Cytoscape Wiki
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...
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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.
Basic Usage
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.
All panels can be shown or hidden using the View → Show/Hide functions.
attachment:cytopanel-menu-items_25.png
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