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 single networks and network collections between [http://www.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. *** ## Known Issues and Limitations - **CyNDEx** can be used with **Cytoscape 3.3.x, 3.4.x or 3.5.x**. If you are running Cytoscape 3.6 or higher, please use the **[http://apps.cytoscape.org/apps/cyndex2 Cyndex-2 App]** instead (CyNDEx-2 has become a "Core Cytoscape App" starting from Cytoscape 3.6.1). - **When a network imported from NDEx is saved as a `Cytoscape session file (.cys)`, the session file loaded at a later time and the network re-exported to NDEx, some data loss may occur.** _We recommend you import and export networks back to NDEx rather than save them as session files_. *** ##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. *** ##Reporting Bugs To report a bug in this app, please use the **[http://www.home.ndexbio.org/report-a-bug/ NDEx Bug Report Form]** and make sure to select "CyNDEx" from the **Product** dropdown menu. *** ***
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4.0.3

Works with Cytoscape 3.3

Release Notes

1. Saving certain networks no longer gives warnings in NDEx. 2. Fixed a compatibility issue when reading networks created with old Cytoscape aspects such as ` visualProperties `. 3. Import function change: when a network doesn’t have a layout, apply ` force-directed ` layout when the network is small (< 5000 edges) and apply ` grid ` layout otherwise.

4.0.2

Works with Cytoscape 3.3

Release Notes

1. Cytoscape and CyNDEx version is recorded in the Provenance History when a user saves or updates a network in NDEx. 2. Added support to export multiple Cytoscape views on a network. A user can choose a view and export it as a singleton network or export all views on all networks as a network collection. 3. When a user exports a **singleton network**, the name column on each node is used to populate the ` name ` field of that node in CX. The value in ` Shared name ` will be ignored if the value in ` name ` field is different from the ` Shared name` field. If a user exports a network as a **Cytoscape collection**, the values in both ` shared name ` and ` name ` will be preserved. **Bug fixes:** The visual mappings were not exported correctly when: 1. The column name, which the mapping was on, has ` , ` or ` = ` in it. 2. There is a discrete mapping on a column and one of the values of the column has ` , ` or ` = ` in it. 3. Other visual styles that has ` , ` or ` = ` in the serialized value.

4.0.1

Works with Cytoscape 3.3

Release Notes

**Bug fixes:** - Use default cytoscape visual style when the ` cyVisualProperties ` aspect is missing in the CX network. - Catches more importing errors. - Convert default edge mapping on interaction column to 'shared interaction' during import.

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**.
CYTOSCAPE 3

Version 4.0.3

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Released 5 Feb 2018

Works with Cytoscape 3.3

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