A proxy server is a server that acts as an intermediary between computers seeking resources from other servers.  Typically these are used to add a layer of security to a network by screening what goes in and out of a network.

If your institution uses a proxy server and a FlowJo site license you will need to add the proxy settings to FlowJo so that your site license can be validated on start up.  When FlowJo is started initially, or anytime subsequently without an internet connection, a proxy setting screen will appear.



Contact your IT department to find out your companies specific host name, what port should be used, and what your user name and password are.


If you are a network administrator

Setting up the proxy for all users can be done by creating / modifying a preference file, as FlowJo licensing variables are stored in the preferences file, and sharing this file with all users.  The preference file is located in:

  • PC – C:UsersYour user nameAppDataRoamingFlowJo10
  • Mac – UsersYour user nameLibraryPreferences

The FlowJo preferences are an XML file called “FlowJo10.prefs”. To create a new preference file, you can start with this example stub, and fill it out with your specific information:

<Prefs version=”17.0″>
<License serialNumber=”” proxyport=”” proxyhost=”” proxyuser=”name” proxypassword=”cGFzcw==”/>


If you open an existing preference file and modify it, you’ll need to add the proxy attributes to the ‘License serialNumber’ object following the format above.

Automating proxy settings using environment variables

Starting with FlowJo version 10.0.7 site wide installation of a proxy can also be done with environment variables.  FlowJo will look at the environment variables:


If these variables have usable values, FlowJo will use them accordingly. This way if you can set these prior to FlowJo installation (and in case of FLS SN, after user-registration on FLS, ) you fly through all the network/licensing dialogs, which would otherwise sequentially come up for /first time/ clean /re / installs.