ArticleSLAS technology2019
Standardizing Automated DNA Assembly: Best Practices, Metrics, and Protocols Using Robots.
Article in SLAS technology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
16 citing papers in PubMed.
- Automated linear DNA assembly of A. thaliana's chloroplast and mitochondrial genome.Nucleic acids research · 2026Article
- CloneCoordinate: Open-Source Software for Collaborative DNA Construction.ACS synthetic biology · 2025Article
- Self-documenting plasmids.Trends in biotechnology · 2025Review
- Engineering biology and automation-Replicability as a design principle.Engineering biology · 2024Review
- Automated high-throughput DNA synthesis and assembly.Heliyon · 2024Review
- Enabling technology and core theory of synthetic biology.Science China. Life sciences · 2023Review
- PyLabRobot: An Open-Source, Hardware Agnostic Interface for Liquid-Handling Robots and Accessories.bioRxiv : the preprint server for biology · 2023Article
- AssemblyTron: flexible automation of DNA assembly with Opentrons OT-2 lab robots.Synthetic biology (Oxford, England) · 2023Article
- Advancing reproducibility can ease the 'hard truths' of synthetic biology.Synthetic biology (Oxford, England) · 2023Review
- Standardization of Synthetic Biology Tools and Assembly Methods forACS synthetic biology · 2022Review
- A linear programming-based strategy to save pipette tips in automated DNA assembly.Synthetic biology (Oxford, England) · 2022Article
- Enabling high-throughput biology with flexible open-source automation.Molecular systems biology · 2021Article
- Setting Up an Automated Biomanufacturing Laboratory.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Biological Materials: The Next Frontier for Cell-Free Synthetic Biology.Frontiers in bioengineering and biotechnology · 2020Review
- Modular cell-free expression plasmids to accelerate biological design in cells.Synthetic biology (Oxford, England) · 2020Article
- DNA-BOT: a low-cost, automated DNA assembly platform for synthetic biology.Synthetic biology (Oxford, England) · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
12 authors.
Funding
Abstract
The advancement of synthetic biology requires the ability to create new DNA sequences to produce unique behaviors in biological systems. Automation is increasingly employed to carry out well-established assembly methods of DNA fragments in a multiplexed, high-throughput fashion, allowing many different configurations to be tested simultaneously. However, metrics are required to determine when automation is warranted based on factors such as assembly methodology, protocol details, and number of samples. The goal of our synthetic biology automation work is to develop and test protocols, hardware, and software to investigate and optimize DNA assembly through quantifiable metrics. We performed a parameter analysis of DNA assembly to develop a standardized, highly efficient, and reproducible MoClo protocol, suitable to be used both manually and with liquid-handling robots. We created a key DNA assembly metric (Q-metric) to characterize a given automation method's advantages over conventional manual manipulations with regard to researchers' highest-priority parameters: output, cost, and time. A software tool called Puppeteer was developed to formally capture these metrics, help define the assembly design, and provide human and robotic liquid-handling instructions. Altogether, we contribute to a growing foundation of standardizing practices, metrics, and protocols for automating DNA assembly.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.