Open source liquid handling automation at EnginZyme

Liquid handling robots are the best friends of the wet lab scientist. A liquid handling robot plays a key role when you need to screen for thousands of process conditions and enzyme candidates — as we do at EnginZyme.

In our early automation efforts, we relied on OT-2s for liquid handling. These inexpensive little fellows were easy to install, but they would only do what they had been instructed. One had to program the robots to move around, aspirate or dispense liquids while ensuring that the program, or protocol, uploaded to the robot represented the exact intentions of the scientist.

EnginZyme facilities
Liquid handling robots — the best friend of any wet lab scientist

Programming robots…

Opentrons Labworks, the company behind the OT-2s, open-sourced both the hardware and software design so that any engineer can tinker under the hood and extend the robot’s functionalities. By reading the design blueprints and code repositories, we could integrate custom accessories in the robot’s deck and build software plugins that connect to other parts of our company’s IT ecosystem.

The OT-2’s robot computer is a Raspberry Pi running a Linux distribution, and the robot protocols are python scripts written using the opentrons python library. In the beginning, scientists that were not familiar or very comfortable with python coding had to ask for help to create their protocols. Over time, we identified many common parameters and actions that we could copy/paste across protocols. This was the beginning of our own systematic protocol designer: restricting the humongous possibilities of a python script to a set of instructions that included:

  • The definition of the robot’s pipettes and labware
  • A series of liquid handling actions with aspiration and dispense locations and volumes
  • A series of miscellaneous instructions, like repeating a step or sending a notification

Scientists would sketch the liquid handling instructions from which a python script had to be written

Generating a robot protocol from a set of instructions simplified the life of the automation engineers since they could very quickly iterate a design by modifying the instructions file. The next step was to take the engineer out of the loop and let the scientist design and shuffle the liquid handling steps at will.

…with a “no-code” Protocol Designer

Our scientists and software developers started planning how to generate the robot protocol’s python code without having to deal with the intricate syntax details of a programming language. The “no-code” solution was a web application where users could create an instructions file and then generate a protocol file that would be uploaded to the robots.