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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, with a silent K and standing for Knowledge Network Miner, is a suite of open-source software tools for gene mining and biological knowledge discovery.">
<meta name="Keywords" content="KnetMiner, software, tool, Gene, Genome, QTL, Ondex, GWAS, Plant, Crop, Big Data, Data Mining, Candidate Gene, Ranking, Prioritization, Bioinformatics, Visualization" />
<!-- 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]-->
<script src="https://use.fontawesome.com/a90751c39e.js"></script>
<!-- Google Analytics -->
<script>
(function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
(i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
})(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/releases">What's new?</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">KnetMiner web app and knowledge graphs</h1>
<h2>Making biological discoveries faster and fun</h2>
</div>
</div>
<div class="item">
<img class="slide" src="images/3field.jpg" alt="Second Slide">
<div class="carousel-caption">
<h1 class="subtitle">Telling the stories of complex traits</h1>
<h2>From genotype to phenotype via gene networks</h2>
</div>
</div>
<div class="item">
<img class="slide" src="images/test2.jpg" alt="Third Slide">
<div class="carousel-caption">
<h1 class="subtitle">Connecting data, technology and humans</h1>
<h2>To provide the best user experience</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>
<li data-target="#Carousel" data-slide-to="2"></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/KnetMiner-About.mp4" type="video/mp4"/>
</video>
<h4 class="text-video"><strong>Introducing KnetMiner</strong></h4>
<p class="text-video">Short clip to introduce the KnetMiner approach</p>
</div>
<div class="col-xs-12 col-sm-4 col-md-4">
<video controls width="300" class="video-geno">
<source src="videos/Wheat-KnetMiner-v2.mp4" type="video/mp4"/>
</video>
<h4 class="text-video"><strong>KnetMiner Overview</strong></h4>
<p class="text-video">KnetMiner user interface and key features</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 Networks</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">
<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/KnetMiner-Intro.mp4" type="video/mp4"/>
</video>
<h4 class="text-video"><strong>KnetMiner walkthrough</strong></h4>
<p class="text-video">Using the KnetMiner search interface and exploring networks</p>
</div>
</div><!--.row-->
</div><!--.item-->
<div class="item">
<div class="row">
<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 more 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/KnetMiner-About.mp4" type="video/mp4"/>
</video>
<h4 class="text-video"><strong>Introducing KnetMiner</strong></h4>
<p class="text-video">Short clip to introduce the KnetMiner approach</p>
</div>
<div class="item">
<video controls width="300" class="video-geno">
<source src="videos/Wheat-KnetMiner-v2.mp4" type="video/mp4"/>
</video>
<h4 class="text-video"><strong>KnetMiner Overview</strong></h4>
<p class="text-video">KnetMiner user interface and key features</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>KnetMiner Networks</strong></h4>
<p class="text-video">Visualising knowledge networks in the interactive KnetMaps.js</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">
<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="item">
<img class="video-geno" src="images/new-videos.jpg"/>
<h4 class="text-video"><strong>We are working on new videos</strong></h4>
</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 -->
</div><!-- 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>Examples of public KnetMiner species</h4>
</div>
<div class="col-xs-12 col-sm-7 col-md-7 col-lg-8"> <!-- div images-->
<!-- KetMiner Wheat -->
<div class="network-images col-xs-4 col-sm-4 col-md-4 col-lg-4">
<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>Triticum aestivum</br>
IWGSC RefSeq v1.1</p>
</div>
<span><p>Wheat</p></span>
</div>
</div>
</a>
</div>
<!-- KetMiner Arabidopsis -->
<div class="network-images col-xs-4 col-sm-4 col-md-4 col-lg-4">
<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 thaliana</br>
TAIR10</p>
</div>
<span><p>Arabidopsis</p></span> <!-- needed to center short names-->
</div>
</div>
</a>
</div>
<!-- KetMiner Rice (IRRI) -->
<div class="network-images col-xs-4 col-sm-4 col-md-4 col-lg-4">
<a href="http://knetminer.rothamsted.ac.uk/Oryza_sativa/">
<div class="subqtl">
<div class="testpics">
<img class="testpics" src="images/Rice.jpg" width="170" height="170"/>
<div class="mask">
<p>Oryza sativa Japonica</br>
IRGSP-1.0</p>
</div>
<span><p>Rice</p></span> <!-- needed to center short names-->
</div>
</div>
</a>
</div>
<!-- KetMiner 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>Zea mays</br>
AGPv4</p>
</div>
<span><p>Maize</p></span>
</div>
</div>
</a>
</div> -->
<!-- KetMiner B.oleracea -->
<!-- <div class="network-images col-xs-4 col-sm-4 col-md-4 col-lg-3">
<a href="https://qtlnetminerboleracea.appliedbioinformatics.com.au/">
<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> -->
<!-- KetMiner Cicer -->
<!-- <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> -->
<!-- KetMiner Poplar -->
<!-- <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>Populus trichocarpa</br>
Version 3.1</p>
</div>
<span><p>Poplar</p></span>
</div>
</div>
</a>
</div> -->
<!-- KetMiner Solanaceae -->
<!-- <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> -->
<!-- KetMiner Potato -->
<!-- <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>Solanum tuberosum</br>
SolTub_3.0</p>
</div>
<span><p>Potato</p></span>
</div>
</div>
</a>
</div> -->
<!-- KetMiner Barley -->
<!-- <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>Hordeum vulgare</br>
ASM32608v1</p>
</div>
<span><p>Barley</p></span>
</div>
</div>
</a>
</div> -->
<!-- KetMiner Chicken -->
<!-- <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> -->
<!-- KetMiner Cow -->
<!-- <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/">
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<h4><strong>About KnetMiner</strong></h4>
<p>KnetMiner, with a silent "K" and standing for Knowledge Network Miner, is a web-app that makes biological knowledge discovery faster and fun.
It helps scientists to connect and search across databases and the scientific literature to find links between genes, traits, diseases and many other types of biological information.
Try one of the public KnetMiner demo species.
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<h4><strong>KnetMiner knowledge graphs</strong></h4>
<p >KnetMiner knowledge graphs are built using the open-source <a title="Ondex-KnetBuilder" class="links-text" target="_blank" href="https://github.com/Rothamsted/ondex-knet-builder">
Ondex data integration platform</a> and are available in different flavours such as <a class="links-text" title="RDF" target="_blank" href="https://www.w3.org/RDF/">RDF</a> and <a class="links-text" title="Neo4j" target="_blank" href="https://www.neo4j.com">Neo4j</a>.
We are experts in data integration and offer our expertise as a service. We can build bespoke knowledge graphs for your species of interest.
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<h4><strong>Searching knowledge graphs</strong></h4>
<p>KnetMiner performs over 70 graph queries of varying depths to find paths between genes and evidence nodes.
It highlights paths that are more important and provides features to gradually expand networks.
KnetMiner knowledge graphs can also be searched programmatically through web APIs, Cypher and SPARQL endpoints.
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<h4><strong>Deploy KnetMiner in the cloud</strong></h4>
<p>KnetMiner can be deployed in the AWS Cloud using Docker. KnetMiner is also available as an App in the <a class="links-text" title="Genestack" target="_blank" href="http://www.genestack.com">Genestack</a> platform.
The KnetMiner-Genestack App allows users to integrate their own private data into the knowledge graph. For more information, read our <a class="links-text" title="KnetMiner-Genestack" target="_blank" href="https://www.rothamsted.ac.uk/news/visualising-data-connections-promises-faster-discoveries">press release</a> and request the <a class="links-text" title="KnetMiner-Genestack" target="_blank" href="https://genestack.com/landings/ebook-knetminer-multi-omics-network-mining/">KnetMiner-Genestack eBook</a>.
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<h4><strong>KnetMiner Gene Rank</strong></h4>
<p>The KnetMiner Gene Rank algorithm takes into account the specificity, connectivity and distance of each piece of evidence in the gene knowledge graph.
It is very fast through the use of a graph database and a pre-build index.
It's not always easy to rank genes, so KnetMiner allows users to refine the results using their own domain expertise and assumptions.
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<h4><strong>Working with us</strong></h4>
<p>Get in touch with us if you need <a class="links-text" title="Contact" target="_blank" href="contact.html">help</a>, have <a class="links-text" title="Git Issues" target="_blank" href="https://github.com/Rothamsted/knetminer/issues">feature requests</a> or would like to contribute to one of our <a class="links-text" title="GitHub" target="_blank" href="https://github.com/Rothamsted">open-source projects</a>.
KnetMiner is used by thousands of users around the world from academia to industry. We aim to provide top user experience and always value user feedback.</p>
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