= Semantic Network Summary Basic Tutorial =
== Outline ==
This tutorial will guide a user through the basic functioning of the Semantic Network Summary plugin using the Cytoscape session file provided.  See the Semantic Summary [[GSoC2010_ParameterTutorial|Parameter Tutorial]] for a more detailed examples on using and changing the parameters available for the Semantic Network Summary.

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

3. Be careful not to change the set of selected nodes for the network titled "EM1_Enrichment Map" as this will change the results that you will get.

'''The example network with the correct set of nodes selected:'''

''' {{attachment:Selected_Nodes.png|Selected_Nodes.jpg}} '''

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

5. 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.  For now you can leave all other values at their defaults.

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.

'''Expected Result:'''

''' {{attachment:Original_Cloud.png|Original_Cloud.jpg}} '''

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. Expand the Advanced Parameters section of the Input panel by clicking on the black triangle next to the section name.  Change Network Normalization value to 0.5.  For a more detailed example on how the parameters affect the Semantic Network Summary see the Parameter Tutorial.

9. Click on the Update button to update the cloud to reflect the parameter change.

 * 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.

'''Expected Result:'''

''' {{attachment:Updated_Cloud.png|Updated_Cloud.jpg}} '''

10. In the word cloud, click on the word "Cancer" to see all the nodes in the network that contain this word become highlighted.

'''The example network with all nodes containing the word Cancer in the attribute EM1_GS_DESCR highlighted:'''

{{attachment:Cancer_Nodes.png|Cancer_Nodes.jpg}}

11. Click on the cloud in the cloud list on the top section of the Input panel to re-select the set of selected nodes that the cloud was built from.

12. With the cloud highlighted, choose the Delete button from bottom of the input panel to remove the cloud from your list of clouds.