CyNDEx

CyNDEx allows users to seamlessly transfer networks between NDEx and Cytoscape as well as perform network updates in NDEx.
*** ###Description CyNDEx is a lightweight app that allows import/export of network objects between [http://home.ndexbio.org The Network Data Exchange (NDEx)] and Cytoscape. Users can conveniently install or update the CyNDEx app directly from Cytoscape using the built-in App Manager. *** ###Installation In order to install CyNDEx, you must have **Java 8** and **Cytoscape v3.3** or higher installed on your system. Once installed, CyNDEx controls can be found in the **Apps** menu item as shown in the screenshot below. <a href="http://apps.cytoscape.org/apps/cyndex"> <img src="http://home.ndexbio.org/img/cyndexpro3.jpg"></a> *** ###Tutorial The NDEx Team has put together a step by step **[http://home.ndexbio.org/ndex-cyapp-tutorial-alt/ CyNDEx Tutorial]** to help you get started using this app and provide additional useful information. *** ###Issues To report a bug in this app, please use the **[http://home.ndexbio.org/ndex-cyapp-tutorial-alt/ NDEx Bug Report Form]** and make sure to select "CyNDEx" from the **Product** dropdown menu. *** *** ###Coming soon... We are pleased to announce that we're working on a major upgrade for this app, to be called **CyNDEx 2**. It will be based on JxBrowser, a lightweight Swing/JavaFX component for seamless integration of Chromium browser into Java applications on Windows, Linux, and macOS. For additional info, please visit: <a href="https://www.teamdev.com/jxbrowser"> <img src="http://chianti.ucsd.edu/~bdemchak/JxBrowser/2017-04-11.png" alt="JxBrowser by TeamDev"></a> ***

4.0.0

Works with Cytoscape 3.3

Release Notes

1. Lossless data round trip from NDEx to Cytoscape then back to NDEx. When you import a network from NDEx to Cytoscpae, all non-Cytoscape aspects (for example, an ‘@context’ aspect in your network) will be preserved when you save this network back to NDEx. All the node and edge identifiers will also be preserved during the round trip, so you can use these ids to reference network elements before and after the network import and export. 2. When a user exports a single network from Cytoscape to NDEx, CyNDEx will no longer export it as a "Cytoscape Network Collection"; this means that node and edge attributes will no longer be moved to a Cytoscape subnetwork when a network is exported to NDEx. In addition, Cytoscape internal attributes (such as "selected", "shared name" etc.) will not be added to the network during export. 3. Minimal improvements to streamline the user interface and guide first time users through basic operations. 4. Better error reporting when importing/exporting networks. 5. CyNDEx now uses the NDEx 2.0 REST API to communicate with the NDEx server. 6. Various bug fixes.

3.3.0

Works with Cytoscape 3.3


CYTOSCAPE 3

Version 4.0.0

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Released 11 May 2017

Works with Cytoscape 3.3

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