I find that Bio-Linux works like Ubuntu 10.04 version. whenever it asks for upgrade it does not upgrade saying that the third-party software is disabled. I don't get where this third-party software is and what are those. can anyone please suggest how can I upgrade ?
There is specific information on how to upgrade Bio-Linux on the project website, including an official update helper script that is designed to handle the known issues related to third-party software sources.
If you still have problems after following these instructions, the Bio-Linux mailing list is probably the best place to ask for help.