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| [PICTURE GOES HERE] | attachment:file_import.png |
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| === Basic Usage === | === Example #1: Retrieving Data from !IntAct === |
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| 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''. | |
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| All panels can be shown or hidden using the View → Show/Hide functions. | |
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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:
[http://www.ebi.ac.uk/intact/site/index.jsf IntAct]: an open source database of protein interaction data, hosted at EMBL-EBI.
[http://www.pathwaycommons.org Pathway Commons]: an open source portal, providing access to multiple integrated data sets, including: Reactome, IntAct, HPRD, HumanCyc, MINT, the MSKCC Cancer Cell Map, and the NCI/Nature Pathway Interaction database.
Example #1: Retrieving Data from !IntAct