Autoprotocol started from two basic beliefs: that a huge lack of reproducibility in biological research stems from the ambiguity inherent in natural-language protocols, and that lab automation was too hard to use and too fragmented. We observed wealthy labs buying $200,000 robots that would sit idle on the bench after six months because they were too complex for regular use. We struggled with reliable biology in our own hands believing that it got better at bigger companies, only to read Amgen's 2012 article in Nature where they attempted to reproduce 53 "landmark" cancer studies and could only validate six.
What Is Autoprotocol?
- Autoprotocol is a formal language for specifying experimental protocols.
- Autoprotocol is an answer to the question: how do we encode experimental protocols such that they are completely unambiguous?
- Autoprotocol is unambiguous.
- It is impossible to encode "mix gently" or "incubate overnight" in Autoprotocol. You must specify all parameters needed to fully describe the operation in question.
- Autoprotocol-encoded protocols are just data.
- Protocols don't need any interpretation or evaluation: autoprotocol is not a programming language and encoded protocols contain no logic.
What Is Autoprotocol Not?
- Autoprotocol is not a programming language.
- Autoprotocol-encoded protocols contain no logic and are guaranteed to complete in a fixed amount of time. Autoprotocol can be generated by programming languages and consumed by programs of all kinds, but Autoprotocol itself is just a data standard. You can do very sophisicated things like autonomous directed evolution or running self-healing assays using code that generates Autoprotocol, but such logic is "external" to the protocol itself.
- Autoprotocol contains no specific knowledge of biology.
- Autoprotocol is designed to be very flexible with no embedded "domain knowledge" with respect to what the protocol encodes, but has been developed with the life sciences in mind.
- Autoprotocol does not necessarily imply robotics or automation.
- Autoprotocol is just a standard way of unambiguously specifying experimental protocols. You can use that specification for any number of things, ranging from mining patterns in published protocols to generating English-language text to perform by hand.
- Autoprotocol is not a Transcriptic product.
- Autoprotocol is a formal open standard that was originated at Transcriptic, but is not at all dependent on Transcriptic. You can use Autoprotocol without a Transcriptic account or having to use any other Transcriptic services. You are free to build new software and hardware that understands Autoprotocol without paying anything to Transcriptic.