I'm interested in building my own motherboard from scratch. tried doing searches and all i can find is prototyping motherboard manufactures.
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M$2 Answers
If it's the former, here's some links that might be interesting:
http://hackaday.com/2009/01/10/n8vem-single-board-z80-computer/
http://chaokhun.kmitl.ac.th/~kswichit/68k/68k.html
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M$Wire wrapping is how this is (or at least was) handled in the day, then you would literally stack your proto boards on top of one another with ribbon cable jumpers connecting the layers.
First step would be to get some reference designes, see whats involved, then decide if you want to peruse it further.
Experience
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M$
sounds too kool - so id start with finding designs or is there software?
here's something interesting
http://www.cs.binghamton.edu/~reckert/sbc.htm
i think this might be a good start for me
no its the latter
im sure that the first prototype was not all printed on a circuit board someone cobbled together pieces and parts to work together ugly big and somewhat limited it was
but with work they refined it id like that experience.