Tutorial:Community Structure Layout

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Slideshow Community_Structure_Layout (about ?? minutes)
Handout Community_Structure_Layout.pdf (?? pages)

Tutorial Sources
Tutorial Curators Anna Kuchinsky, Alex Pico


Community Structure Layout

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.

Procedure

  1. Start by loading the GLay.jar and MetaNodePlugin2.jar plugins from Plugins->Manage Plugins.
    1. Currently, the GLay file is not available from the Manage Plugins menu. You can download the file here: File:GLAY.jar
  2. After you have placed all the plugin jars in the folder, load Glay from the plugins tab. Also, load the preferred network. In this example, use galFiltered.sif.
  3. Next, tune the parameters. Right now, we have two clustering algorithms and two layout algorithms. Just go with the default.Tune your Parameters
  4. Next, you may interact with all the clusters from the cluster browsing panel. You may select multiple clusters by holding the shift key. This will activate clusters by changing visual styles.
  5. Clusters can be expanded or collapsed by right-clicking on the nodes to bring up the contextual menu. Expanding clusters
  6. Toolticons can be used to perform various tasks.

Other Tutorials

Video

A video tutorial is available, in two parts, on YouTube:

  1. http://www.youtube.com/watch?v=W79Kb28348g
  2. http://www.youtube.com/watch?v=OD3fUF62Gd8

Mini Poster

GLay Mini Poster