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Cytoscape Hands-On Tutorial for SDCSB Cytoscape Workshop 12/4/2012

Cytoscape Hands-On Tutorial for SDCSB Cytoscape Workshop 12/4/2012

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Published by Keiichiro Ono
Handouts for hands-on tutorial for Cytoscape workshop at Salk Institute on 12/4/2012.

Basic tutorials for Cytoscape.
Handouts for hands-on tutorial for Cytoscape workshop at Salk Institute on 12/4/2012.

Basic tutorials for Cytoscape.

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Categories:Types, Research
Published by: Keiichiro Ono on Dec 04, 2012
Copyright:Attribution Non-commercial

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12/04/2012

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CytoscapeBasicTutorial
SDCSBCytoscapeWorkshop12/4/2012KeiichiroOno
 
NavigatingCytoscape
NavigatingCytoscape
ThissectionwillintroducetheCytoscapeuserinterface.FirstofallwewilllookatthebasicUIofCytoscape.ThenwewillshowallmenufeaturesofCytoscapeandtheextendedfunctionalityprovidedbyplugins.
CytoscapeLayoutandUserInterface
LaunchCytoscape.Youshouldseeawindowthatlookslikethis:
 
 
At the top of the Cytoscape Desktop window is the toolbar, which contains the commandbuttons. The name of each command button is shown when the mouse pointer hoversover it.
 
In the upper right is the Main Network View window, where network data will bedisplayed. This region is initially blank.
 
At left is the Control Panel (Network Management) Panel. This lists the availablenetworks by name and provides information on the number of nodes and edges.
 
Immediately below the Control Panel is the Network Overview Pane
 
At lower right is the Data Panel which can be used to display node, edge, and networkattribute data
 
TheNetworkManagementandDatabrowserpanelsaredockabletabbedpanelsknownasCytoPanels.YoucanundockanyofthesepanelsbyclickingontheFloatWindowcontrolintheupper-rightcorneroftheCytoPanel.TheDataPanelstartsoffwiththreetabs:
Node AttributeBrowser
,
EdgeAttributeBrowser
,and
NetworkAttribute
Browser
;theNetworkManagementpanelstartsoffwithfourtabs:
Network 
,
VizMapper
,
Editor
,and
Filters
.LoadedpluginsmightaddtabstoeitheroftheseCytoPanels.
CytoscapeMenus
WewillbrieflyrunthroughallthemenusavailableinCytoscape.
File
TheFilemenucontainsbasicfilefunctionality:
 
File
à
Open
for opening a Cytoscape session file
 
File
à
New
for creating a new network
 
File
à
Save
for saving a session file
 
File
à
Import
for importing data such as networks and attributes
 
File
à
Export
for exporting data and images.
 
File
à
Print
allows printing
 
File
à
Quit
closes all windows of Cytoscape and exits the program
Edit
TheEditmenucontains:
 
Undo and Redo functions which undo and redo edits made in the Attribute Browser, theNetwork Editor and the Layout.
 
Options for creating and destroying views (graphical representations of a network) andnetworks
 
Options for deleting selected nodes and edges from the current network.
 
All deleted nodes and edges can be restored to the network via
Edit
à
Undo
.
 
Edit
à
Preferences
à
Properties
to edit preferences for properties and plugins
View
TheViewmenuallowsyoutodisplayorhide:
 
The network management panel (Control Panel)
 
The attribute browser (Data Panel)
 
Results Panel
 
VizMapper
 Select
TheSelectmenucontains:
 
Options for selecting nodes and edges
 
The
Select
à
Use Filters
option allows filters to be created for automatic selection of portions of a network whose node or edge attributes meet a filtering criterion (see belowfor the filters section).
Layout
TheLayoutmenuhasanarrayoffeaturesforvisuallyorganizingthenetwork:

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