Sorry for the plug, but you can kind of simulate that process in the nand2tetris.org course (also available on Coursera). In that course, you build a computer

Sorry for the plug, but you can kind of simulate that process in the nand2tetris.org course (also available on Coursera). In that course, you build a computer (through hardware simulators) that can run binary programs. Then you build up a programming toolchain: stack based virtual machine language that compiles to assembly, and a high level language that you compile to the VM language. You also write the assembler that translates your assembly into ones and zeros, which are like the punch cards. So you can simulate what it's like to be writing the binaries: if you take out the compilers, you can go through the process of manually translating your high level code into punchcards. The high-level lines become stack operations, which become assembly commands, which become binary words. (For efficiency reasons, you'd probably program directly in assembly where possible, but you can add on the abstraction levels.)