Differences between revisions 1 and 7 (spanning 6 versions)

ClusterMaker

John 'Scooter' Morris

University of California, San Francisco

Biological Use Case: Find possible complexes, protein families, functional relationships and view in biological context.

Recipe

Cytoscape version: Version number (2.6)

Plugins to Load: ClusterMaker (from what URL?)

GUI steps:

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

Story	Action	Remarks
Start with expression data for studies into mechanism for galactose utilization.	open galfiltered.cys session	galfilterd may be replaced by time series data from Nathan Salomonis, AllanK will follow up on this
run clustering to determine interesting subnets	select plugins -> cluster -> hierarchical cluster. For settings, use maximal linkage, cluster attributes as well as nodes, cluster on just expression data
visualize and navigate the clusters	on treeview window, explore by clicking on points on the dendogram	shows Eisen treeview visualization. Clicking/selecting a particular row in the heatmap will result in the expression values for that column being overlaid on the network view
	use shift-drag to draw a box and see results on network
	use shift-click to pick individual columns

Data Files: Attach data files

Presentation: Attach your presentation

Webstart: Attach a webstart

Video: Attach a video link

-  ← Revision 1 as of 2008-08-13 18:06:46 →
  Size: 581
  Editor: scsiapat1
  Comment:
+  ← Revision 7 as of 2008-08-13 18:31:56 →
  Size: 1582
  Editor: scsiapat1
  Comment:
-Deletions are marked like this.
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-= Your Title =

'''Your name '''
+= ClusterMaker =

'''John 'Scooter' Morris '''
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-''Your institute''
+''University of California, San Francisco''
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-'''__Biological Use Case__''': Describe a real biological problem.
+'''__Biological Use Case__''': Find possible complexes, protein families, functional relationships and view in biological context.
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 ''__Cytoscape version__'': Version number (2.6)
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-''__Plugins to Load__'': Plugins and urls
+''__Plugins to Load__'': ClusterMaker (from what URL?)
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 ''__GUI steps__'':
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-|| ''Story'' || ''Action'' || ''Remarks'' ||

||  ||  ||  ||
+||''Story'' ||''Action'' ||''Remarks'' ||

||Start with expression data for studies into mechanism for galactose utilization.   || open galfiltered.cys session|| galfilterd may be replaced by time series data from Nathan Salomonis, AllanK will follow up on this||

||run clustering to determine interesting subnets || select plugins -> cluster -> hierarchical cluster.  For settings, use maximal linkage, cluster attributes as well as nodes, cluster on just expression data || ||

|| visualize and navigate the clusters || on treeview window, explore by clicking on points on the dendogram || shows Eisen treeview visualization.  Clicking/selecting a particular row in the heatmap will result in the expression values for that column being overlaid on the network view ||

|| || use shift-drag to draw a box and see results on network|| ||

|| ||use shift-click to pick individual columns || ||

|| || || ||

|| || || ||

|| || || ||

|| || || ||
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+Line 31:
 '''__Presentation__''': Attach your presentation

Diff for "ClusterMakerRecipe"

ClusterMaker