I am about to start my thesis this January 2008. I pick java as my PL but I don't know any database right now.. is there any database than i could learn easily and also fit to java? please help me..

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it's not as if your DB will be a part of the programming language.
I would suggest you to use MySQL, it's free, and thus used for lots of examples you can find on the web.
if you would like to have a DB written in Java, there's Derby, but since I never used it myself, I won't say whether it's a good choice or not.

You need to ramp up on JDBC , it works with various databases.

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