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Obviously, I can't get to the BIOS after the OS is loaded.

But is it somehow possible to invoke BIOS functionality/interact with it from within the OS? Does the OS do it? Is it possible for a user mode applications? (all of this in protected mode, because I've read it's possible in real mode.)

Or is the BIOS only needed before the OS loads?

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It depends on a few things. For starters on the OS.

  • If you boot DOS (ancient, I know) then DOS will do most of its jobs via BIOS calls.
  • If you use a modern OS then that will generally take over control from the BIOS.

Secondly, do you consider ACPI part of the BIOS?
That part keeps on running even after a modern OS is loaded).

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DOS (or OpenDOS) boots are not completely obsolete. Diagnostics often run that way. – Isaac Rabinovitch Apr 22 '13 at 7:08

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