Hanalyzer: A 3R System

How To Explore the Network in the PLoS paper

The Cytoscape files used in the analysis as described in the Leach et al. are available on this SourceForge site. You can download the network here: networkInHanalyzerPaper_cytoscapeFiles.tar.gz

In order to view the network, you will need to install Cytoscape. Please visit the Cytoscape website and following the download and installation instructions for your operating system.

Once you have Cytoscape installed you will want to install the Cytoscape plugins that have been developed to support Hanalyzer network navigation. Please see the Hanalyzer Cytoscape Plugins Support Page for details on installing and using the Cytoscape plugins.

You should now be ready to explore the network from the PLoS paper.

  1. Unpack the networkInHanalyzerPaper_cytoscapeFiles.tar.gz into a directory of your choosing ([NETWORK-DIR]).

  2. Start Cytoscape

  3. File --> Open --> Select [NETWORK-DIR]/cytoscape-files/networkInHanalyzerPaper.cys

  4. Select the network you would like to explore by clicking on one listed in the left-most panel

  5. Plugins --> CommonAttributes --> Select [NETWORK-DIR]cytoscape-files/commonattributes-plugin-files

You should now be able to right-click on an edge and see the experts that asserted that edge in the CommonAttributes menu.