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At school I've always rotate clockwise, with $90^0$ being straight up.

But I see some system operates with $0$ being straight up and clockwise rotation, does someone know why this is?

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It gets worse; in more advanced mathematics, it's common for $0$ to be to the right, and angle to increase as you rotate counterclockwise. It's just convention, doing what's most convenient at the time. – Gerry Myerson Apr 17 '13 at 6:35
The second system you describe is what is used in navigational "bearing". Due North is 0º (sometimes called 000), 90º is East (or 090), South is 180, and West, 270. Conventions for different sorts of measurements comes from particular disciplinary, historical, or even regional practices. The more kinds of work you do, the more you run into this: you come to accept that and learn them. It is a lot like dealing with dialects of a language... – RecklessReckoner Apr 18 '13 at 17:49

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