Flexible automation for robotic bioengineering

Jimmy Day/MIT Media Lab

Liquid handling robots are key components of modern biotechnology labs, but they largely function to spare humans from laborious or repetitive protocols. We decided they could do more.

Upgrading Hamilton robots

Many companies offer superb liquid-handling robots, but their software is narrowly designed to automate traditional hand-pipetting protocols and struggles to harness the full capabilities of robotic manipulation. 

To change that for our two Hamilton robots—and through open-source, all Hamilton robots—we developed Pyhamilton, an open-source Python package that eliminates these constraints, enabling experiments that could never be done by hand. 

We used Pyhamilton to double the speed of automated bacterial assays over current software and execute complex pipetting patterns to simulate population dynamics, and incorporated feedback-control to maintain hundreds of remotely monitored bacterial cultures in log-phase growth without user intervention. 

Finally, we applied these capabilities to comprehensively optimize bioreactor protein production by maintaining and monitoring fluorescent protein expression of nearly 500 different continuous cultures to explore the carbon, nitrogen, and phosphorus fitness landscape. Our results demonstrate Pyhamilton’s empowerment of existing hardware to new applications ranging from biomanufacturing to fundamental biology.