Community Structure Layout

Gang Su 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.


Cytoscape version: Version number (2.6.1)

Plugins to Load: GLay.jar , MetaNodePlugin2.jar

GUI steps:

Describe each step (story), the GUI action to take, and probable 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


Then, you may tune the parameters. Right now we have two clustering algorithms and two layout algorithms. Just go with the default.


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.


Clusters can be expanded or collapsed by right click on the nodes to bring up the contextual menu.


Toolticons can be used to perform various tasks.


Here's a miniposter for FYI

And abstract FYI

Data / Session Files: Attach (preferably) a session file or else the data files used in the workflow

Presentation: Presentation.ppt

Webstart: Attach a webstart

Video: Video Tutorial:, ; High resolution video tutorial: GangScreen.wmv

CommunityStructureLayoutRecipe (last edited 2009-02-12 01:04:09 by localhost)

Funding for Cytoscape is provided by a federal grant from the U.S. National Institute of General Medical Sciences (NIGMS) of the Na tional Institutes of Health (NIH) under award number GM070743-01. Corporate funding is provided through a contract from Unilever PLC.

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