Imperial College London
Portrait Picture

Guy-Bart Stan

Faculty of Engineering, Department of Bioengineering

Visiting Professor
 
 
 
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Contact

 

+44 (0)20 7594 6375g.stan Website

 
 
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Location

 

B703Royal School of MinesSouth Kensington Campus

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Summary

 

Publications

Citation

BibTex format

@article{Sechkar:2022:synbio/ysac004,
author = {Sechkar, K and Tuza, ZA and Stan, G-B},
doi = {synbio/ysac004},
journal = {Synthetic Biology},
pages = {1--8},
title = {A linear programming-based strategy to save pipette tips in automated DNA assembly},
url = {http://dx.doi.org/10.1093/synbio/ysac004},
volume = {7},
year = {2022}
}
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RIS format (EndNote, RefMan)

TY  - JOUR
AB  - 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 optimizationof how DNA assembly reaction mixes are prepared remains largely unexplored. Here, we focus on reducing the pipettetip consumption of a liquid-handling robot as it delivers DNA parts across a multi-well plate where several constructsare being assembled in parallel. We propose a linear programming formulation of this problem based on the capacitatedvehicle routing problem, as well as an algorithm which applies a linear programming solver to our formulation, henceproviding a strategy to prepare a given set of DNA assembly mixes using fewer pipette tips. The algorithm performedwell in randomly generated and real-life scenarios concerning several modular DNA assembly standards, proving capableof reducing the pipette tip consumption by up to 59% in large-scale cases. Combining automatic process optimizationand robotic liquid-handling, our strategy promises to greatly improve the efficiency of DNA assembly, either used aloneor combined with other algorithmic DNA assembly optimization methods.
AU  - Sechkar,K
AU  - Tuza,ZA
AU  - Stan,G-B
DO  - synbio/ysac004
EP  - 8
PY  - 2022///
SN  - 2397-7000
SP  - 1
TI  - A linear programming-based strategy to save pipette tips in automated DNA assembly
T2  - Synthetic Biology
UR  - http://dx.doi.org/10.1093/synbio/ysac004
UR  - https://academic.oup.com/synbio/article/7/1/ysac004/6552983
UR  - http://hdl.handle.net/10044/1/95959
VL  - 7
ER  -
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