CyNDEx-2

Core App: CyNDEx-2 is a user-friendly app for browsing, importing, and exporting networks to an NDEx server.
# Welcome to CyNDEx-2! *** The latest **CyNDEx-2** build available here on the App Store (**v2.3.0**) is distributed as core app with the new Cytoscape 3.7 release. *** **While we keep working to improve the app and fix a few minor issues as described in the section below, we strongly encourage you to use CyNDEx-2, provide feedback and report issues to help us improve our product and better serve the scientific community** *** ###[http://chianti.ucsd.edu/cyto_web/bugreport/bugreport.php CLICK HERE TO REPORT A BUG IN CyNDEx-2] *** ## Known Issues and Limitations - **CyNDEx-2 v2.3.0** is only compatible with Cytoscape 3.7 or higher. - If you are running Cytoscape 3.6.x, please use **CyNDEx-2 v2.2.3**. - If you are running a Cytoscape version older than 3.6.0, please use the [http://apps.cytoscape.org/apps/cyndex **CyNDEx App**] instead. - **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_. *** *** ## To Find and Load a Network When installed, a new search bar will be added to the search widget in Cytoscape's network control panel. To activate it, pull down the list of data sources and choose the NDEx Database option. You can enter your query directly into the adjoining text box; your query can be a keyword, a public network's UUID, a gene symbol or a private network's "Sharable URL". The search bar also provides a pop up panel containing search tips as shown below: <a href="http://home.ndexbio.org/img/sshot1.png"> <img src="http://home.ndexbio.org/img/sshot1.png"></a> Alternatively, you can use the convenient NDEx button in the Cytoscape toolbar: <a href="http://home.ndexbio.org/img/sshot2.png"> <img src="http://home.ndexbio.org/img/sshot2.png"></a> Once you click the search button, the CyNDEx-2 Finder window will appear where you can customize display options and import one or more networks into Cytoscape. <a href="http://home.ndexbio.org/img/Cyndex2-browser.png"> <img src="http://home.ndexbio.org/img/Cyndex2-browser.png"></a> *** ## To Save a Network Saving a network to NDEx is very simple: as for loading networks, you can use the NDEx button in the Cytoscape toolbar as shown below: <a href="http://home.ndexbio.org/img/sshot3.png"> <img src="http://home.ndexbio.org/img/sshot3.png"></a> Alternatively, you can open the File menu, -> Export -> and choose to save to NDEx either an individual network or a network collection: <a href="http://home.ndexbio.org/img/exportmenu.png"> <img src="http://home.ndexbio.org/img/exportmenu.png"></a> Finally, you can simply right-click on your network and use the new context menu item to save your network to NDEx. A similar context menu item is also available when you right-click on a collection. <a href="http://home.ndexbio.org/img/sshot4.png"> <img src="http://home.ndexbio.org/img/sshot4.png"></a> After selecting the suitable export option, the CyNDEx-2 Saver window will be opened: here you can fill out network metadata, choose whether you want to keep the network PRIVATE or make it PUBLICLY visible to other NDEx users and visitors as well as decide whether you want to save a new copy or update the existing one. **IMPORTANT NOTE: in order to save a network to NDEx, you must log in to your NDEx account using the built-in "Account Manager" available in the upper right hand corner of both the Finder and Saver windows as shown below: <a href="http://home.ndexbio.org/img/export-browser.png"> <img src="http://home.ndexbio.org/img/export-browser.png"></a> *** ## Managing your NDEx Profiles CyNDEx-2 comes with a nifty account manager. Both the CyNDEx-2 Finder and Saver have a menu in the upper right hand corner that can be used to add a userID/password for any NDEx server you wish to save and load networks from. Simply click on the account manager box in the upper right hand corner, and the account manager will open. You may add multiple profiles, which will then be available in a list when hovering over the account manager. <a href="http://home.ndexbio.org/img/accountmanager.png"> <img src="http://home.ndexbio.org/img/accountmanager.png"></a> *** ## Sharing you NDEx Networks After succesfully saving a network to NDEx, you will be presented a confirmation screen showing the UUID of the network you just saved. The screen also gives you the option to enable the "Sharable URL" for that network and copy it to your clipboard so that you can easily share it with collaborators via email or include it in a grant proposal or publication: <a href="http://home.ndexbio.org/img/after-export.png"> <img src="http://home.ndexbio.org/img/after-export.png"></a> *** ***

2.3.0

Works with Cytoscape 3.7

Release Notes

1. Added new NDEx Toolbar button with import and export menu items. 2. Added context menu options for saving networks or collections to NDEx. 3. Reduced app size: JXBrowser JARs no longer packaged with app. 4. Added CyREST endpoint for importing pure CX. **Bug Fixes**: 1. Dialog window is always on top, non-modal to allow interaction with CyNDEx2 and Cytoscape simultaneously. 2. Cytoscape Annotations survive round trip. 3. Disabled Property Editor when saving collections. 4. Better parameter checking for CyREST API.

2.2.3

Works with Cytoscape 3.6

Release Notes

1. Supports the updated CX specification. These CX data types: ‘float’, short’, ‘byte’ and ‘char’ are deprecated. cyNDEx-2 supports reading in CX networks that have these data types, but will convert them to double, long or string in the output. 2. Augmented the cyREST endpoints to take Google ID token as an authentication method. 3. Added new cyREST endpoint to allow users to load a CX network to Cytoscape. 4. Added the “Import Network from NDEx” and “Export Network to NDEx” button to the menu bar. 5. Added File -> Import -> Network from NDEx … item in the menu. 6. Added “Export Network to NDEx…” item in the network context menu in the Network panel. 7. Reduced the size of cyNDEx-2 app to about 8M from about 170M. 8. Faster start up time. 9. Setting visibility is no longer allowed when user updates a network. The system status of the old network will be kept when updating a network. 10. Added progress bar when loading network from NDEx. 11. Network without a view can be exported to NDEx now. **Bug fixes**: 1. CX float data type issues. 2. Network that has group nodes can round trip to NDEx now. 3. Issues in continuous mapping when using long values. 4. Issues of potential conflict on port 2222, which was used to serve the web pages used in cyNDEx-2. 5. cyRest and cy-NDEx start up racing condition issue. 6. When exporting a network as a public network. A URL is returned in the dialog window instead of asking user to create a sharable URL.

2.2.2

Works with Cytoscape 3.6

Release Notes

Bug fix: 1. CyNDEx-2 failed to initialize in certain conditions. Core apps are now intialized taking into account dependencies.

2.2.1

Works with Cytoscape 3.6

Release Notes

1. Anonymous users can be added on any server now. 2. Sharable URL can be created on servers other than public server. 3. Removed error message when image fails to be saved after network is successfully exported. 4. Added 10px at bottom of search tips pop-up window. 5. Saving cocanet certain networks no longer gives warnings in NDEx. 6. Added warning when the user has both cyNDEx1 and cyNDEx2 installed. The message only pops up the first time when the user opens the search or export windows . 7. Fixed a compatibility issue when reading networks created with old Cytoscape aspects such as “visualProperties”. 8. Adding a warning message when a user tries to import a large (>200000 edges) network. 9. Removed the Cytoscape warning for importing large network, because it was covered by the browser window and user wouldn't be aware they need to respond to the dialog box. 10. CyNDEx-2 import logic 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. 11. Cytoscape and CyNDEx version is recorded in the provenance when a user saves or updates a network in NDEx. 12. Supports exporting 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. 13. When a user exports a singleton network, the name column on each node is used to populate the ‘name’ field in the 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 saves a network as a Cytoscape collection in NDEx, the values in both ‘shared name’ and ‘name’ will be preserved. 14. When upgrading CyNDEx-2, the old Cyndex-2 directory was removed instead of overwriting it with new files. JxBrowser cache is also cleared during update. 15. Date string is reformatted to be consistent with NDEx web app. 16. Network description was displayed as a tooltip in the browser window, the tooltip is removed from this release. 17. Description and link are added to the dropdown menu of NDEx search bar. Bug fixes: 1. Sharable URL search only works for URLs from public server. 2. the visual mappings were not exported correctly when: * The column name, which the mapping was on, has ‘,’ or ‘=’ in it. * There is a discrete mapping on a column and one of the values of the column has ‘,’ or ‘=’ in it. * Other visual styles that has “,” or “=” in the serialized value.

2.2.0

Works with Cytoscape 3.6

Release Notes

- Lossless data round-trip between NDEx and Cytoscape - Search feature allows "Share URLs" - Enforced minimum annotation requirements when saving a network as Public - Added post-export feature to enable "Share URL" - Individual menu items for exporting single networks or collections

CYTOSCAPE 3

Version 2.3.0

Released 25 Oct 2018

Works with Cytoscape 3.7

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