" id="xmlDiff"></div>
<div class="row" id="bivesReport"></div>
<div class="row" id="sbgnJson"></div> -->
</div>
<div class="offcanvas offcanvas-start" tabindex="-1" id="offcanvasExample" aria-labelledby="offcanvasExampleLabel">
<div class="offcanvas-header">
<h5 class="offcanvas-title" id="offcanvasExampleLabel">Difference Visualisation</h5>
<button id="dismissCanvas" type="button" class="btn-close text-reset" data-bs-dismiss="offcanvas"
aria-label="Close"></button>
</div>
<div class="offcanvas-body">
<p>
This prototype showcases our method to visualise differences between versions of biochemical models in a
standardized format.
</p>
<p>
Select two model versions from your local system with the menu at the top or choose examples from below.
</p>
<div class="accordion accordion-flush" id="accordionFlushExample">
<div class="accordion-item">
<h2 class="accordion-header" id="flush-heading1">
<button class="accordion-button collapsed" type="button" data-bs-toggle="collapse"
data-bs-target="#flush-collapse1" aria-expanded="false" aria-controls="flush-collapse">
Example #1 - Oscillation
</button>
</h2>
<div id="flush-collapse1" class="accordion-collapse collapse" aria-labelledby="flush-heading1"
data-bs-parent="#accordionFlushExample">
<div class="accordion-body">
<p>Kummer2000 - Oscillations in Calcium Signalling
<br>BioModel: <a href="https://www.ebi.ac.uk/biomodels/BIOMD0000000329">000329</a>
</p>
<button id="e1Kummer" type="button" class="btn btn-outline-primary btn-sm">Compute</button>
</div>
</div>
</div>
<div class="accordion-item">
<h2 class="accordion-header" id="flush-heading2">
<button class="accordion-button collapsed" type="button" data-bs-toggle="collapse"
data-bs-target="#flush-collapse2" aria-expanded="false" aria-controls="flush-collapse2">
Example #2 - B.subtilis transcription
</button>
</h2>
<div id="flush-collapse2" class="accordion-collapse collapse" aria-labelledby="flush-heading2"
data-bs-parent="#accordionFlushExample">
<div class="accordion-body">
<p>Liebal2012 - B.subtilis transcription inhibition model
<br>BioModel: <a href="https://www.ebi.ac.uk/biomodels/BIOMD0000000461">000461</a>
</p>
<button id="e2Liebal" type="button" class="btn btn-outline-primary btn-sm">Compute</button>
</div>
</div>
</div>
<div class="accordion-item">
<h2 class="accordion-header" id="flush-heading3">
<button class="accordion-button collapsed" type="button" data-bs-toggle="collapse"
data-bs-target="#flush-collapse3" aria-expanded="false" aria-controls="flush-collapse3">
Example #3 - Dupreez models
</button>
</h2>
<div id="flush-collapse3" class="accordion-collapse collapse" aria-labelledby="flush-heading3"
data-bs-parent="#accordionFlushExample">
<div class="accordion-body">
<p>Comparison of the Dupreez models 6 and 7
<br>JWS Online: <a
href="https://jjj.biochem.sun.ac.za/models/?id=dupreez&organism=&process=&jwsmodel__model_type=">Dupreez
models</a>
</p>
<button id="e3Dupreez" type="button" class="btn btn-outline-primary btn-sm">Compute</button>
</div>
</div>
</div>
<div class="accordion-item">
<h2 class="accordion-header" id="flush-heading4">
<button class="accordion-button collapsed" type="button" data-bs-toggle="collapse"
data-bs-target="#flush-collapse4" aria-expanded="false" aria-controls="flush-collapse4">
Example #4 - NaviCentas Th2 submap
</button>
</h2>
<div id="flush-collapse4" class="accordion-collapse collapse" aria-labelledby="flush-heading4"
data-bs-parent="#accordionFlushExample">
<div class="accordion-body">
<p>Comparison of two versions of the Th2 submap
<br>from <a href="https://www.sbi.uni-rostock.de/minerva/index.xhtml?id=NaviCenta">
NaviCenta</a>.
</p>
<button id="e4Julia" type="button" class="btn btn-outline-primary btn-sm">Compute</button>
</div>
</div>
</div>
<!-- <div class="accordion-item">
<h2 class="accordion-header" id="flush-headingThree">
<button class="accordion-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#flush-collapseThree" aria-expanded="false" aria-controls="flush-collapseThree">
Accordion Item #3
</button>
</h2>
<div id="flush-collapseThree" class="accordion-collapse collapse" aria-labelledby="flush-headingThree" data-bs-parent="#accordionFlushExample">
<div class="accordion-body">
<button id="e1Kummer" type="button" class="btn btn-outline-primary btn-sm">Compute</button>
</div>
</div>
</div> -->
</div>
<p>
This project relies on <a href="https://d3js.org/">D3</a> and <a
href="http://bives.bio.informatik.uni-rostock.de/">BiVeS</a>. Styling and Layout is based on
Bootstrap 5.
</p>
</div>
<div class="offcanvas-body mt-auto" id="offcanvasFooter">
<p>Contact: <a class="text-light" href="https://www.sbi.uni-rostock.de/team/detail/tom-gebhardt">Tom
Gebhardt</a>, University of Rostock
<br>E-Mail: tom.gebhardt@uni-rostock.de</p>
<div id="foot">This was started as part of SEMS (funded by the German Federal Ministry of Education and
Research in the e:Bio programme SEMS, FKZ 031 6194).
Maintenance and further development were part of INCOME (funded by the German Federal Ministry of
Education and Research in the e:Med programme FKZ 01ZX1705C)
and EU-Stands4PM (funded by the Horizon2020 framework programme, Grant Agreement #825843).
</div>
</div>
</div>
<script src="javascriptAndCss/bootstrap.bundle.min.js"></script>
<script src="javascriptAndCss/init.js"></script>
</body>
</html>