= 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|| galfiltered 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.  Press 'map colors onto network' diagram || 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 ||
|| || adjust contrast by settings -> contrast || ||
|| || use shift-drag to draw a box and see results on network|| ||
|| ||use shift-click to pick individual columns || ||
|| || select an individual row by clicking on it || ||
|| animate expression values over time || select 'options'.  On popup, click on specific attributes to select.  Optionally order attributes.  Select all attributes and click on 'animate'. || will show nicely if we have time series data.  TODO: AllanK check with Nathan on this ||


'''__Data Files__''': Attach data files

'''__Presentation__''': Attach your presentation

'''__Webstart__''': Attach a webstart

'''__Video__''': Attach a video link