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YASP (Yet Another Simple Processor) is a 8-bit microprocessor with microcontroller capabilities (I/O ports, REQ, ACK) that can be used as a small computer for educational purposes. Its development environment includes simulators and assemblers.
Tori assim is an assembler for the educational Txori assembly language and simulator for the bird processor. It's being developed as an open source clone for the closed source and windows only BIRD.
The CLOWN virtual machine is a microcomputer simulator for operating system research. CLOWN emulates a realistic, though vastly simplified computer system. Besides the simulator itself, it includes assembler, linker, and disk maintenance tools.