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. 2025 Apr 11;10(1):ysaf009.
doi: 10.1093/synbio/ysaf009. eCollection 2025.

OT-Mation: an open-source code for parsing CSV files into Python scripts for control of OT-2 liquid-handling robotics

Alex Laverick  1 , Katherine Convey  1 , Catherine Harrison  1   2 , Jenny Tomlinson  2 , Jem Stach  1 , Thomas P Howard  1
Affiliations

OT-Mation: an open-source code for parsing CSV files into Python scripts for control of OT-2 liquid-handling robotics

Alex Laverick et al. Synth Biol (Oxf). .

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 utilizing 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. Graphical Abstract.

Keywords: Opentrons OT-2; robotic liquid handling; statistical design of experiments.

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Conflict of interest statement

None declared.

Figures

None
Graphical abstract
Figure 1.
Figure 1.
OT-Mation workflow. OT-Mation was designed to support the iterative, sequential workflow required in statistical DoE but can be applied in any iterative design–build–test–learn cycle. In a cyclic experimental process, after results from an experiment have been analysed, new factor combinations or parameters are chosen. Using OT-Mation, only the ‘Experimental Parameters’ CSV file (red) needs to be changed to generate a new protocol—and this is compatible with the output format of many statistical packages removing the need for human intervention in transferring data.
Figure 2.
Figure 2.
Layout of the four user defined CSV Files central to OT-Mation. A. Experimental Parameters. B. Labware Inventory. C. Stock Inventory. D. Pipette Settings.
See this image and copyright information in PMC

References

    1. Jessop-Fabre MM, Sonnenschein N. Improving reproducibility in synthetic biology. Front Bioeng Biotechnol 2019;7:18. doi: 10.3389/fbioe.2019.00018 - DOI - PMC - PubMed
    1. Kong F, Yuan L, Zheng YF et al. Automatic liquid handling for life science: a critical review of the current state of the art. J Lab Autom 2012;17:169–85. doi: 10.1177/2211068211435302 - DOI - PubMed
    1. Storch M, Haines MC, Baldwin GS. DNA-BOT: a low-cost, automated DNA assembly platform for synthetic biology. Synth Biol (Oxf) 2020;5:ysaa010. doi: 10.1093/synbio/ysaa010 - DOI - PMC - PubMed
    1. Whitehead E, Rudolf F, Kaltenbach HM et al. Automated planning enables complex protocols on liquid-handling robots. ACS Synth Biol 2018;7:922–32. doi: 10.1021/acssynbio.8b00021 - DOI - PubMed
    1. Baker M. 1,500 scientists lift the lid on reproducibility. Nature 2016;533:452–54. doi: 10.1038/533452a - DOI - PubMed

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