Cytoscape 3.2 update#
Cytoscape 3.2 archive#

You can change the suggested file name/path using the You can choose the format using the dialog drop-down box.Ī file name is automatically suggested based on the network name and selected format, with the file pathĭefaulting to the current working directory. The default format is SIF, which is a simple tab-delimited network format that provides CX JSON (for Cytoscape Cyberinfrastructure network exchange).Cytoscape.js JSON (can be used with Cytoscape.js, a tool described in future sections).Network data can be exported in a number of formats, including: Will include data attributes and visual information if the chosen format supports it Network data includes the nodes and edges in the network, and also For more sharing options, see the NDEx Public Server website.įurther information on NDEx is available at the NDEx Informational/Doc website. The UUID is suitable for e-mailing to colleagues so they can load your network via their Cytoscape Search bar (provided you selected the Save as Public option). When the export to NDEx is complete, you will be given an opportunity to capture the network’s UUID in your clipboard. Menu actions have also been added to the network and collection context menus in the Cytoscape Network panel, as another method of accessing the network save dialog. Choose the Save as Public option to enable collaborators to load your network. If you choose to make your network public, you must fill in the Version and Description attributes.

Cytoscape 3.2 update#

The Update Existing Network option enables you to overwrite an existing NDEx network if you have permission. You can set the name of your network by editing the Network Name attribute at the bottom. To save a network, you must add an NDEx account profile to the CyNDEx-2 Browser (by filling out the profile form reachable by clicking on the Anonymous credential in the upper right), and then make it current. When you select either option, the CyNDEx-2 Browser dialog will appear and enable you to provide metadata that will be displayed during subsequent NDEx searches. This option is closest to saving an entire Cytoscape session, except that only the current collection is saved. If you import this collection (using the Cytoscape Search bar), the entire collection will be loaded. The Collection to NDEx option saves all networks in the collection containing the currently selected network.

If you import this network (using the Cytoscape Search bar), only the single network will be loaded. Such networks are suitable for processing by other applications and web services, as they contain only the nodes and edges in the selected network – other networks and the nodes and edges unique to them are not written. The Network to NDEx option saves only the currently selected network to your NDEx account. To store a network, you must have an NDEx account, which you can create by visiting the NDEx Public Server website.

Cytoscape 3.2 archive#

You can use an NDEx server as a cloud-based store for your networks, as a means of sharing networks with collaborators, or to archive networks for publication. The Network to NDEx and Collection to NDEx options are used to store a network on a public NDEx server. Network Data Exchange (NDEx) Public Database ¶