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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">
<!-- The above 3 meta tags *must* come first in the head; any other head content must come *after* these tags -->
<title>KnetMiner</title>
<!-- Bootstrap -->
<link href="css/bootstrap.css" rel="stylesheet">
<link href="style_knetminer.css" rel="stylesheet">
<link href="https://fonts.googleapis.com/css?family=Kanit|Play" rel="stylesheet"> <!-- used font is Play -->
<link rel="shortcut icon" href="images/favicon.ico" >
<meta name="description" content="KnetMiner - Mining and prioritizing candidate genes in integrated Ondex networks for plant and animal genomes.">
<meta name="Keywords" content="KnetMiner, tool, Gene, Genome, QTL, Ondex, Plant, Animal, Data Mining, Candidate Gene, Ranking, Prioritization, Bioinformatics" />
<!-- 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:// -->
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<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
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<![endif]-->
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<script>
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})(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
ga('create', 'UA-88753233-1', 'auto');
ga('send', 'pageview');
</script>
</head>
<body>
<nav class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container-fluid">
<!-- mobile display -->
<div class="navbar-header">
<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#bs-example-navbar-collapse-1" aria-expanded="false">
<span class="sr-only">Menue hide/unhide</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<a href="http://knetminer.rothamsted.ac.uk/"><img class="logo-top" src="images/logo-regular.png" height="50" alt="Logo"></a>
</div>
<div class="navi collapse navbar-collapse" id="bs-example-navbar-collapse-1">
<ul class="nav navbar-nav" id="top">
<li><a target="_blank" href="https://github.com/Rothamsted/knetminer/">GitHub</a></li>
<li><a target="_blank" href="http://knetminer.rothamsted.ac.uk/KnetMiner_Tutorial.pdf">User Guide</a></li>
<li><a href="publications.html">Publications</a></li>
</ul>
</div>
</div>
</nav> <!-- end navbar -->
<div class="carousel">
<!--carousel -->
<div id="my-carousel" class="carousel slide" data-interval="false">
<ol class="carousel-indicators">
<li data-target="#my-carousel" data-slide-to="0" class="active"></li>
<li data-target="#my-carousel" data-slide-to="1"></li>
<li data-target="#my-carousel" data-slide-to="2"></li>
</ol>
<div class="carousel-inner" role="listbox">
<div class="item active">
<img class="slide" src="images/first-pic2.jpg" alt="First Slide">
<div class="carousel-caption">
<h1 class="subtitle">Evidence-based Gene Discovery</h1>
<h2>User friendly, systematic gene selection for desktop and mobile devices</h2>
</div>
</div>
<div class="item">
<img class="slide" src="images/3field.jpg" alt="Second Slide">
<div class="carousel-caption">
<h1 class="subtitle">From Genotype to Phenotype via Networks</h1>
<h2>Understanding the genes and networks controlling complex traits</h2>
</div>
</div>
<div class="item">
<img class="slide" src="images/test2.jpg" alt="Third Slide">
<div class="carousel-caption">
<h1 class="subtitle">Fast search and query of large knowledge networks</h1>
<h2>Interactive apps to filter, visualise and explore data</h2>
</div>
</div>
</div> <!-- End carousel-inner -->
<!-- Glyphicon carousel -->
<a class="left carousel-control" href="#my-carousel" role="button" data-slide="prev">
<span class="glyphicon glyphicon-chevron-left" aria-hidden="true"></span>
</a>
<a class="right carousel-control" href="#my-carousel" role="button" data-slide="next">
<span class="glyphicon glyphicon-chevron-right" aria-hidden="true"></span>
</a>
</div>
</div> <!-- End carousel -->
<!-- Video carousel -->
<div class="slider-container hidden-xs">
<div class="row">
<div class="col-xs-12 col-sm-12 col-md-12">
<div id="Carousel" class="carousel slide" data-interval="false">
<ol class="carousel-indicators">
<li data-target="#Carousel" data-slide-to="0" class="active"></li>
<li data-target="#Carousel" data-slide-to="1"></li>
</ol>
<!-- Carousel items -->
<div class="carousel-inner">
<div class="item active">
<div class="row">
<div class="col-xs-12 col-sm-4 col-md-4">
<video controls width="300" class="video-geno">
<source src="videos/video_search_interface.mp4" type="video/mp4"/>
</video>
<h4 class="text-video"><strong>KnetMiner Search Interface</strong></h4>
<p class="text-video">Finding a link between drought tolerance and trehalose</p>
</div>
<div class="col-xs-12 col-sm-4 col-md-4">
<video controls width="300" class="video-geno">
<source src="videos/GenoMap.mp4" type="video/mp4"/>
</video>
<h4 class="text-video"><strong>KnetMiner Map View</strong></h4>
<p class="text-video">Visualising GWAS, QTL, SNP and genes in the interactive GenoMaps.js</p>
</div>
<div class="col-xs-12 col-sm-4 col-md-4">
<video controls width="300" class="video-geno">
<source src="videos/Video2.mp4" type="video/mp4" />
</video>
<h4 class="text-video"><strong>KnetMiner Network View</strong></h4>
<p class="text-video">Visualising knowledge networks in the interactive KnetMaps.js</p>
</div>
</div><!--.row-->
</div><!--.item-->
<div class="item">
<div class="row">
<div class="col-sm-4 col-md-4">
<video controls width="300" class="video-geno">
<source src="videos/Video3.mp4" type="video/mp4" />
</video>
<h4 class="text-video"><strong>Connecting the dots with KnetMiner</strong></h4>
<p class="text-video">Interrogating GWAS and interaction data to unveil complex traits in Arabidopsis.</p>
</div>
<div class="col-sm-4 col-md-4">
<img class="video-geno" src="images/new-videos.jpg"/>
<h4 class="text-video"><strong>We are working on new videos</strong></h4>
</div>
<div class="col-sm-4 col-md-4">
<img class="video-geno" src="images/new-videos.jpg"/>
<h4 class="text-video"><strong>We are working on new videos</strong></h4>
</div>
</div><!--.row-->
</div><!--.item-->
</div><!--.carousel-inner-->
<a data-slide="prev" href="#Carousel" class="left carousel-control">‹</a>
<a data-slide="next" href="#Carousel" class="right carousel-control">›</a>
</div><!--.Carousel-->
</div>
</div>
</div><!--.container-->
<!--video carousel for mobile devices-->
<div id="video-carousel" class="carousel hidden-sm hidden-md hidden-lg">
<!--carousel -->
<div class="carousel slide">
<ol class="carousel-indicators">
<li data-target="#video-carousel" data-slide-to="0" class="active"></li>
<li data-target="#video-carousel" data-slide-to="1"></li>
<li data-target="#video-carousel" data-slide-to="2"></li>
<li data-target="#video-carousel" data-slide-to="3"></li>
<li data-target="#video-carousel" data-slide-to="4"></li>
<li data-target="#video-carousel" data-slide-to="5"></li>
</ol>
<div class="carousel-inner" role="listbox">
<div class="item active">
<video controls width="300" class="video-geno">
<source src="videos/first-video.mp4" type="video/mp4"/>
</video>
<h4 class="text-video"><strong>Introducing KnetMiner with a use case</strong></h4>
<p class="text-video">Demo of the KnetMiner user interface and its capabilities for evidence-based gene discovery.</p>
</div>
<div class="item">
<video controls width="300" class="video-geno">
<source src="videos/GenoMap.mp4" type="video/mp4"/>
</video>
<h4 class="text-video"><strong>New Map View using GenoMaps.js</strong></h4>
<p class="text-video">Visualisation of GWAS, QTL, SNP and KnetMiner genes on an interactive chromosome map.</p>
</div>
<div class="item">
<video controls width="300" class="video-geno">
<source src="videos/Video2.mp4" type="video/mp4" />
</video>
<h4 class="text-video"><strong>New Network View using KnetMaps.js</strong></h4>
<p class="text-video">Visualise and explore the biological knowledge networks produced by KnetMiner.</p>
</div>
<div class="item">
<video controls width="300" class="video-geno">
<source src="videos/Video3.mp4" type="video/mp4" />
</video>
<h4 class="text-video"><strong>Connecting the dots with KnetMiner</strong></h4>
<p class="text-video">Interrogating GWAS and interaction data to unveil complex traits in Arabidopsis.</p>
</div>
<div class="item">
<img class="video-geno" src="images/new-videos.jpg"/>
<h4 class="text-video"><strong>We are working on new videos</strong></h4>
</div>
<div class="item">
<img class="video-geno" src="images/new-videos.jpg"/>
<h4 class="text-video"><strong>We are working on new videos</strong></h4>
</div>
</div> <!-- End carousel-inner -->
<!-- Glyphicon carousel -->
<a class="left carousel-control" href="#video-carousel" role="button" data-slide="prev">
<span class="glyphicon glyphicon-circle-arrow-left" aria-hidden="true"></span>
</a>
<a class="right carousel-control" href="#video-carousel" role="button" data-slide="next">
<span class="glyphicon glyphicon-circle-arrow-right" aria-hidden="true"></span>
</a>
</div>
</div><!-- End carousel -->
<!-- End slider for mobile -->
<!-- beginning of content -->
<div id="content" class="col-xs-12 col-sm-12 col-md-12 col-lg-12 container-fluid">
<div class="col-xs-12 col-sm-12 col-md-8 col-lg-8">
<h4>Available KnetMiners for Plant and Animal networks</h4>
</div>
<div class="col-xs-12 col-sm-7 col-md-7 col-lg-8"> <!-- div imgages-->
<div class="network-images col-xs-4 col-sm-4 col-md-4 col-lg-3">
<a href="http://knetminer.rothamsted.ac.uk/Arabidopsis_thaliana/">
<div class="subqtl">
<div class="testpics">
<img class="testpics" src="images/pic_arabidopsis1.png" width="170" height="170"/>
<div class="mask">
<p>Arabidopsis </br>
Araport 11</p>
</div>
<span><p>Arabidopsis</p></span> <!-- needed to center short names-->
</div>
</div>
</a>
</div>
<div class="network-images col-xs-4 col-sm-4 col-md-4 col-lg-3">
<a href="http://knetminer.rothamsted.ac.uk/Hordeum_vulgare/">
<div class="subqtl">
<div class="testpics">
<img class="testpics" src="images/pic_barley1.jpg" width="170" height="170"/>
<div class="mask">
<p>Barley</br>
ASM32608v1</p>
</div>
<span><p>Barley</p></span>
</div>
</div>
</a>
</div>
<div class="network-images col-xs-4 col-sm-4 col-md-4 col-lg-3">
<a href="https://qtlnetminerboleracea.appliedbioinformatics.com.au/">
<!-- <a href="https://knetbole.appliedbioinformatics.com.au/Brassica_oleracea/"> -->
<div class="subqtl">
<div class="testpics">
<img class="testpics" src="images/pic_boleracea_new.png" width="170" height="170"/>
<div class="mask">
<p>B.oleracea</br>
Version 3.0.0</p>
</div>
<span><p>B.oleracea</p></span>
</div>
</div>
</a>
</div>
<div class="network-images col-xs-4 col-sm-4 col-md-4 col-lg-3">
<a href="http://qtlnetminercicer.appliedbioinformatics.com.au/">
<div class="subqtl">
<div class="testpics">
<img class="testpics" src="images/chickpea.png" width="170" height="170"/>
<div class="mask">
<p>Chickpea</br>
Version 3.0.0</p>
</div>
<span><p>Chickpea</p></span>
</div>
</div>
</a>
</div>
<!-- new QTLNetMiner Maize -->
<div class="network-images col-xs-4 col-sm-4 col-md-4 col-lg-3">
<a href="http://knetminer.rothamsted.ac.uk/Zea_mays/">
<div class="subqtl">
<div class="testpics">
<img class="testpics" src="images/pic_maize.png" width="170" height="170"/>
<div class="mask">
<p>Maize</br>
AGPv4</p>
</div>
<span><p>Maize</p></span>
</div>
</div>
</a>
</div>
<div class="network-images col-xs-4 col-sm-4 col-md-4 col-lg-3">
<a href="http://knetminer.rothamsted.ac.uk/Populus_trichocarpa/">
<div class="subqtl">
<div class="testpics">
<img class="testpics" src="images/pic_poplar1.png" width="170" height="170"/>
<div class="mask">
<p>Poplar</br>
Populus trichocarpa v3.1</p>
</div>
<span><p>Poplar</p></span>
</div>
</div>
</a>
</div>
<div class="network-images col-xs-4 col-sm-4 col-md-4 col-lg-3">
<a href="http://knetminer.rothamsted.ac.uk/Solanum_tuberosum/">
<div class="subqtl">
<div class="testpics">
<img class="testpics" src="images/pic_potato1.png" width="170" height="170"/>
<div class="mask">
<p>Potato</br>
SolTub_3.0</p>
</div>
<span><p>Potato</p></span>
</div>
</div>
</a>
</div>
<div class="network-images col-xs-4 col-sm-4 col-md-4 col-lg-3">
<a href="http://knetminer.rothamsted.ac.uk/Solanaceae/">
<div class="subqtl">
<div class="testpics">
<img class="testpics" src="images/sol1.png" width="170" height="170"/>
<div class="mask">
<p>Solanacea</br>
SL2.50</p>
</div>
<span><p>Solanaceae</p></span>
</div>
</div>
</a>
</div>
<div class="network-images col-xs-4 col-sm-4 col-md-4 col-lg-3">
<a href="http://knetminer.rothamsted.ac.uk/Triticum_aestivum/">
<div class="subqtl">
<div class="testpics">
<img class="testpics" src="images/pic_wheat1.png" width="170" height="170"/>
<div class="mask">
<p>Wheat</br>
TGAC_v1</p>
</div>
<span><p>Wheat</p></span>
</div>
</div>
</a>
</div>
<div class="network-images col-xs-4 col-sm-4 col-md-4 col-lg-3">
<a href="http://knetminer.rothamsted.ac.uk/Gallus_gallus/">
<div class="subqtl">
<div class="testpics">
<img class="testpics" src="images/pic_chicken.png" width="170" height="170"/>
<div class="mask">
<p>Chicken</br>
Version 3.0.1</p>
</div>
<span><p>Chicken</p></span>
</div>
</div>
</a>
</div>
<!-- <div class="network-images col-xs-4 col-sm-4 col-md-4 col-lg-3">
<a href="http://knetminer.rothamsted.ac.uk/Bos_taurus/">
<div class="subqtl">
<div class="testpics">
<img class="testpics" src="images/pic_cow1.png" width="170" height="170"/>
<div class="mask">
<p>Cow</br>
Version 3.0.1</p>
</div>
<span><p>Cow</p></span>
</div>
</div>
</a>
</div> -->
<div class="network-images col-xs-4 col-sm-4 col-md-4 col-lg-3">
<a href="http://knetminer.rothamsted.ac.uk/Sus_scrofa/">
<div class="subqtl">
<div class="testpics">
<img class="testpics" src="images/pic_pig1.png" width="170" height="170"/>
<div class="mask">
<p>Pig</br>
Version 3.0.1</p>
</div>
<span><p>Pig</p></span>
</div>
</div>
</a>
</div>
<!-- <div class="network-images col-xs-4 col-sm-4 col-md-4 col-lg-3">
<a href="http://knetminer.rothamsted.ac.uk/Salix_viminalis/">
<div class="subqtl">
<div class="testpics">
<img class="testpics" src="images/willow.jpg" width="170" height="170"/>
<div class="mask">
<p>Willow</br>
Version 3.0.1</p>
</div>
<span><p>Willow</p></span>
</div>
</div>
</div> -->
<div class="network-images col-xs-4 col-sm-4 col-md-4 col-lg-3">
<a href="http://knetminer.rothamsted.ac.uk/HumanDisease/">
<div class="subqtl">
<div class="testpics">
<img class="testpics" src="images/humanDisease.png" width="170" height="170"/>
<div class="mask">
<p>Human Diseases</br>
Version 3.0.1</p>
</div>
<span><p>Human Diseases</p></span>
</div>
</div>
</a>
</div>
<div class="network-images col-xs-4 col-sm-4 col-md-4 col-lg-3">
<a href="http://knetminer.rothamsted.ac.uk/Fusarium_graminearum/">
<div class="subqtl">
<div class="testpics">
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<p>Fusarium graminearum</br>
Version RR.34</p>
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<a href="http://knetminer.rothamsted.ac.uk/Zymoseptoria_tritici/">
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<p>Zymoseptoria tritici</br>
Version MG2.34</p>
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<span><p>Z.tritici</p></span> <!-- needed to center short names-->
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<h1 style="padding-left:20px;">Description and Features<span style="color:darkorange;opacity: 0.7;">...</span></h1>
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<h4><strong>About KnetMiner</strong></h4>
<p>KnetMiner (with a silent K) stands for Knowledge Network Miner and is a suite of tools to integrate, search and explore large biological knowledge networks.
It is used to accelerate gene discovery, decision making and hypothesis generation across species.</p>
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<h4><strong>Building knowledge networks</strong></h4>
<p >Knowledge networks are generated from public and private data using either the free <a title="Ondex KnetBuilder" class="links-text" target="_blank" href="https://github.com/Rothamsted/ondex-knet-builder">
Ondex-KnetBuilder</a> (limited support) or the paid <a class="links-text" title="Genestack-KnetMiner" target="_blank" href="https://genestack.com/blog/2017/02/06/pag-our-thoughts-workshop-slides-and-recordings/">
Genestack-KnetBuilder</a> App (web-interface, good support). For more information, visit our <a class="links-text" title="Wiki" target="_blank" href="https://github.com/Rothamsted/ondex-knet-builder/wiki/Building-Knowledge-Networks">wiki</a> and read our paper <a class="links-text" title="Hassani-Pak et al.(2016)" target="_blank" href="http://www.sciencedirect.com/science/article/pii/S2212066116300308/"> Hassani-Pak et al. (2016)</a>.
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<h4><strong>Searching knowledge networks</strong></h4>
<p>KnetMiner performs over 70 graph queries to find direct or indirect links between genes and user provided search terms.
It is very fast through smart graph-indexing and has features like real-time user feedback and query term suggestions.
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<h4><strong>Develop your own KnetMiner</strong></h4>
<p>The KnetMiner code is open-source and customisable. You can host your own KnetMiner server or use the paid Genestack-KnetMiner Platform to easily deploy a KnetMiner server in the cloud. <a class="links-text" title="Contact Page" href="contact.html">Contact us</a> for more information.</p>
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<h4><strong>Candidate gene prioritisation</strong></h4>
<p>The gene ranking algorithm takes into account how specific each evidence concept is to a gene and the frequency of all evidence concepts in a gene-evidence network. We are constantly exploring new ways of ranking genes.
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<h4><strong>Recently funded Projects</strong></h4>
<p>We currently receive funding through an <a class="links-text" title="UK grant" href=" http://gtr.rcuk.ac.uk/projects?ref=132162/">Innovate UK grant</a> to make KnetMiner accessible in <a class="links-text" title="GeneStack" href="http://www.genestack.com">Genestack</a>,
a <a class="links-text" title=" BBSRC grant" href=" http://gtr.rcuk.ac.uk/projects?ref=BB/N022874/1"> BBSRC grant</a> to develop DiseaseNetMiner for crop-pathogen interactions and another BBSRC grant <a class="links-text" title="DFW" href="https://www.rothamsted.ac.uk/projects/designing-future-wheat-dfw">Designing Future Wheat</a> to improve accessibility of wheat data.</p>
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