التفاصيل البيبلوغرافية
العنوان: |
linear programming-based strategy to save pipette tips in automated DNA assembly. |
المؤلفون: |
Sechkar, Kirill, Tuza, Zoltan A, Stan, Guy-Bart |
المصدر: |
Synthetic Biology (23977000); 2022, Vol. 7 Issue 1, p1-8, 8p |
مصطلحات موضوعية: |
LINEAR programming, DNA, SYNTHETIC biology, AUTOMATION, ROBOTICS |
مستخلص: |
Laboratory automation and mathematical optimization are key to improving the efficiency of synthetic biology research. While there are algorithms optimizing the construct designs and synthesis strategies for DNA assembly, the optimization of how DNA assembly reaction mixes are prepared remains largely unexplored. Here, we focus on reducing the pipette tip consumption of a liquid-handling robot as it delivers DNA parts across a multi-well plate where several constructs are being assembled in parallel. We propose a linear programming formulation of this problem based on the capacitated vehicle routing problem, as well as an algorithm which applies a linear programming solver to our formulation, hence providing a strategy to prepare a given set of DNA assembly mixes using fewer pipette tips. The algorithm performed well in randomly generated and real-life scenarios concerning several modular DNA assembly standards, proving to be capable of reducing the pipette tip consumption by up to |$59\%$| in large-scale cases. Combining automatic process optimization and robotic liquid handling, our strategy promises to greatly improve the efficiency of DNA assembly, either used alone or combined with other algorithmic DNA assembly optimization methods. Graphical Abstract [ABSTRACT FROM AUTHOR] |
|
Copyright of Synthetic Biology (23977000) is the property of Oxford University Press / USA and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.) |
قاعدة البيانات: |
Complementary Index |