I understand that Firefox addins can be created in Javascript and Chrome.
How do they run advanced graphics applications such as CoolIris ?

(source: cooliris.com)
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Cooliris uses native compiled code utilizing graphics acceleration on the platforms it supports.
You can get a full screen GUI if you use Flash, but the user is informed about it (try watching a YouTube vid in fullscreen) and also the user can’t do everything they can otherwise, like type using the keyboard.