But I may have been a bit unclear about my mapping of computer and biology terminology to this question.

I tend to think of a computer programs as being mathematical machines, and proteins as being molecular/chemical machines. Motor proteins "walking" along microtubules is the most vivid example of this.

I'm sort of torn between both worlds here, honestly. I like both perspectives. Viruses especially have a very quinish quality to them in that they're stripped down to just enough stuff to get a host cell to make more viruses.