cMonkey Bicluster Viewing Instructions

All cMonkey Biclusters may be viewed and queried using a series of Java Web Starts. These are Java applications that are downloaded automatically to your computer and started upon the click of a hyperlink. We have developed several such applications, that all communicate with each other via a "Gaggle Boss" to pass selection information between them. The relevant microarray data may also be viewed, queried, and downloaded, using this framework. For more complete instructions on the use of the "Gaggle" and its associated applications ("Geese"), you may view additional documentation at the Gaggle Home Page. To view the biclusters for a given organism, perform the following:

1. Click the "Start the gaggle boss" link to start up the Gaggle Boss. This must be performed FIRST!
2. Click the "Start the bicluster network viewer in Cytoscape" link to start up Cytoscape for viewing the network of associated biclusters.
3. Click the "Start the bicluster viewer" link to start up the Bicluster View application, for displaying the detailed diagrams of each bicluster as shown in the paper.
4. If you are interested in viewing the data associated with the biclusters (and from which the biclusters were generated), click the "Start some other geese" link, and then click the "DMV" (Data Matrix Viewer) link. This will start up the viewer that enables browsing, plotting, and downloading of the microarray data.
   • On this page (if available), you may also start up applications for browsing associations and other bioinformatics information for the genes of each organism. Note that these geese and their availability are organism-specific.
5. Once all of the applications have started up, you can select a bicluster by clicking a rectangular node (representing a bicluster) in the Cytoscape window, and then:
   1. Press the "B" button to broadcast the bicluster's number to the Bicluster Biewer. The Bicluster Biewer should then present a "bicluster view diagram" with detailed information on the bicluster.
   2. Press the "Cl" button to broadcast the bicluster's genes and conditions to other Geese. For example, if you have the DMV running, it will select the submatrix in the expression data which is contained within the bicluster.