Proxy configuration for Cytoscape

In large companies, you often find that direct web access is blocked: you have to ask a proxy server to request web pages on your behalf (The proxy also does stuff like scanning for viruses and malware). As a consequence, all the software on your computer needs to be configured to be proxy-aware. This is usually done for you, but Bioinformaticians tend to use “non-standard” software that you’ll have to configure yourself.

If you are using Cytoscape 2.X or 3.0 behind a proxy, and you know your proxy settings, you may find the following useful.

Cytoscape has a “proxy server settings” dialog, as described in the manual. The problem is that it doesn’t work – it stores the proxy settings in a special way that only some bits of Cytoscape are aware of. It does not work for plug-ins (sorry, “apps”) that make use of off-the-shelf Java libraries.

Instead, go to your Cytoscape installation directory, and look for a file named Cytoscape.vmoptions. Enter the following lines at the top. Substitute the dummy host ( and port (8080) values for the appropriate values of your proxy.


This method works for Cytoscape internally as well as plug-ins and libraries, so you can just ignore the internal Proxy configuration dialog. I’ve tested this for Cytoscape 2.8.2 and 2.8.3, and it’s also relevant for Cytoscape 3.0. People from the Cytoscape mailinglist inform me that this will be changed in the upcoming Cytoscape 3.1.

I recommend putting the options at the top, because Cytoscape.vmoptions has a maximum of 9 options. Any more are quietly ignored.

In case you want to delete some to make space, I’ll explain the meaning of the default Cytoscape.vmoptions. The first three options increase the memory available to Cytoscape, and are potentially useful to keep if you deal with large networks:


The next two deal with anti-aliasing for font rendering. That’s ancient stuff, I can’t remember the last time I saw a Java application without anti-aliased fonts. I think you can remove them safely, and in the worst case you’ll just get some ugly text.


Finally, a note for Java developers: if you are trying to debug proxy issues, use the following snippet of code just before you make a web request. Sometimes the values of system properties are not what you think they are – with this you can confirm them.

// print out proxy settings for debugging purposes
for (String key : new String[] { "proxySet", "http.proxyHost",
        "http.proxyPort", "https.proxyHost", "https.proxyPort" })
    System.out.printf ("%30s: %40s\n", key, System.getProperty(key));

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