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<h1>D-NetWeaver Overview</h1>
				<p>D-NetWeaver is an application to enable the manipulation and
					analysis of time course
					data matrices, such as gene expression data
					as generated by microarray
					or RNA-seq
					experiments. It is
					specifically
					geared toward reconstructing gene regulatory networks from time
					course gene expression data using differential equation network
					models.
				</p>
				<p>It provides the ability to apply six primary steps to gene
					expression data:
				</p>
				<ol>
					<li>Significant gene detection</li>
					<li>Clustering</li>
					<li>Smoothing</li>
					<li>Functional enrichment analysis</li>
					<li>Regulation identification (otherwise known as variable
						selection of differential equation network models)
					</li>
					<li>Parameter estimation refinement</li>
				</ol>
				<p>The software provides many data manipulation and data visualization features to assist 
				users in exploring their data and interpreting the results of these six primary steps.</p>
				
				<p>The end goal is the creation of a dynamic network
					model.
					Currently, the only supported model is the linear ordinary
					differential equation (ODE) model (Lu et al. (2011); see "Papers"
					in the help menus for the manuscript).
				</p>
				<div id="dl">
				<h2 id="dld"style="border: 0;"> <a id="dla" href="https://cbim.urmc.rochester.edu/software/d-netweaver/dnetweaver.jar" onClick="_gaq.push(['_trackEvent', 'Software', 'Download', 'D-NetWeaver']);">Download D-NetWeaver, version 1.0</a></h2></div>
				<p>D-NetWeaver runs on any major OS, such as Windows, Mac OS, and Linux.  If you already have
				Java installed on your machine, running D-NetWeaver usually requires just double-clicking on
				the jar file.  Otherwise, you can run D-NetWeaver via a command such as:</p>
				
				<code>java -Xmx1g -jar dnetweaver.jar</code>
				
				<p>D-NetWeaver requires Java 1.6 or higher and R 2.15 or higher to run correctly.  You can
				download Java from <a href="http://java.com">Java.com</a> and you can download R from 
				<a href="http://www.r-project.org/index.html">http://www.r-project.org/index.html</a></p>
				
		<h2>Screenshots</h2>
		<h3>Cluster Results</h3>
		<img src="images/cluster_shot.png">
		<p/>
		<h3>Cluster Annotation</h3>
		<img src="images/cluster_annotation.png"/>
		<p/>
		<h3>Network Model</h3>
		<img src="images/network_model.png"/>
		<h2>Acknowledgements</h2>
		<P>Software was created by University of Rochester Center for Biodefense Immune Modeling with funding from NIAID HHSN272201000055C</P>
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