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JEFworksJEFworks
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update website css
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‎_data/carousel.yml

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images:
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- image: /assets/news/bmes_group1.jpg
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- image: /assets/news/lab_retreat_09292024.jpg
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- image: /assets/news/farewell_gohta_06282024.jpg
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- image: /assets/news/lab_bbq_05032024.jpg
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- image: /assets/news/csh_single_cell_analysis_2023-2.jpg
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- image: /assets/news/lab_retreat_fall2023.gif
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- image: /assets/news/farewell_brendan_041423.gif
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- image: /assets/news/PTD_2022.jpg
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- image: /assets/news/lab_retreat_summer2022.jpg
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- image: /assets/news/bioeng22_team.jpeg
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- image: /assets/news/lab_event_062022.jpg
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- image: /assets/news/lab_hike_D3S6934.jpg
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‎_includes/footer.html

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<footer class="footer">
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<footer class="footer" align="center">
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<div class="container">
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<div class="row" align="center">
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<!-- © {{ site.title }} 2015-{{ site.time | date: '%Y' }} --->
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<div class="row">
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© {{ site.title }} {{ site.time | date: '%Y' }}
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<br/>
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<a rel="license" href="http://creativecommons.org/licenses/by/4.0/"><img alt="Creative Commons License" style="border-width:0" src="https://i.creativecommons.org/l/by/4.0/88x31.png" /></a><br /><br />This work by <span xmlns:cc="http://creativecommons.org/ns#" property="cc:attributionName">Jean Fan and team</span> is licensed under a <br/><a rel="license" href="http://creativecommons.org/licenses/by/4.0/" target="_blank">Creative Commons Attribution 4.0 International License</a><br />
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<a rel="license" href="http://creativecommons.org/licenses/by/4.0/"><br><img alt="Creative Commons License" style="padding:8px" src="https://i.creativecommons.org/l/by/4.0/88x31.png"/></a>
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<br/>
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This work by <span xmlns:cc="http://creativecommons.org/ns#" property="cc:attributionName">Jean Fan and team</span> is licensed under a <br/><a rel="license" href="http://creativecommons.org/licenses/by/4.0/" target="_blank">Creative Commons Attribution 4.0 International License</a>
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</div>
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<hr style="height:1px;border-width:0;background-color:#fff;">
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<!---
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<div class="row"><div align="center">
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<p>We are a part of</p>
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<div class="col-xs-4 col-sm-4">
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</div>
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</div></div>
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<!---
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<div class="row"><div align="center">
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<div class="col-xs-4 col-sm-4" align="center">
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<a href="https://www.cis.jhu.edu/" target="_blank">
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</div></div>
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--->
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<hr style="height:1px;border-width:0;background-color:#fff;">
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<div class="row"><div align="center">
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<br>
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<div class="row">
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<p>Our work is made possible thanks to the following publicly funded programs</p>
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<div class="col-xs-4 col-sm-4">
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<img src="/assets/logo/nsf-career.png" width=30%/>
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</div>
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<div class="col-xs-4 col-sm-4">
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<img src="/assets/logo/nih-nigms.png" width=30%/>
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</div>
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<div class="col-xs-4 col-sm-4">
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<img src="/assets/logo/HuBMAP_logo.png" width=60%/>
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</div>
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</div></div>
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<img src="/assets/logo/nsf-career.png" height="100px"/>
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<img src="/assets/logo/nih-nigms.png" height="100px"/>
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<img src="/assets/logo/HuBMAP_logo.png" height="100px"/>
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</div>
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</div>
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</footer>

‎_includes/head.html

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<meta http-equiv="X-UA-Compatible" content="IE=edge">
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<meta name="viewport" content="width=device-width, initial-scale=1">
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<!-- <title>{% if page.title %}{{ page.title }}{% else %}{{ site.title }}{% endif %}</title>
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<title>JEFworks Lab - {% if page.title %}{{ page.title }}{% else %}{{ site.title }}{% endif %}</title>
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<meta name="description" content="{% if page.excerpt %}{{ page.excerpt | strip_html | strip_newlines | truncate: 160 }}{% else %}{{ site.description }}{% endif %}">
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-->
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<title>JEFworks Lab</title>
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<meta name="description" content="Welcome to the JEFworks Lab where Prof. Jean Fan and team work on computational software and statistical approaches to address questions in developmental and cancer biology. We are a bioinformatics research lab in the Department of Biomedical Engineering at Johns Hopkins University. We develop methods for analyzing single-cell spatially resolved transcriptomic sequencing and imaging data. We apply these methods to better understand the impact of cellular heterogeneity on cancer pathogenesis and prognosis.">
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<meta name="keywords" content="bioinformatics, single cell, spatial transcriptomics, spatially resolved transcriptomics, merfish, computational biology, research lab, JHU research opportunities">
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‎_includes/image-gallery.html

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.image-gallery {overflow: auto; margin-left: -5%!important;}
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.image-gallery li {float: left; display: block; margin: 0 0 1% 1%; width: 32%;}
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.image-gallery img {
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width: 300px;
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height: 300px;
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align: center;
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object-fit: cover;
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border-radius: 9px;
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width: 300px;
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height: 300px;
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align: center;
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object-fit: cover;
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border-radius: 9px;
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}
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.image-gallery li a {text-align: center; text-decoration: none!important; color: #777;}
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.image-gallery li a img {width: 100%; display: block;}
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{% for item in site.data.carousel.images %}
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<li>
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<a href="{{ item.image }}">
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<img src="{{ item.image }}"/>
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<img src="{{ item.image }}">
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</a>
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</li>
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{% endfor %}
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</ul>
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<!-- lightbox -->
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<script type="text/javascript" src="/js/lightbox.js"></script>
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<link rel="stylesheet" href="/css/lightbox.css">

‎_includes/topnav.html

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<nav class="navbar navbar-default navbar-fixed-top">
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<header class="navbar navbar-fixed-top" role="navigation">
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<div class="container navbar-container">
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<div class="navbar-header">
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<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false" aria-controls="navbar">
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<span class="sr-only">Toggle navigation</span>
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<span class="icon-bar"></span>
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<span class="icon-bar"></span>
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<span class="icon-bar"></span>
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<button type="button" class="navbar-toggle" data-toggle="collapse" data-target="#navbar" aria-expanded="false" aria-controls="navbar" style="color:#fff">
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<i class="fa fa-bars"></i>
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</button>
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<a class="navbar-brand" href="{{ site.baseurl }}/">
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<span><img src="{{site.baseurl}}/img/logonav.png"></span> {{ site.title }}
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<span><img src="{{site.baseurl}}/assets/logo/jefworks_logo_white.svg"></span> {{ site.title }}
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</a>
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</div>
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<div id="navbar" class="collapse navbar-collapse">
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<ul class="nav navbar-nav navbar-right">
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<li class="nav-item dropdown">
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<a class="nav-link dropdown-toggle" href="#" id="navbarDropdown" role="button" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">
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About Us
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</a>
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<ul class="dropdown-menu" role="menu" aria-labelledby="navbarDropdown">
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<li {% if page.sectionid=='mission' %} class="active" {% endif %}>
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<a class="dropdown-item" href="{{ site.baseurl }}/mission">
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Our Mission
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<!-- Collect the nav links, forms, and other content for toggling -->
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<div id="navbar" class="collapse navbar-collapse navbar-right navbar-main-collapse">
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<ul class="nav navbar-nav">
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<li class="dropdown">
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<a href="#" class="dropdown-toggle" data-toggle="dropdown">
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About Us <b class="caret"></b>
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</a>
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<ul class="dropdown-menu">
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<li align="right">
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<a href="{{ site.baseurl }}/mission">
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Our Mission
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</a>
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<a href="{{ site.baseurl }}/team">
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Meet the Team
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</a>
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<a href="{{ site.baseurl }}/lab">
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Lab Resources
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</a>
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</li>
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</ul>
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</li>
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<li {% if page.sectionid=='team' %} class="active" {% endif %}>
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<a class="dropdown-item" href="{{ site.baseurl }}/team">
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Our Team
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<li>
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<a href="{{ site.baseurl }}/publications">
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Publications
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</a>
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</li>
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<li {% if page.sectionid=='lab' %} class="active" {% endif %}>
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<a class="dropdown-item" href="{{ site.baseurl }}/lab">
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Our Lab
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</a>
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</li>
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<li class="dropdown">
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<a href="#" class="dropdown-toggle" data-toggle="dropdown">
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Contributions <b class="caret"></b>
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</a>
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<ul class="dropdown-menu" role="menu" aria-labelledby="navbarDropdown">
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<li align="right">
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<a class="dropdown-item" href="{{ site.baseurl }}/software">
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Software
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</a>
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<a class="dropdown-item" href="{{ site.baseurl }}/teaching">
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Courses
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</a>
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<a class="dropdown-item" href="{{ site.baseurl }}/talks">
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Talks
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</a>
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</li>
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</ul>
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</li>
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<li {% if page.sectionid=='publications' %} class="active" {% endif %}>
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<a href="{{ site.baseurl }}/publications">
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Our Publications
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</a>
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</li>
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<li class="nav-item dropdown">
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<a class="nav-link dropdown-toggle" href="#" id="navbarDropdown" role="button" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">
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Our Contributions
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<li>
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<a href="{{ site.baseurl }}/join">
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Join
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</a>
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<ul class="dropdown-menu" role="menu" aria-labelledby="navbarDropdown">
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<li {% if page.sectionid=='software' %} class="active" {% endif %}>
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<a class="dropdown-item" href="{{ site.baseurl }}/software">
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Our Software
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</a>
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</li>
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<li {% if page.sectionid=='teaching' %} class="active" {% endif %}>
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<a class="dropdown-item" href="{{ site.baseurl }}/teaching">
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Our Courses
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</a>
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</li>
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<li {% if page.sectionid=='talks' %} class="active" {% endif %}>
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<a class="dropdown-item" href="{{ site.baseurl }}/talks">
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Our Talks
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</a>
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</li>
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</ul>
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</li>
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<li {% if page.sectionid=='blog' %} class="active" {% endif %}>
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<a href="{{ site.posts.first.url | prepend: site.baseurl }}">Blog</a>
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</li>
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<li {% if page.sectionid=='contact' %} class="active" {% endif %}>
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<li>
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<a href="{{ site.baseurl }}/contact">
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Contact
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</a>
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</li>
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<li style="margin:-13px 0px">
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<a href="{{ site.baseurl }}/join">
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<button type="button"
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{% if page.sectionid=='join' %}
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class="btn btn-primary"
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{% elsif page.section != 'join' %}
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class="btn btn-warning"
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{% endif %}
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>Join Us</button>
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</a>
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</li>
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</ul>
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<!---
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<div class="navbar-right">
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<form class="navbar-form navbar-left">
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<div class="form-group has-feedback">
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<input id="search-box" type="text" class="form-control" placeholder="Search...">
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<i class="fa fa-search form-control-feedback"></i>
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</div>
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</form>
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</div>
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--->
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<li>
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<a href="{{ site.posts.first.url | prepend: site.baseurl }}">
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Blog
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</a>
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</li>
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</ul>
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</div>
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</div>
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</nav>
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</div>
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</header>
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‎_layouts/default.html

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{% if page.image != null %}
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<div class='banner' style="
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background: url('/img/pattern.png') top left repeat,
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url( {{ page.image }}) top center / cover no-repeat;
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url( {{ page.image }}) center center / cover no-repeat;
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position: relative;
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">
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{% if page.desc != null %}
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top: 50%;
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transform: translateY(-50%);
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">
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<div class="container"><div class="row"><div class="col-sm-12">
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<h1 class="display-1">{{ page.desc }}</h1>
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</div></div></div>
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<div class="container center-container">
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<div class="col-xs-12 col-md-9">
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<h1>{{ page.desc }}</h1>
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</div>
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</div>
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</div>
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{% endif %}
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</div>
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{% endif %}
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<div class="page-content">
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<div class="wrapper">
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<div class="container">
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<div class="row"><div class="col-sm-12">
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{{ content }}
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</div></div>
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</div>
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</div>
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{{ content }}
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</div>
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{% include footer.html %}

‎_layouts/default2.html

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<!DOCTYPE html>
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<html>
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{% include head.html %}
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<body>
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{% include topnav.html %}
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{% if page.image != null %}
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<div class='banner' style="
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background: url('/img/pattern.png') top left repeat,
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url( {{ page.image }}) center center / cover no-repeat;
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position: relative;
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">
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{% if page.desc != null %}
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<div align="center" style="color: #ffffff; text-shadow: 0px 0px 8px #000000;
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position: absolute;
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width: 100%;
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top: 50%;
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transform: translateY(-50%);
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">
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<div class="container center-container">
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<div class="col-xs-12 col-md-9">
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<h1>{{ page.desc }}</h1>
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</div>
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</div>
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</div>
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{% endif %}
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</div>
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{% endif %}
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<div class="page-content">
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<div class="container page-pad">
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<div class="row">
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{{ content }}
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</div>
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</div>
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</div>
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{% include footer.html %}
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{% include js_files.html %}
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</body>
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</html>

‎_layouts/news.html

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layout: default
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---
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<div class="container">
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<div class="row">
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<h1>{{ page.date | date: "%b %-d, %Y" }}</h1>
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<p>{{ page.title }}</p>
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<div id="markdown-content-container">{{ content }}</div>
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</div>
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</div>

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