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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8"/>
<meta http-equiv="X-UA-Compatible" content="IE=edge"/>
<meta name="viewport" content="user-scalable=no, width=device-width, initial-scale=1, maximum-scale=1">
<title>Juicebox</title>
<meta name="viewport" content="width=device-width, initial-scale=1.0"/>
<link rel="icon" type="image/png" href="https://aidenlab.org/favicon.ico">
<!-- Font Awesome CSS-->
<link rel="stylesheet" href="//maxcdn.bootstrapcdn.com/font-awesome/4.2.0/css/font-awesome.min.css">
<!-- Bootstrap 5 CSS -->
<link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/bootstrap@5.3.8/dist/css/bootstrap.min.css">
<!-- Bootstrap 5 bundle (includes Popper, no jQuery) -->
<script src="https://cdn.jsdelivr.net/npm/bootstrap@5.3.8/dist/js/bootstrap.bundle.min.js"></script>
<!-- Dropbox Chooser API-->
<script src="https://www.dropbox.com/static/api/2/dropins.js" id="dropboxjs" data-app-key="8glijwyao9fq8we"></script>
<script type="module" src="/js/app.js"></script>
</head>
<body id="portfolio">
<nav class="navbar navbar-dark bg-dark fixed-top navbar-expand justify-content-between px-4">
<span class="navbar-brand">Juicebox Web App</span>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#hic-navbar-content">
<span class="navbar-toggler-icon"></span>
</button>
<div id="hic-navbar-content" class="collapse navbar-collapse d-flex flex-row">
<ul class="navbar-nav">
<!-- App Clone -->
<li class="nav-item">
<button id="juicebox-app-clone-button" type="button" class="btn btn-secondary btn-circle btn-sm ms-4 mt-2">
<i class="fa fa-plus"></i>
</button>
</li>
<!-- Contact Map -->
<li class="nav-item">
<div class="dropdown ms-2 mt-1">
<a id="hic-contact-map-dropdown" href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown">
Load Map
</a>
<div id="hic-contact-map-dropdown-menu" class="dropdown-menu">
<!-- Select -->
<a class="dropdown-item" href="#" data-bs-toggle="modal" data-bs-target="#hic-contact-map-modal">
Juicebox Archive
</a>
<!-- ENCODE hosted maps -->
<button id="hic-encode-hosted-contact-map-presentation-button" class="dropdown-item disabled" type="button" data-bs-toggle="modal" data-bs-target="#hic-encode-hosted-contact-map-modal">
ENCODE
</button>
<!-- 4DN maps -->
<button class="dropdown-item" type="button" data-bs-toggle="modal" data-bs-target="#hic-4dn-contact-map-modal">
4DN
</button>
<!-- Local Map File -->
<label class="dropdown-item btn btn-default btn-file">
<div class="igv-app-dropdown-item-cloud-storage">
<div>
Local File
</div>
<div>
<input name="contact-map" type="file" style="display: none;">
</div>
</div>
</label>
<!-- Dropbox -->
<div class="dropdown-item">
<div id="hic-contact-map-dropdown-dropbox-button" class="igv-app-dropdown-item-cloud-storage">
<div>Dropbox File</div>
<div>
<img src="./img/dropbox-dropdown-menu-item.png" width="18" height="18">
</div>
<!-- <div>...</div>-->
</div>
</div>
<!-- URL -->
<a class="dropdown-item" href="#" data-bs-toggle="modal" data-bs-target="#hic-load-url-modal">URL</a>
</div>
</div>
</li>
<!-- Control Map -->
<li class="nav-item">
<div class="dropdown ms-2 mt-1">
<a id="hic-control-map-dropdown" href="#" class="nav-link dropdown-toggle disabled" data-bs-toggle="dropdown">
Load "B" Map
</a>
<div id="hic-control-map-dropdown-menu" class="dropdown-menu">
<!-- Select -->
<a class="dropdown-item" href="#" data-bs-toggle="modal" data-bs-target="#hic-contact-map-modal">
Juicebox Archive
</a>
<!-- ENCODE hosted maps -->
<button id="hic-encode-hosted-control-map-presentation-button" class="dropdown-item" type="button" data-bs-toggle="modal" data-bs-target="#hic-encode-hosted-contact-map-modal">
ENCODE
</button>
<!-- 4DN maps -->
<button class="dropdown-item" type="button" data-bs-toggle="modal" data-bs-target="#hic-4dn-contact-map-modal">
4DN
</button>
<!-- Local Map File -->
<label class="dropdown-item btn btn-default btn-file">
<div class="igv-app-dropdown-item-cloud-storage">
<div>
Local File
</div>
<div>
<input name="contact-map" type="file" style="display: none;">
</div>
</div>
</label>
<!-- Dropbox -->
<div class="dropdown-item">
<div id="hic-control-map-dropdown-dropbox-button" class="igv-app-dropdown-item-cloud-storage">
<div>Dropbox File</div>
<div>
<img src="./img/dropbox-dropdown-menu-item.png" width="18" height="18">
</div>
<!-- <div>...</div>-->
</div>
</div>
<!-- URL -->
<a class="dropdown-item" href="#" data-bs-toggle="modal" data-bs-target="#hic-load-url-modal">URL</a>
</div>
</div>
</li>
<!-- Tracks -->
<li class="nav-item">
<div class="dropdown ms-2 mt-1">
<a id="hic-track-dropdown-button" href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown">
Load Tracks
</a>
<div id="hic-track-dropdown-menu" class="dropdown-menu">
<!-- toggle sequence track-->
<div class="dropdown-item">
<div>
<input type="checkbox" id="hic-sequence-track-checkbox">
Sequence
</div>
</div>
<!-- toggle ref-seq-genes track-->
<div class="dropdown-item">
<div>
<input type="checkbox" id="hic-ref-seq-genes-track-checkbox">
Genes
</div>
</div>
<!-- Local File -->
<label class="dropdown-item btn btn-secondary btn-file">
<div class="igv-app-dropdown-item-cloud-storage">
<div>
Local File ...
</div>
<div>
<input id="hic-local-track-file-input" name="local-track-file" type="file"
style="display: none;">
</div>
</div>
</label>
<!-- Dropbox -->
<div class="dropdown-item">
<div id="hic-track-dropdown-dropbox-button" class="igv-app-dropdown-item-cloud-storage">
<div>Dropbox File</div>
<div>
<img id="igv-app-track-dropbox-button-image" width="18" height="18">
</div>
</div>
</div>
<!-- URL -->
<a class="dropdown-item" href="#" data-bs-toggle="modal" data-bs-target="#track-load-url-modal">URL ...</a>
<!-- Genome Annotations (Frequently Used) -->
<a class="dropdown-item" href="#" data-bs-toggle="modal" data-bs-target="#hic-annotation-datalist-modal">Frequently
Used</a>
<!-- 2D Annotations -->
<a class="dropdown-item" href="#" data-bs-toggle="modal" data-bs-target="#hic-annotation-2D-datalist-modal">2D
Annotations</a>
<div id="hic-annotations-section" class="dropdown-divider">
</div>
</div>
</div>
</li>
<!-- Share -->
<li class="nav-item">
<div class="dropdown ms-2 mt-1">
<a id="hic-share-button" href="#" class="nav-link" data-bs-toggle="modal" data-bs-target="#hic-share-url-modal">
Share
</a>
</div>
<!-- <button id="hic-share-button" class="btn btn-outline-light btn-sm ms-2 mt-2" type="button" data-bs-toggle="modal" data-bs-target="#hic-share-url-modal">Share</button>-->
</li>
<!-- Session -->
<li class="nav-item">
<div class="dropdown ms-2 mt-1">
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown">
Session
</a>
<div id="igv-session-dropdown-menu" class="dropdown-menu">
<!-- Session Local file -->
<label class="dropdown-item btn btn-default btn-file">
<div class="igv-app-dropdown-item-cloud-storage">
<div>
Local File ...
</div>
<div>
<input id="igv-app-dropdown-local-session-file-input" type="file" name="file" style="display: none;">
</div>
</div>
</label>
<!-- Session Dropbox -->
<!-- Session Google Drive -->
<!-- Session URL -->
<button class="dropdown-item" type="button" data-bs-toggle="modal" data-bs-target="#igv-app-session-url-modal">
Load URL ...
</button>
<div class="dropdown-divider"></div>
<!-- Save Session Local file -->
<button id="igv-app-save-session-button" class="dropdown-item" type="button" data-bs-toggle="modal" data-bs-target="#igv-app-session-save-modal">
Save ...
</button>
</div>
</div>
</li>
<!-- Info -->
<li class="nav-item ms-4">
<div class="dropdown ms-4 mt-1">
<button type="button" class="btn btn-outline-light dropdown-toggle" data-bs-toggle="dropdown">
<svg xmlns="http://www.w3.org/2000/svg" width="24" height="24" fill="currentColor" class="bi bi-info-circle" viewBox="0 0 16 16">
<path d="M8 15A7 7 0 1 1 8 1a7 7 0 0 1 0 14zm0 1A8 8 0 1 0 8 0a8 8 0 0 0 0 16z"/>
<path d="m8.93 6.588-2.29.287-.082.38.45.083c.294.07.352.176.288.469l-.738 3.468c-.194.897.105 1.319.808 1.319.545 0 1.178-.252 1.465-.598l.088-.416c-.2.176-.492.246-.686.246-.275 0-.375-.193-.304-.533L8.93 6.588zM9 4.5a1 1 0 1 1-2 0 1 1 0 0 1 2 0z"/>
</svg>
</button>
<div class="dropdown-menu">
<div class="d-flex flex-column">
<a class="dropdown-item" href="https://www.aidenlab.org/index.html" target="_blank" rel="noopener">Aiden Lab</a>
</div>
<div class="dropdown-divider"></div>
<div class="d-flex flex-column">
<div>
<a class="dropdown-item" href="https://aidenlab.org/aboutus.html" target="_blank" rel="noopener">Team</a>
</div>
<div>
<a class="dropdown-item" href="https://news.tc4ga.com/" target="_blank" rel="noopener">News</a>
</div>
<div>
<a class="dropdown-item" href="https://aidenlab.org/join.html" target="_blank" rel="noopener">Join</a>
</div>
</div>
<div class="dropdown-divider"></div>
<div class="d-flex flex-column">
<div>
<a class="dropdown-item" href="https://aidenlab.org/research.html" target="_blank" rel="noopener">Projects</a>
</div>
<div>
<a class="dropdown-item" href="https://aidenlab.org/publications.html" target="_blank" rel="noopener">Publications</a>
</div>
<div>
<a class="dropdown-item" href="https://aidenlab.org/software.html" target="_blank" rel="noopener">Software</a>
</div>
<div>
<a class="dropdown-item" href="https://aidenlab.org/documentation.html" target="_blank" rel="noopener">Documentation</a>
</div>
<div>
<a class="dropdown-item" href="https://aidenlab.org/data.html" target="_blank" rel="noopener">Data</a>
</div>
</div>
<div class="dropdown-divider"></div>
<div class="d-flex flex-column">
<div>
<a class="dropdown-item" href="https://aidenlab.org/contactus.html" target="_blank" rel="noopener">Contact</a>
</div>
</div>
<div class="dropdown-divider"></div>
<div class="d-flex flex-column">
<div>
<a class="dropdown-item" href="https://aidenlab.org/forum.html" target="_blank" rel="noopener">Forum</a>
</div>
</div>
<div class="dropdown-divider"></div>
<div class="d-flex flex-column">
<div>
<a class="dropdown-item" href="https://aidenlab.org/assembly" target="_blank" rel="noopener">Assembly</a>
</div>
</div>
<div class="dropdown-divider"></div>
<div class="d-flex flex-column">
<a class="dropdown-item" href="https://aidenlab.github.io/juicebox-web/" target="_blank" rel="noopener">Help</a>
</div>
</div>
</div>
</li>
</ul>
</div>
<ul class="navbar-nav">
<li class="nav-item">
<a href="https://aidenlab.github.io/juicebox-web/" target="_blank">
Help
</a>
</li>
</ul>
</nav>
<main id="hic-main" class="container-fluid">
<!-- App container -->
<div class="row">
<div class="col-md-12">
<!-- app + caption container-->
<div id="app-caption" class="juicebox-app-caption-container">
<!-- app container-->
<div id="app-container" class="juicebox-app-clone-container">
</div>
<!-- caption -->
<div id="hic-caption" class="hic-caption-container" contenteditable="true">
</div>
</div>
</div>
</div>
<div class="row">
<div class="col-md-4">
<div>
<span> </span>
<span>Version @VERSION </span>
<!-- <span id="hic-version-number">version</span>-->
</div>
</div>
</div>
<div class="row header">
<div class="text-center col-md-offset-2 col-md-8 col-md-offset-2">
<br>
<h5>
<a href="https://github.com/igvteam/juicebox.js" target="_blank">Juicebox.js</a> is cloud-based
visualization software for Hi-C data created by <a href="https://github.com/jrobinso" target="_blank">Jim
Robinson</a> and <a href="https://github.com/turner" target="_blank">Douglass Turner</a> of the <a
href="https://igv.org" target="_blank">IGV</a> team, in collaboration with <a
href="https://github.com/nchernia" target="_blank">Neva C. Durand</a> and the <a
href="https://aidenlab.org" target="_blank">Aiden Lab</a>. You can also download a full-fledged
<a href="https://github.com/theaidenlab/juicebox/wiki/Download" target="_blank">desktop version of
Juicebox</a>.
</h5>
<br>
<h5>
If you use Juicebox in your research, please cite:
</h5>
<br>
<h5>James T. Robinson, Douglass Turner, Neva C. Durand, Helga Thorvaldsdóttir, Jill P. Mesirov, Erez
Lieberman Aiden.
<em>"Juicebox.js Provides a Cloud-Based Visualization System for Hi-C Data."</em> <i>Cell Systems</i> 6(2),2018.
</h5>
<br>
</div>
</div>
<!-- Share URL Modal -->
<div id="hic-share-url-modal" class="modal fade">
<div class="modal-dialog modal-lg">
<div class="modal-content">
<div class="modal-header">
<div class="modal-title">Share</div>
<button type="button" class="btn-close" data-bs-dismiss="modal" aria-label="Close"></button>
</div>
<div class="modal-body">
<div class="container-fluid">
<!-- copy url -->
<div class="row">
<div class="col-md-9">
<div class="mb-3">
<input id="hic-share-url" type="text" class="form-control" placeholder="">
</div>
</div>
<div class="col-md-3">
<button id="hic-copy-link" type="button" class="btn btn-default">
COPY
</button>
</div>
</div>
<!-- social buttons -->
<div class="hic-social-button-container">
<div id="emailButtonContainer">
<a id="emailButton" href="mailto:?body=https://aidenlab.org/juicebox">
EMAIL
</a>
</div>
<div id="hic-embed-button">
EMBED
</div>
<div id="hic-qr-code-button">
QR CODE
</div>
</div>
<!-- qr code image -->
<div class="row">
<div id="hic-qr-code-image" class="col-md-offset-4 col-md-4">
</div>
</div>
<!-- embed widget -->
<div id="hic-embed-container" class="row">
<div class="col-md-9 mb-3">
<textarea id="hic-embed" class="form-control" rows="4">
</textarea>
</div>
<div class="col-md-3">
<button id="hic-embed-copy-link" type="button" class="btn btn-default">
COPY
</button>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</main>
<div id="footer-white" style="background:#414B5B;">
<div class="container">
<div class="row" align="center">
<div class="newsletter" style="width:60%;">
<div class="signup clearfix">
<p style="text-align:center;">
Sign up for our newsletter and we'll inform you of updates on projects in the lab.
</p>
<form role="form" id="newsletter-form" method="post" action="../newsletter.php">
<input type="text" name="email" class="form-control" placeholder="Your email address">
<input type="submit" name="submit" value="Sign up">
</form>
</div>
</div>
</div>
<div class="row credits">
<div class="col-md-12">
Copyright © 2017. Aiden Lab
</div>
</div>
</div>
</div>
</body>
</html>