![]() Library, and so enable not only viewing but also Cytoscape-style All solutions leverage the cytoscape.js drawing With each choice representing tradeoffs between ease, simplicity, andĬustomization options. The Web is an excellent platform for data sharing and collaboration, andĬytoscape (as of version 3.2.0) provides a number of ways to publish your network on the web, Press OK to export with the selected options. ![]() 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 If you want to share your network with external collaborators or for more sharing options, please refer to the guide for Uploading and Sharing Networks in NDEx.įurther information on NDEx is available at the NDEx Informational/Doc website. When the export operation is complete, a confirmation dialog will be displayed as shown below. Once the profile is created, you are allowed to export your network to NDEx.Įxport commands 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.įinally, the NDEx button in the toolbar provides an additional convenient way to both Import and Export to NDEx. To export your network, you must first associate your NDEx account credentials with the CyNDEx-2 Browser by filling out the profile form (red oval in screenshot below). We recommend to provide as much metadata as possible, and always provide at least Version and Description attributes. The Update Existing Network option enables you to overwrite the existing copy of the network (if you have permission to do so). You can set the name of your network by editing the Network Name attribute. When you select either option, the CyNDEx-2 Browser dialog will appear and enable you to provide various metadata to annotate the network and make it findable in subsequent NDEx searches. This option is closest to saving an entire Cytoscape session. If you later re-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 later re-import this network (using the Cytoscape Search bar), only the single network you saved 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 views 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 first create a free NDEx account, which you can easily do by visiting the NDEx Public Server website. You can use the NDEx public server to store your networks on the cloud, for 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 the public NDEx server. Network Data Exchange (NDEx) Public Database ¶
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