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Add page on workbench, add workbench publicaton to publications
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@pvanheus
pvanheus authored Jul 25, 2022
2 parents 43b68e8 + fb25a43 commit 72b101c
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2 changes: 1 addition & 1 deletion index.html
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Expand Up @@ -179,7 +179,7 @@ <h3>combatTB-NeoDB</h3>
<h3>combatTB Workbench</h3>
<p>A customizable platform for variant discovery and annotation and phylogeny construction.
</p>
<a href="https://github.com/COMBAT-TB/irida-galaxy-deploy">Read more</a>
<a href="/workbench">Read more</a>
</div>
</div>
<!-- /about -->
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11 changes: 11 additions & 0 deletions publications.html
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Expand Up @@ -139,6 +139,17 @@ <h2>Publications</h2>
</tr>
</thead>
<tbody>
<tr>
<td>The COMBAT-TB Workbench: Making Powerful Mycobacterium tuberculosis Bioinformatics Accessible</td>
<td>van Heusden, P. et al. </td>
<td>Feb 2022</td>
<td>mSphere</td>
<td>
<a
href="https://doi.org/10.1128/msphere.00991-21">10.1128/msphere.00991-21</a>
</td>
</tr>

<tr>
<td>COMBAT-TB-NeoDB: fostering tuberculosis research through integrative analysis
using graph database technologies</td>
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276 changes: 276 additions & 0 deletions workbench.html
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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="width=device-width, initial-scale=1">
<meta name="Description" content="COMBAT-TB: Computational Bacterial Analytical ToolKit for Tuberculosis.">

<title>COMBAT-TB</title>

<link rel="apple-touch-icon" sizes="152x152" href="/img/apple-touch-icon.png">
<link rel="icon" type="image/png" sizes="32x32" href="/img/favicon-32x32.png">
<link rel="icon" type="image/png" sizes="16x16" href="/img/favicon-16x16.png">
<link rel="manifest" href="/img/site.webmanifest">
<link rel="mask-icon" href="/img/safari-pinned-tab.svg" color="#5bbad5">
<meta name="msapplication-TileColor" content="#da532c">
<meta name="theme-color" content="#ffffff">

<!-- Google font -->
<link href="https://fonts.googleapis.com/css?family=Montserrat:400,700%7CVarela+Round" rel="stylesheet">

<!-- Bootstrap -->
<link type="text/css" rel="stylesheet" href="/css/bootstrap.min.css" />

<!-- Owl Carousel -->
<link type="text/css" rel="stylesheet" href="/css/owl.carousel.css" />
<link type="text/css" rel="stylesheet" href="/css/owl.theme.default.css" />

<!-- Magnific Popup -->
<link type="text/css" rel="stylesheet" href="/css/magnific-popup.css" />

<!-- Font Awesome Icon -->
<link rel="stylesheet" href="/css/font-awesome.min.css">

<!-- Custom stlylesheet -->
<link type="text/css" rel="stylesheet" href="/css/style.css" />

<!-- DataTables stlylesheet -->
<link type="text/css" rel="stylesheet" href="/css/dataTables.bootstrap.min.css" />
<link rel="stylesheet" type="text/css" href="https://cdn.datatables.net/v/bs/dt-1.10.18/datatables.min.css" />

<!-- HTML5 shim and Respond.js for IE8 support of HTML5 elements and media queries -->
<!-- WARNING: Respond.js doesn't work if you view the page via file:// -->
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
<![endif]-->
</head>

<body>

<!-- Header -->
<header id="workbench">
<!-- Background Image -->
<div class="bg-img" style="background-image: url('/img/ctbbackground.jpg');">
<div class="overlay"></div>
</div>
<!-- /Background Image -->

<!-- Nav -->
<nav id="nav" class="navbar">
<div class="container">

<div class="navbar-header">
<!-- Logo -->
<div class="navbar-brand">
<a href="/">
<img class="logo" src="/img/ctb-logo-alt.png" alt="logo">
</a>
</div>
<!-- /Logo -->

<!-- Collapse nav button -->
<div class="nav-collapse">
<span></span>
</div>
<!-- /Collapse nav button -->
</div>

<!-- Main navigation -->
<ul class="main-nav nav navbar-nav navbar-right">
<li>
<a href="/">Home</a>
</li>
<li>
<a href="/index.html#services">Services</a>
</li>
<li>
<a href="/index.html#about">About</a>
</li>
<li>
<a href="/index.html#team">Team</a>
</li>
<li>
<a href="/index.html#funders">Funders</a>
</li>
<li>
<a href="/index.html#contact">Contact</a>
</li>
</ul>
<!-- /Main navigation -->

</div>
</nav>
<!-- /Nav -->

<!-- header wrapper -->
<!-- <div class="header-wrapper sm-padding bg-grey">
<div class="container">
<h2>Publications</h2>
<ul class="breadcrumb">
<li class="breadcrumb-item">
<a href="/#home">Home</a>
</li>
<li class="breadcrumb-item active">Publications</li>
</ul>
</div>
</div> -->
<!-- /header wrapper -->

</header>
<!-- /Header -->

<!-- Publications -->
<div id="blog" class="section md-padding">
<div class="overlay"></div>

<!-- Container -->
<div class="container">

<!-- Row -->
<div class="row">

<!-- Main -->
<main>
<h2>combatTB and combat-SARS-Cov-2 Workbench</h2>

<p>The combatTB project has produced two Workbench platforms, for analysis of <em>M. tuberculosis</em> (Mtb)
and SARS-CoV-2 sequence data. The first of these, for analysis Mtb data, is described in this
<a href="https://journals.asm.org/doi/10.1128/msphere.00991-21">publication</a> in mSphere. Code
for deploying the combatTB Workbench can be found
<a href="https://github.com/COMBAT-TB/irida-galaxy-deploy">here</a>.
</p>

<p>The work on the combatTB Workbench led to the development of a similar Workbench for SARS-CoV-2.
The code for deploying the "combat-SARS-Cov-2 Workbench" can be found
<a href="https://github.com/combat-sars-cov-2/workbench-deploy">here</a>. Funding from the
Africa CDC <a href="https://africacdc.org/institutes/ipg/">Institute for Pathogen Genomics (IPG)</a>
allowed us to deploy an instance of the Workbench at
<a href="https://workbench.sanbi.ac.za/login">workbench.sanbi.ac.za</a> for use by labs
supported by the IPG's Pathogen Genomics Initiative.
</p>
</main>
<!-- /Main -->

</div>
<!-- /Row -->

</div>
<!-- /Container -->

</div>
<!-- /Publications -->

<!-- Footer -->
<footer id="footer" class="sm-padding bg-dark">

<!-- Container -->
<div class="container">

<!-- Row -->
<div class="row">

<div class="col-md-12">

<!-- footer logo -->
<div class="footer-logo">
<a href="/index.html">
<img src="/img/ctblogo-alt.png" alt="logo">
</a>
</div>
<!-- /footer logo -->

<!-- footer follow -->
<ul class="footer-follow">
<li>
<a href="https://github.com/COMBAT-TB" aria-label="COMBAT-TB">
<i class="fa fa-github"></i>
</a>
</li>
<li>
<a href="https://twitter.com/SANBI_SA" aria-label="SANBI_SA">
<i class="fa fa-twitter"></i>
</a>
</li>
</ul>
<!-- /footer follow -->

<!-- footer copyright -->
<div class="footer-copyright">
<p>Copyright ©
<script>
document.write(new Date().getFullYear())

</script>. All Rights Reserved.
</p>
<p>
<small>
With
<i class="fa fa-heart"></i>
by
<a href="https://thobalose.co.za" target="_blank" rel="noopener">Thoba Lose</a>
</small>
</p>

</div>
<!-- /footer copyright -->

</div>

</div>
<!-- /Row -->

</div>
<!-- /Container -->

</footer>
<!-- /Footer -->

<!-- Back to top -->
<div id="back-to-top"></div>
<!-- /Back to top -->

<!-- Preloader -->
<div id="preloader">
<div class="preloader">
<span></span>
<span></span>
<span></span>
</div>
</div>
<!-- /Preloader -->

<!-- jQuery Plugins -->
<script type="text/javascript" src="/js/jquery.min.js"></script>
<script type="text/javascript" src="/js/bootstrap.min.js"></script>
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<script type="text/javascript" src="/js/jquery.dataTables.min.js"></script>
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<script type="text/javascript" src="/js/dataTables.bootstrap.min.js"></script>
<script>
$(document).ready(function () {
$('#manuscripts').DataTable();
});

</script>

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