AUTOPROTOCOL SUMMIT 2016 - PUSHING REPRODUCIBILITY AND USABILITY

Ben Miles on 7/13/16 6:01 PM

We recently hosted the second annual Autoprotocol Summit at our new San Francisco office. With the gorgeous city of San Francisco as a backdrop, we took the day to think about how Autoprotocol has changed since the first Autoprotocol Summit in 2016, and how we can make it even better.

Joined by developers and vendors from a number of companies and organizations, we met to celebrate the achievements of the last six months and focus on making Autoprotocol more usable and reproducible. Here's a report from the trenches!

We began with a recap of the progress made since the last summit.

Highlights included:

  1. An increase in Autoprotocol's scientific coverage with 15 new Autoprotocol Standard Changes (ASCs) allowing for new instructions like magnetic transfer for DNA, RNA, protein, and cellular bead based purification to purification by gel electrophoresis.

  2. Improvements in developer tools for writing and analyzing Autoprotocol with the release of Autoprotocol-Utilities, updates to Autoprotocol-Python, and to the data analysis components of the Transcriptic Python Library (TxPy).

  3. The ability to increase reproducibility with the addition of time constraints as a top level feature in Autoprotocol.

Overall, it's never been easier to write and use Autoprotocol.

Next we took a look at how Autoprotocol is being used in the wild. We heard about all of the projects using Autoprotocol inside and outside of Transcriptic including autoprotocol-ruby, assaytools, and “How to make any protein you want for $360”.

Developer's perspective from Brian Naughton

Developer's perspective from Brian Naughton

Autoprotocol developer Brian Naughton presented his experiences using and contributing to Autoprotocol. Brian felt that Autoprotocol's underlying JSON and Python infrastructure was a strong choice for standard adoption because it was very accessible to scientists. Brian, who uses Autoprotocol mainly in conjunction with Transcriptic, also described how the development of TxPy has made it much easier to launch his experiments. Finally Brian concluded with a brief mention of his plans to look at generating sequences of experiments with workflow tools to make chained experiments a reality.

In the Q&A period, Brian touched on the need for greater transparency in how Autoprotocol is translated to a physical experiment (especially with regards to inventory) as well as the need for more tools to help abstract away some lower-level decisions which scientists may be less interested in (like liquid-handling parameters).

The Need for Platform Independence by Conner Warnock

The Need for Platform Independence by Conner Warnock

Next, Connor Warnock from Notable Labs brought a vendor's perspective to the day. Connor shared a common pain point faced by many automation startups: the lack of standardization around devices and their protocols. His presentation focused on the possibility for Autoprotocol to become a universal common interface and compared the current stage of Autoprotocol to the early days of HTTP, where the long-term payoff is clear, but more immediate payoff is required for driving adoption. As a part of becoming a better layer for lab automation, there was substantial discussion around the possibility of broadening the scope of Autoprotocol to cover open-sourcing Lab Inventory Management Systems (LIMS) as well as open-sourcing device-driver wrappers.

After the two presentations, everyone headed to the Goals session excited to move Autoprotocol forward. After a short icebreaker, we went into brainstorming mode to discuss the problems which are confronted by Autoprotocol's users and potential users. There was a lively discussion with potential users ranging widely from pharmaceuticals to developing countries to even the FBI. The brainstorming led to three key areas for future Autoprotocol growth:

  1. Visualization and Intent
  2. Reproducibility
  3. Community Adoption

With the topics to be tackled agreed upon, we broke for lunch and started informal discussions.

Following lunch, we looked into the possibility of improving the ASC contribution process. There was general consensus that the current process should be made more transparent and explicit. As one action item moving forwards, the public discussion around submitting new ASCs will begin much earlier in the developers forums, and interested parties should join in on the contribution process. There was also substantial discussion on changing the underlying format of Autoprotocol to more naturally support the communication of experimental intent which would make it easier and more natural for scientists to use Autoprotocol for communicating scientific protocols.

Finally, we broke into small groups to tackle the three key areas of Visualization, Reproducibility, and Community Adoption brought up earlier. The room came up with a lot of great ideas and rapid prototypes. To highlight a few, there were mocks of better protocol visualization tools, a drag-and-drop system for creating Autoprotocol, and the groundwork for more comprehensive standards for reagents and data. Be on the lookout for more specific implementations to come!

Thank you all who attended Autoprotocol Summit 2016. None of the growth in Autoprotocol would be possible without the enthusiasm and care of the developer community. Shoutouts go to external developers such as Brian Naughton and Transon Nguyen & Connor Warnick from Notable Labs. Thanks as well to Ben Miles and Yang Choo for leading and organizing the sessions and Taylor Murphy for handling the logistics. Thanks also for the support of the Autoprotocol Curators including Tali Herzka from Verily and Vanessa Biggers, Jeremy Apthorp & Peter Lee from Transcriptic. And of course, a big thank you to the Autoprotocol community. We are looking forward to another great year of Autoprotocol ahead.