Go to www.cytoscape.org and click in upper right corner ‘Download Cytoscape 2.6.3’
Fill in the information and click ‘Proceed to Download’.
Chose the Platform specific bundle and click on your operating system, this will start the download. When it has finished install the program.
NB: If you are using the CBS portable computers you must install cytoscape on the Desktop, you do not have permissions to install it in Program Files.
If you do not have Java Runtime Environment installed, download and install it from: http://www.java.com/en/download/manual.jsp.
Installing BiNGO plugin
Navigate via the Cytoscape website to PlugIns and select ‘Functional Enrichment’ and then BiNGO or go directly to http://www.psb.ugent.be/cbd/papers/BiNGO/. If the other sites are down you can also download it directly from here.
Click Download and then ‘I Agree’ which will start the download of the BiNGO.jar file. Place it in the /plugins directory under your Cytoscape installation directory and BiNGO is ready to use.