# Welcome to CyNDEx-2!
The latest **CyNDEx-2** build available here on the App Store (**v3.0.1**) is a recommended update!
**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 versions 2.3.0 and up** are 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:
Alternatively, you can use the convenient NDEx button in the Cytoscape toolbar:
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.
## 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:
Alternatively, you can open the File menu, -> Export -> and choose to save to NDEx either an individual network or a network collection:
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.
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:
## 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.
## Sharing your 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: