= Community Structure Layout =
'''Gang Su'''

sugang@umich.edu
{{attachment:CLogo.png}}

''Bioinformatics Program, University of Michigan, Ann Arbor''

'''__Biological Use Case__''': This plugin is aimed to find community structures in large biological networks, which may infer protein complexes and biological pathways. We also utilize the community structure information to improve visualization of large interaction networks.

'''__Recipe__'''

''__Cytoscape version__'': Version number (2.6.1)

''__Plugins to Load__'': [[attachment:GLay.jar]] , [[attachment:MetaNodePlugin2.jar]]

''__GUI steps__'':

Describe each step (story), the GUI action to take, and probable remarks
|| ''Story'' || ''Action'' || ''Remarks'' ||
|| First of all, you need to load Glay. After you placed all the plugins jars in the folder, load Glay from the plugins tab. Also please load the preferred network. Here we used galFiltered.sif || {{attachment:screen1.jpg}} || ||
|| Then, you may tune the parameters. Right now we have two clustering algorithms and two layout algorithms. Just go with the default. || {{attachment:screen2.jpg}} || ||
|| Next, you may interact with all the clusters from the cluster browsing panel; you may select multiple clusters from by holding the shift key. This will 'activate' clusters my changing visual styles. || {{attachment:screen3.jpg}} || ||
|| Clusters can be expanded or collapsed by right click on the nodes to bring up the contextual menu. || {{attachment:screen4.jpg}} || ||
|| Toolticons can be used to perform various tasks. || {{attachment:screen5.jpg}} || ||


Here's a miniposter for FYI

 . {{attachment:GLayMiniPoster.jpg}}
And abstract FYI

 . [[attachment:GLayAbstract.pdf]]
'''__Data / Session Files__''': Attach (preferably) a session file or else the data files used in the workflow

'''__Presentation__''': [[attachment:Presentation.ppt]]

'''__Webstart__''': Attach a webstart

'''__Video__''': Video Tutorial: http://www.youtube.com/watch?v=W79Kb28348g, http://www.youtube.com/watch?v=OD3fUF62Gd8 ; High resolution video tutorial: [[attachment:GangScreen.wmv]]