= Semantic Network Summary Tutorial and Examples =
== Outline ==
This tutorial and set of examples will guide a user through the basic functioning of the Semantic Network Summary plugin using the Cytoscape session file provided.

Pre-requisites -

 * Cytoscape >= 2.7.0 must be installed
 * The Semantic Network Summary plugin must be in the Cytoscape-v2.7.x/plugins folder
 * Download the test data

Go to this page to [[GSoC2010_SoftwareDownload|download the plugin and test data]]

== Instructions ==
=== Version 0.5 or newer ===
1. Open Cytoscape

2. Click on Plugins / Semantic Network Summary / Settings - this will bring up the Semantic Network Summary Input and Display panels.

3. Open the provided [[GSoC2010_SoftwareDownload|sample data file]] (File / Open / select the file GSnames_AlzheimerEM.cys)

4. On the Network tab of the Control Panel make sure to select the network titled "EM1_Enrichment Map"

5. Select a set of at least one node in the network in the network titled "EM1_Enrichment Map".

6. Create a new cloud using one of the following three options:

 A. Right click on one of the nodes in the network and select the option for "Create Cloud"
 A. Click on Plugins / Semantic Network Summary / Create Cloud
 A. Click on the Create button on the bottom right corner of the Semantic Summary Input panel.

7. Right click on the cloud in the Semantic Network Summary and choose "Edit Cloud Name".  Provide a new name for the cloud that is not a duplicate of a name already given to any clouds for this network and select OK.

8. In the Semantic Analysis section of the Input panel change the attribute used from nodeID to EM1_GS_DESCR.  This will change what node attribute is used when performing the semantic analysis and creating the cloud.

9. Click on the Update button to update the cloud to reflect the change in node attribute.

 * The Update functionality only applies to the cloud currently selected from the list of clouds in the top section of the Input panel.

 * If you have changed the set of selected nodes from when the cloud was originally created or last updated a warning will appear at this time.  The warning will ask if you want to use the set of currently selected nodes, or if you want to revert back to last set of selected nodes.