Flexible Open-Source Automation for Robotic Bioengineering
bioRxiv preprint doi: https://doi.org/10.1101/2020.04.14.041368; this version posted April 16, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Flexible open-source automation for robotic bioengineering Emma J Chory1,2,3 *, Dana W Gretton1 *✝ , Erika A DeBenedictis1,4, Kevin M Esvelt1 1Media Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA 2Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA 3Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA 4Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA * Designates equal-contriBution ✝ Designates primary correspondence for software development INTRODUCTION Liquid handling robots have become a biotechnology staple1,2, allowing laBorious or repetitive protocols to Be executed in high- throughput. However, software narrowly designed to automate traditional hand-pipetting protocols often struggles to harness the full capaBilities of roBotic manipulation. Here we present 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. Next, we 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.
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