Show HN: The Autoprotocol Language Standard for Biology

What is the overall process when using autoprotocol? I presume there are standardized robotic workstations with the capability to - 'do biology'. My experience of microbiology is limited to high school biology experiments 20 years ago -sequencing DNA and culturing bacteria on a petri dish. What is it exactly like to do biology in a modern research setting? (rough high-level description/example appreciated :) )

Re: Show HN: The Autoprotocol Language Standard for Biology

#6

Post by nornagon » Wed, Feb 11, 2015, 5:29 AM UTC

dflock wrote: post #3

What's the 3rd party hardware/software support for this like?

Software-wise, there are a couple of unannounced things from our partners coming down the line that work with Autoprotocol, and several of our customers have been building on top of the autoprotocol-python[1] and autoprotocol-core[2] libraries. Hardware-wise, Autoprotocol is a description language, it could even be executed on a sufficiently meticulous "human" device. (We have a project in the works that transforms Autoprotocol into human-readable instructions suitable for inclusion in a publication.) Transcriptic is the only fully automated system today that accepts Autoprotocol, but we're working with other groups building low-cost hardware systems (in particular, OpenTrons) who want to build on top of the Autoprotocol standard.

[1]: https://github.com/autoprotocol/autoprotocol-python [2]: https://github.com/autoprotocol/autoprotocol-core

Re: Show HN: The Autoprotocol Language Standard for Biology

#7

Post by zevets » Wed, Feb 11, 2015, 5:42 AM UTC

nornagon wrote: post #4

Another of the devs here along with @therzka, happy to answer questions :)

This is neat, but you guys have failed on the basic human motivation. A python file isn't something I can take into the lab with me to reproduce an experiment. Does this spit out a useful human readable set of instruction?

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.

Re: Show HN: The Autoprotocol Language Standard for Biology

#8

Post by therzka » Wed, Feb 11, 2015, 7:02 AM UTC

zevets wrote: post #7

nornagon wrote: post #4

Another of the devs here along with @therzka, happy to answer questions :)

This is neat, but you guys have failed on the basic human motivation. A python file isn't something I can take into the lab with me to reproduce an experiment. Does this spit out a useful human readable set of instruction? 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.

Does this spit out a useful human readable set of instruction?

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

Re: Show HN: The Autoprotocol Language Standard for Biology

#9

Post by therzka » Wed, Feb 11, 2015, 7:31 AM UTC

fsloth wrote: post #5

What is the overall process when using autoprotocol? I presume there are standardized robotic workstations with the capability to - 'do biology'. My experience of microbiology is limited to high school biology experiments 20 years ago -sequencing DNA and culturing bacteria on a petri dish. What is it exactly like to do biology in a modern research setting? (rough high-level description/example appreciated :) )

At Transcriptic we perform experiments using what we call a workcell - a set of devices like liquid handlers (automated pipettors), PCR machines, and plate readers all linked together via a common interface and a robotic arm that moves containers between devices. That interface understands Autoprotocol and executes the instructions accordingly. Autoprotocol itself was designed to be an agreed upon standard for different types of laboratory automation (not just ours) to execute protocols.

An example of an experiment someone could run through our cloud laboratory interface would be to monitor the growth rate of bacteria expressing different genes. This would be done using a protocol that contains some pipetting steps to dilute the bacteria and then alternates between incubating the plate at 37 degrees and reading OD600 of its wells using a plate reader at a specified interval for a certain number of repetitions.

Re: Show HN: The Autoprotocol Language Standard for Biology

#10

Post by endeavour » Wed, Feb 11, 2015, 9:28 AM UTC

This is a really neat idea. I wrote test-scripts for cell culture machines a few years back. Great fun moving giant robotic arms around!

If you can indeed encode all the primitives needed to more formally describe an experiment this would be great.

Are you worried the language will endlessly grow in complexity as you find edge cases it doesn't support?