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A great book and accompanying software imo lacks just 2 things.

1:the building of the Nand gate itself and 2: the building of a flip flop.

Both these tasks can be easily accomplished with reference to the book 'Code' by Charles Petzold (http://www.amazon.com/Code-Language-Computer-Hardware-Softwa...)

and software such as this http://logic.ly/

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I haven't read 'Code' yet, but I think starting from NAND gates is right; it has to stop at some level. I feel CMOS, MOSFETs, semiconductor physics.. are all interesting topics, but this book is already too broad.

Code actually starts with relays.

Code is a great book. What I think is the most powerful and interesting point is that a computer can be built from (a sufficiently large number of) any component that can perform logic functions.

I stopped reading Nand2Tetris in any great amount of detail and just skimmed the rest after I saw that it confused Harvard (separate code and data) and Von Neumann (combined) architectures.

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