Differences between revisions 1 and 2
Revision 1 as of 2008-03-07 15:41:11
Size: 1899
Editor: cerami
Comment:
Revision 2 as of 2008-03-07 17:41:09
Size: 862
Editor: cerami
Comment:
Deletions are marked like this. Additions are marked like this.
Line 7: Line 7:
[PICTURE GOES HERE] attachment:file_import.png
Line 14: Line 14:
=== Basic Usage === === Example #1: Retrieving Data from !IntAct ===
Line 16: Line 16:
Cytoscape includes four !CytoPanels: '''''Control Panel''''' on the left, '''''Tool Panel''''' on the bottom of ''Control Panel'', '''''Data Panel''''' on the bottom, and '''''Result Panel''''' on the right. By default, ''Control Panel'' and ''Data Panel'' will appear. ''Result Panel'' may appear, depending on the mix of Cytoscape plugins that you currently have installed. ''Tool Panel'' will appear when you select the following commands under the ''Layout'' menu: ''Rotate'', ''Scale'', and ''Align and Distribute''.
Line 18: Line 17:
All panels can be shown or hidden using the View → Show/Hide functions.
Line 20: Line 18:
attachment:cytopanel-menu-items_25.png
Line 22: Line 19:
In addition, !CytoPanels can be floated or docked by selecting the icon at the top right corner of each !CytoPanel. The icon and tooltip will change based on the !CytoPanel state. If the !CytoPanel is docked, clicking on the icon will float the !CytoPanel, as indicated by the “Float Window” tooltip. Alternatively, if the !CytoPanel is floating, clicking on the icon will dock the !CytoPanel, as indicated by the “Dock Window” tooltip.

attachment:cytopanel-float-dock-icon.png
=== Example #2: Retrieving Data from Pathway Commons ===

Importing Networks from External Databases

Cytoscape includes the ability to import networks and pathways directly from external databases.

To get started, select: File → Import → Network from web services...

attachment:file_import.png

By default, Cytoscape provides direct access to the following external resources:

Example #1: Retrieving Data from !IntAct

Example #2: Retrieving Data from Pathway Commons

Cytoscape_User_Manual/ImportingNetworksFromWebServices (last edited 2010-07-28 03:24:29 by KeiichiroOno)

Funding for Cytoscape is provided by a federal grant from the U.S. National Institute of General Medical Sciences (NIGMS) of the Na tional Institutes of Health (NIH) under award number GM070743-01. Corporate funding is provided through a contract from Unilever PLC.

MoinMoin Appliance - Powered by TurnKey Linux