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I have several applications including Mathematica and VirtualBox(with Ubuntu) that I constantly run in the background.

Ideally I would like these applications to automatically start at boot but hide to system tray where I can access them if needed.

I would ideally like the application to be open source(and maybe paid) solely because of security reasons. Back in the day I used to minimize using the middle click applications to the system tray and there are applications which do this but then I have to manually minimize each application I want to start automatically which is annoying.

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