Differences between revisions 1 and 11 (spanning 10 versions)

Community Structure Layout

Gang Su

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 , MetaNodePlugin2.jar

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

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

-  ← Revision 1 as of 2008-08-20 18:22:24 →
  Size: 694
  Editor: www
  Comment:
+  ← Revision 11 as of 2008-08-20 20:28:53 →
  Size: 2011
  Editor: www
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 6:
-'''__Biological Use Case__''': Describe a real biological problem.
+'''__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.
 Line 12:
-''__Plugins to Load__'': GLay Plugin; MetaNodePlugin2;
+''__Plugins to Load__'': attachment:GLay.jar , MetaNodePlugin2.jar



''__Plugins to Load__'': attachment:GLay.jar , attachment:MetaNodePlugin2.jar
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+Line 20:
-|| || || ||
+|| 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 || || ||
-Line 21:
+Line 27:
+Here's a miniposter for FYI



 . attachment:GLayMiniPoster.jpg
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+Line 32:
-'''__Presentation__''':
+'''__Presentation__''': attachment:Presentation.ppt
-Line 27:
+Line 36:
-'''__Video__''': Attach a video link
+'''__Video__''': Video Tutorial: http://www.youtube.com/watch?v=W79Kb28348g, http://www.youtube.com/watch?v=OD3fUF62Gd8

Diff for "CommunityStructureLayout"

Community Structure Layout