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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<title>National Resource for Network Biology</title>
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<meta name="description" content="">
<meta name="author" content="">
<!-- Le styles -->
<link href="assets/css/bootstrap.css" rel="stylesheet">
<link href="assets/css/bootstrap-responsive.css" rel="stylesheet">
<link href="assets/css/nrnb.css" rel="stylesheet">
<!-- HTML5 shim, for IE6-8 support of HTML5 elements -->
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<script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script>
<![endif]-->
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<link rel="shortcut icon" href="assets/ico/favicon.ico">
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</head>
<body>
<div class="belt top">
<div class="container">
<div class="row top-right">
<div class="span5 offset7">
<div class="row">
<img class="logo-big" src="images/NRNB_white.svg" />
<h2>National Resource for Network Biology</h2>
</div>
<div class="row buttons">
<a class="button-flat" href="projects.html">Research Projects</a>
<a class="button-flat" href="tools.html">Tools</a>
<a class="button-flat" href="training.html">Training</a>
<a class="button-flat" href="outreach.html">Collaboration</a>
<a class="button-flat" href="#highlights">Research Highlights</a>
</div>
<!-- Begin iQuery widget-->
<div class="row">
<div class="col-md-4 col" style="padding-top: 25px">
<h2>Analyze Your Genes With NDEx iQuery</h2>
<div class="form-group blue-border-focus" style="margin-bottom: 0px auto">
<textarea style="padding-top: 5px; width: 338px" class="form-control" id="geneSet_input" rows="2" placeholder="Type or paste your list of genes here..."></textarea>
</div>
<div class="row-buttons">
<input type="submit" value="Analyze Now!" style="float:left; margin-top: 0px" id="openGeneSetButton" class="button-flat btn-blue" disabled="">
</div>
<script>
document.getElementById("geneSet_input").addEventListener("keyup", function() {
var nameInput = document.getElementById('geneSet_input').value;
if (nameInput != "") {
document.getElementById('openGeneSetButton').removeAttribute("disabled");
} else {
document.getElementById('openGeneSetButton').setAttribute("disabled", null);
}
});
document.getElementById('openGeneSetButton').disabled = true;
document.getElementById('openGeneSetButton').addEventListener('click', function(e) {
var geneSet = document.getElementById("geneSet_input").value;
geneSet = geneSet.replace(/\s/g, ",")
console.log(geneSet)
var baseUrl = 'https://www.ndexbio.org/iquery?genes=';
console.log(baseUrl + encodeURIComponent(geneSet));
window.open(baseUrl + encodeURIComponent(geneSet));
e.preventDefault();
return false;
});
</script>
</div>
</div>
<!--End iQuery widget-->
</div>
</div>
</div>
</div>
<div class="belt white">
<div class="container">
<div class="row section">
<h3>What is NRNB?</h3>
</div>
<div class="row">
<div class="span4">
<iframe width="100%" src="https://www.youtube.com/embed/_nbqSe4Zaps?rel=0" frameborder="0" allowfullscreen></iframe>
</div>
<div class="span8">
<p>
The aim of the <b>National Resource for Network Biology (NRNB)</b>
is to advance the new science of
Biological Networks through analytic tools, visualizations, databases and computing resources.
Biomedical research is increasingly dependent on knowledge of biological networks of multiple
types and
scales, including gene, protein and drug interactions, cell-cell and cell-host communication,
and vast
social networks. Our technologies enable researchers to assemble and analyze these networks and
to
use
them to better understand biological systems and, in particular, how they fail in disease. NRNB
leverages the <a href="http://www.cytoscape.org/" target="_blank">Cytoscape</a> Cyberinfrastructure,
a widely-used network analysis
platform which we further support through a rich set of tutorials, workshops, 24/7 help desk
assistance,
and over 100 collaboration and service projects.</p>
<p> We are developing freely available, open source software
technologies to enable network-based visualization, analysis, and
biomedical discovery. We are driving research and development <a href="projects.html"><b>projects</b></a>, coordinating <a href="training.html"><b>training</b></a> opportunities, and
actively seeking new <a href="outreach.html"><b>collaborations</b></a>
to develop NRNB <a href="tools.html"><b>tools</b></a> and apply
them to biomedical research.
</p>
</div>
</div>
</div>
</div>
<div id="renewed"></div>
<div class="belt white">
<div class="container">
<div class="row section">
<h3>5-Year Funding Renewal</h3>
</div>
<div class="row">
<div class="span3">
<img src="images/NRNB_black.png" alt="nrnb logo">
</div>
<div class="span9">
<p>
We have been awarded another five years of funding by <a href="https://www.nigms.nih.gov/" target="_blank">NIGMS</a>
for the National Resource of Network Biology until 2025. We have identified three major themes of Differential Networks,
From Descriptive to Predictive and Multi-scale Network Representations in Network Biology that will define our
technology research and development projects. With this renewed investment, we will also continue to pursue a broad
range of <a href="./outreach">collaboration</a> and <a href="./training.html">training</a> opportunities.
</p>
</div>
</div>
</div>
</div>
<div id="highlights"></div>
<div class="belt white">
<div class="container">
<div class="row section">
<h3>Research Highlights</h3>
</div>
<div class="row belt">
<div class="span3">
<img src="images/NeXO.png" alt="image">
</div>
<div class="span9">
<p><b>Network Approach to Building Gene Ontologies</b><br />
<a href="http://nexontology.org/" target="_blank">NeXO</a> (The Network Extracted Ontology) uses a principled
computational approach which integrates evidence from hundreds of thousands of individual gene and
protein interactions to construct a complete hierarchy of cellular components and processes. This
data-derived ontology aligns with known biological machinery in the GO Database and also uncovers
many new structures.
</p>
</div>
</div>
<div class="row belt">
<div class="span3">
<img src="images/nbs.png" alt="image">
</div>
<div class="span9">
<p><b>Network-based stratification of tumor mutations</b><br />
<a href="http://www.nature.com/nmeth/journal/v10/n11/full/nmeth.2651.html" target="_blank">NBS</a> is a method for stratification (clustering) of patients in a cancer cohort based on somatic mutations and a gene interaction network. The method uses network propagation to integrate genome wide somatic mutation profiles for each patient over a gene interaction network, and a non-negative matrix factorization based clustering approach in order to derive biologically meaningful stratification of a patient cohort.
</p>
</div>
</div>
<div class="row belt">
<div class="span3">
<img src="images/cyappstore1.png" alt="image">
</div>
<div class="span9">
<p><b>Cytoscape App Store</b><br />
The overarching goals of the <a href="http://apps.cytoscape.org" target="_blank">Cytoscape App Store</a> are to
highlight the important features apps add to Cytoscape, to enable researchers to find apps they
need, and for developers to promote their apps. The Cytoscape App Store highlights the important
features that apps add to Cytoscape, enable researchers to find and install apps they need, and help
developers promote their apps.
</p>
</div>
</div>
<div class="row belt">
<div class="span3">
<img src="images/cBioPortal_2.png" alt="image">
</div>
<div class="span9">
<p><b>Network Analysis Tools</b><br />
Our research programs are exploring an array of new approaches to network analysis, such as how to
use
molecular networks to stratify cancer patient genomes (Network-Based Stratification) or how to
assemble
a gene ontology of the cell directly from molecular network data (<a href="http://www.nexontology.org/" target="_blank">nexontology.org</a>). In recent years
we
have released a number of widely-used network analysis resources, including the Cancer Biology
Portal
(<a href="http://www.cbioportal.org/public-portal/" target="_blank">cBioPortal.org</a>), the GeneMANIA network
database (<a href="http://genemania.org/" target="_blank">genemania.org</a>), and the Cytoscape Appstore
(<a href="http://apps.cytoscape.org/" target="_blank">apps.cytoscape.org</a>).
</p>
</div>
</div>
<a class="btn button-flat btn-gray pull-right" href="https://www.ncbi.nlm.nih.gov/pubmed/?term=GM103504" target="_blank">
Recent NRNB Publications
</a>
</div>
</div>
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