OT-Mation: an open-source code for parsing CSV files into python scripts for control of OT-2 liquid handling robotics
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Abstract
OT-Mation is an open-source Python script designed to automate the programming of OT-2 liquid handling robots, making combinatorial experiments more accessible to researchers. By parsing user-defined CSV files containing information on labware, reagents, pipettes, and experimental design, OT-Mation generates a bespoke Python script compatible with the OT-2 system. OT-Mation enhances reproducibility, reduces human error, and streamlines workflows, making it a valuable addition to any laboratory utilising OT-2 robotics for liquid handling. While OT-Mation can be used for setting up any type of experiment on the OT-2, its real utility lies in making the connection between multifactorial experimental design software outputs (i.e. Design of Experiments arrays) and liquid-handling robot executable code. As such, OT-Mation helps bridge the gap between code-based flexibility and user-friendly operation, allowing researchers with limited programming skills to design and execute complex experiments efficiently.
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As this tool simplifies the programming process, it also allows researchers with limitedcoding experience to leverage the full capabilities of the OT-2
I really like this approach to making structured and reproducible Opentrons protocols without generating entire new scripts each time. I'm curious how LLMs might fit in upstream of this, could you describe your protocol in plain language, have the LLM generate the csv files, then run protocol generation script? Could the LLM just generate the protocol at this point?
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