Cytoscape WikiThere are 4 different ways of creating networks in Cytoscape:
- Importing pre-existing, formatted network files.
- Importing pre-existing, unformatted text or Excel files.
- Importing networks from Web Service.
- Creating an empty network and manually adding nodes and edges.
Import Fixed-Format Network Files
Network files can be specified in any of the formats described in the Supported Network Formats chapter. Networks are imported into Cytoscape through the "Import Network" window, which can be accessed by going to File → Import → Network (multiple file types). The network file can either be located directly on the local computer, or found on a remote computer (in which case it will be referenced with a URL).
Load Networks from Local Computer
In order to load network from local files you can select File → Import → Network → File... or click on 
on the tool bar. Choose the correct file in the file chooser dialoge and press Open. Some sample network files of different types have been included in the sampleData folder in Cytoscape.
Network files in SIF, GML, and XGMML formats may also be loaded directly from the command line using the –N option.
Load Networks from a Remote Computer (URL import)
To load network from remote files you can select File → Import → Network → URL... or click on 
on the tool bar. In the import network dialoge, insert the appropriate URL, either manually or using URL bookmarks. Bookmarked URLs can be accessed by clicking on the arrow to the right of the text field (see the Bookmark Manager in Preferences for more details on bookmarks). Also, you can drag and drop links from web browser to the URL text box. Once a URL has been specified, click on the OK button to load the network.
