Is there a sample output spec, compared with the norm of human readable input? As is, this seems like a solution for computers, not folks in the lab.
At its core, Autoprotocol is just a way to agree on how to capture all of the information about an experimental method, which in itself turns out to be deceptively complex (though looks a little obvious afterwards when you see it). That description is just JSON: it can be generated by scripts, UIs, or written by hand (and we at Transcriptic + customers do all three) and it can be consumed by lots of different things. If you have a lab of your own, we'll release our to-english converter soon! You can also post the protocol JSON to Transcriptic to run it in our cloud lab environment, which produces a preview of the instructions that looks like this: http://imgur.com/EOBfZfW
I know the main use-case may be inter-device, but someday you might want to embed a short hint or explanation along with a particularly arcane set of instructions or parameters.