"The Elements of Computing Systems: Building a Modern Computer from First Principles" by Noam Nisan and Shimon Schocken is a project-based book that demonstrates how to build a computing system from the ground up. One learns about combinatorial & sequential logic, ALU & memory chips, CPU & von Neumann architecture, machine & assembly language, assemblers, virtual machines, parsing and code generation.
The hardware part is built using a freely provided Hardware Simulator and the software part can be tackled in any programming language(s) you choose. You can get started right now by going to the book's website @ http://www1.idc.ac.il/tecs/ which has some sample chapters and all the tools (like the Hardware Simulator) one will need to complete these projects.
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