## *Core App*: CyNDEx-2
### Note: This app is pre-installed in Cytoscape 3.9 or later
**_You should not download this app_ from the store yourself. If Cytoscape detects that a new version is available in the App Store, it will notify you as it's starting and will give you a chance to download it directly.**
**_You should not download this app_ if your Cytoscape is earlier than 3.9. An earlier version of this app is pre-installed in your Cytoscape, and this app cannot replace it.**
# Welcome to CyNDEx-2!
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We strongly recommend you always use the latest Cytoscape version available as well as the latest versions of all "Core" apps, including CyNDEx-2.
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**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**
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###[http://chianti.ucsd.edu/cyto_web/bugreport/bugreport.php CLICK HERE TO REPORT A BUG IN CyNDEx-2]
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## Known Issues and Limitations
- If you are running Cytoscape 3.7.x, please use **CyNDEx-2 v3.0.1**.
- 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.
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## 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 allowing you to 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>
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## 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 -> Network to NDEx.
<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 and decide whether you want to save a new copy of the network or update the existing one. Starting from CyNDEx-2 v3.3.0, it is now possible to update a target network even after opening a session file or interrupting a work session in Cytoscape. To manually specify the UUID of the target network to update, click the icon indicated by the red arrow below. In order to update a target network in NDEx, the user still needs to have edit permission on that network.
**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 indicated by the red oval below:
<a href="http://home.ndexbio.org/img/export-browser.png">
<img src="http://home.ndexbio.org/img/export-browser.png"></a>
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## Managing your NDEx Profiles
CyNDEx-2 comes with a simple account manager. Both the CyNDEx-2 Finder and Saver have a button 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 as shown in the screenshot below, and the account manager will open.
You may add multiple profiles, which will then be available in a list when clicking over the account manager button.
Once a profile is created and selected, the "Export" button in the bottom right corner (red oval) will be enabled allowing you to save your network to NDEx.
<a href="http://home.ndexbio.org/img/accountmanager.png">
<img src="http://home.ndexbio.org/img/accountmanager.png"></a>
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