fixed broken links, layout

tools.html

@@ -73,7 +73,7 @@ <h3>NRNB Tools</h3>
         <div class="tab-content">
 
             <div class="tab-pane fade" id="amatreader-tab">
-                <iframe src="tools/amatreader.html" width="1170" height="1500"
+                <iframe src="tools/amatreader.html" width="1170" height="900"
                         frameborder="0" scrolling="auto"></iframe>
             </div>
 
@@ -128,7 +128,7 @@ <h3>NRNB Tools</h3>
             </div>
 
             <div class="tab-pane fade" id="string-tab">
-                <iframe src="tools/stringapp.html" width="1170" height="950"
+                <iframe src="tools/stringapp.html" width="1170" height="1100"
                         frameborder="0" scrolling="auto"></iframe>
             </div>
 

tools/cbioportal.html

@@ -31,22 +31,21 @@ <h3>cBio Portal</h3>
 	<h5>Documentation</h5>
 	<ul>
 	<li><a href="http://www.cbioportal.org" target="_blank">cBio Portal Website</a></li>
-	<li><a href="http://www.cbioportal.org/public-portal/tutorial.jsp" target="_blank">Tutorials</a>
+	<li><a href="https://docs.cbioportal.org/user-guide/overview/" target="_blank">Tutorials</a>
 	</li>
 	</ul>
 
 	<h5>Developer Resources</h5>
 	<ul>
-	<li><a href="http://www.cbioportal.org/public-portal/web_api.jsp" target="_blank">Web API</a></li>
-	</li>	
+	<li><a href="https://docs.cbioportal.org/web-api-and-clients/" target="_blank">Web API</a></li>	
 	</ul>
 
 	<h5>How to Cite</h5>
 	<ul>
 	<li><a href="http://cancerdiscovery.aacrjournals.org/content/2/5/401.long" target="_blank">
 	The cBio Cancer Genomics Portal: An Open Platform for Exploring Multidimensional Cancer Genomics Data.</a>
 	 Cerami et al., <i>Cancer Discovery</i> 2012</li>
-	<li><a href="http://stke.sciencemag.org/cgi/content/full/sigtrans;6/269/pl1" target="_blank">Integrative 
+	<li><a href="https://www.science.org/doi/10.1126/scisignal.2004088" target="_blank">Integrative 
 	Analysis of Complex Cancer Genomics and Clinical Profiles Using the cBioPortal.</a>
 	 Gao et al., <i>Science Signalling</i> 2013.</li>
 	</ul>

tools/clustermaker.html

@@ -18,7 +18,7 @@
 
 <h3>clusterMaker</h3>
 	<p>
-	The Cytoscape app <a href="http://www.rbvi.ucsf.edu/cytoscape/cluster/clusterMaker.shtml" target="_blank" >
+	The <a href="http://www.rbvi.ucsf.edu/cytoscape/cluster/clusterMaker.shtml" target="_blank" >
 	clusterMaker Cytoscape app</a>
 	unifies different clustering techniques and displays into a single interface. Current clustering algorithms include hierarchical, k-medoid, AutoSOME, and k-means for clustering expression or genetic data; and MCL, transitivity clustering, affinity propagation, MCODE, community clustering (GLAY), SCPS, and AutoSOME for partitioning networks based on similarity or distance values. Hierarchical, k-medoid, AutoSOME, and k-means clusters may be displayed as hierarchical groups of nodes or as heat maps. All of the network partitioning cluster algorithms create collapsible "meta nodes" to allow interactive exploration of the putative family associations within the Cytoscape network, and results may also be shown as a separate network containing only the intra-cluster edges, or with inter-cluster edges added back.	
 	</p>

tools/cynitoolbox.html

@@ -17,10 +17,9 @@
 <!-- PASTE HERE -->
 
 <h3>Cyni Toolbox</h3>
-<p>
-The Cytoscape app <a href="http://www.proteomics.fr/Sysbio/CyniProject" target="_blank" >
+<p>The Cytoscape app <a href="https://github.com/schwikowskilab/cyniProject" target="_blank" >
 Cyni Toolbox</a> puts together several tools 
-that allow infering networks from biological data. Each of the tools can be used independently or together to perform several tasks.<BR>
+that allow infering networks from biological data. Each of the tools can be used independently or together to perform several tasks.
 The goal of Cyni is to make network inference more accessible to biologists by providing user-friendly solution as well as provide a 
 framework to bio-informaticiens to develop and apply their new techniques. Data imputation and discretization techniques are provided 
 along with several known inference algorithms to make this tool fully operational for any kind inference requirement. While data 
@@ -51,7 +50,7 @@ <h5>Image Gallery</h5>
 <div class="thumbnail">
 <a href="../images/inferenceUIList.png" target="_blank"><img src="../images/inferenceUIList.png"
 alt="Cyni Toolbox 1" /></a>
-<div>
+    </div>
 </li>
 
 <li class="span4">
@@ -84,6 +83,6 @@ <h5>Image Gallery</h5>
 </li>
 </ul>
 </div>
-
+    </body>
 <!-- END PASTE -->
 </html>

tools/cytoscape.html

@@ -58,7 +58,7 @@ <h5>How to Cite</h5>
 	<h5>Image Gallery</h5>
 	<p>
 	In addition to these images, also see <a
-	href="http://cytoscape-publications.tumblr.com/" target="_blank">published figures using Cytoscape</a>.
+	href="https://www.ncbi.nlm.nih.gov/pmc/?term=(cytoscape+AND+network)&report=imagesdocsum&dispmax=100" target="_blank">published figures using Cytoscape</a>.
 	</p>
 
 	<div class="row-fluid">

tools/genemania.html

@@ -35,7 +35,7 @@ <h5>Documentation</h5>
 	<h5>Developer Resources</h5>
 	<ul>
 	<li><a href="http://pages.genemania.org/data/" target="_blank">Download Data</a></li>
-	<li><a href="http://pages.genemania.org/help/#linking-to-genemania/" target="_blank">Linking to GeneMANIA</a></li>	
+	<li><a href="https://pages.genemania.org/help/#linking-to-genemania" target="_blank">Linking to GeneMANIA</a></li>	
 	</ul>
 
 	<h5>How to Cite</h5>

tools/ndex.html

@@ -38,7 +38,7 @@ <h5>Documentation</h5>
 <h5>Developer Resources</h5>
 <ul>
     <li><a href="https://home.ndexbio.org/disclaimer-license/" target="_blank">Disclaimer, License and Code Repository</a></li>
-    <li><a href="http://openapi.ndextools.org/" target="_blank">NDEx REST API</a></li>
+    <li><a href="https://home.ndexbio.org/using-the-ndex-server-api/" target="_blank">NDEx REST API</a></li>
 </ul>
 
 <h5>How to cite</h5>

tools/noa.html

@@ -34,7 +34,6 @@ <h5>Documentation</h5>
 	<h5>Developer Resources</h5>
 	<ul>
 	<li><a href="http://nrnb.org/tools/noa/#techdocs" target="_blank">Technical Documentation</a></li>
-	<li><a href="http://svn.cgl.ucsf.edu/svn/genmappcs/trunk/avalon/noa/" target="_blank">Code Repository</a></li>
 	</ul>
 
 	<h5>How to Cite</h5>

tools/noctua.html

@@ -27,7 +27,6 @@ <h5>Documentation</h5>
 	<li><a href="http://noctua.berkeleybop.org/" target="_blank">Noctua website</a></li>
 	<li><a href="https://vimeo.com/channels/Noctua" target="_blank">Video demos</a></li>
 	<li><a href="https://docs.google.com/document/d/18ihslb7prB6CWtu2yjF-pMHZBTY1-AdXJAu-ZyuyXS4/edit#" target="_blank">Modeling guide</a></li>
-	<li><a href="http://geneontology.org/article/gaf-gpad-and-lego" target="_blank">GO announcement</a></li>
 	</ul>
 
 	<h5>Developer Resources</h5>
@@ -37,7 +36,7 @@ <h5>Developer Resources</h5>
 
 	<h5>How to Cite</h5>
 	<ul>
-	<li>Paper coming soon, cite the <a href="https://github.com/geneontology/noctua">GitHub repo</a> for now.</li>
+	<li>Paper coming soon, cite the <a href="https://github.com/geneontology/noctua" target="_blank">GitHub repo</a> for now.</li>
 	</ul>
 
 	<hr />

tools/pathvisio.html

@@ -26,23 +26,21 @@ <h3>PathVisio</h3>
 	<h5>Documentation</h5>
 	<ul>
 	<li><a href="http://www.pathvisio.org/" target="_blank">PathVisio Website</a></li>
-	<li><a href="http://www.pathvisio.org/documentation/tutorials/" target="_blank">Tutorials</a></li>
-	<li><a href="http://www.pathvisio.org/documentation/" target="_blank">User Documentation</a></li>
+	<li><a href="https://pathvisio.org/tutorials" target="_blank">Tutorials</a></li>
+	<li><a href="https://pathvisio.org/documentation" target="_blank">User Documentation</a></li>
 	</ul>
 
 	<h5>Developer Resources</h5>
 	<ul>
-	<li><a href="http://developers.pathvisio.org/" target="_blank">Developers Documentation</a></li>
 	<li><a href="https://github.com/PathVisio/pathvisio" target="_blank">Code Repository</a></li>
-	<li><a href="http://developers.pathvisio.org/apidoc/" target="_blank">API</a></li>	
 	</ul>
 
 	<h5>How to Cite</h5>
 	<ul>
         <li><a href="http://www.biomedcentral.com/1471-2105/9/399" target="_blank">Presenting and exploring 
         biological pathways with PathVisio.</a> van Iersel et al., <i>BMC Bioinformatics</i> 2008.</li>
 	<li><a href="http://nar.oxfordjournals.org/content/40/D1/D1301" target="_blank">WikiPathways: building research 
-	communities on biological pathways.</a> Kelder et al., <i>NAR> 2011.</li>
+        communities on biological pathways.</a> Kelder et al., <i>NAR</i> 2011.</li>
 	</ul>
 
 	<hr />

tools/pihelper.html

@@ -18,13 +18,13 @@
 
 <h3>PiHelper</h3>
 	<p>
-	<a href="https://bitbucket.org/armish/pihelper" target="_blank">PiHelper</a> is a drug- and antibody-target 
+	PiHelper is a drug- and antibody-target 
 	information aggregator and provider service. The data aggregated by PiHelper can be accessed either 
 	programmatically via a Java API or through a web user interface. The framework works in a human-gene centric 
 	manner and model drug-target and antibody-target relationships accordingly.	
 	</p>
 
-	<h5>Documentation</h5>
+<!--	<h5>Documentation</h5>
 		<ul>
 		<li><a href="https://bitbucket.org/armish/pihelper" target="_blank">PiHelper Website</a></li>
 		</ul>
@@ -33,7 +33,7 @@ <h5>Developer Resources</h5>
 		<ul>
 		<li><a href="https://bitbucket.org/armish/pihelper/src" target="_blank">Source Code and Documentation
 		</a></li>
-		</ul>
+		</ul>-->
 
 	<h5>How to Cite</h5>
 		<ul>

tools/stringapp.html

@@ -35,7 +35,7 @@ <h3>stringApp</h3>
 	<h5>Documentation</h5>
 	<ul>
 	<li><a href="http://www.cgl.ucsf.edu/cytoscape/stringApp/index.shtml" target="_blank">stringApp Website</a></li>
-	<li><a href="http://jensenlab.org/training/stringapp/" target="_blank">Tutorial</a></li>
+	<li><a href="https://cytoscape.org/cytoscape-tutorials/protocols/stringApp/#/" target="_blank">Tutorial</a></li>
 	</ul>
 
 	<h5>Developer Resources</h5>