PASIV: A Pooled Approach-Based Workflow to Overcome Toxicity-Induced Design of Experiments Failures and Inefficiencies

Casas, Alexis; Bultelle, Matthieu; Motraghi, Charles; Kitney, R.I.

doi:10.1021/acssynbio.1c00562

Cited by 4 publications

(1 citation statement)

References 58 publications

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“…Gate assembly 5,6 , where multiple restriction enzymes are utilised and assemblies not conforming to standard transcriptional units e.g., operons, are not supported. Notably, BASIC DNA assembly was successfully applied to several areas of Synthetic Biology and Life Sciences research including combinatorial pathway engineering 3,11,12 , synthetic operon 10 & sRNA circuit design 13 , combinatorial gRNA expression for gene editing 14 , ribosome binding site (RBS) tuning and fusion protein engineering 7 .…”

Section: Basic Compares Favourably With Modular Methods Based On Goldenmentioning

confidence: 99%

basicsynbio and the BASIC SEVA collection: Software and vectors for an established DNA assembly method

Haines

Carling

Marshall

et al. 2022

Preprint

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Standardized DNA assembly methods utilizing modular components provide a powerful framework to explore design spaces and iterate through Design-Build-Test-Learn cycles. Biopart Assembly Standard for Idempotent Cloning (BASIC) DNA assembly uses modular parts and linkers, is highly accurate, easy to automate, free for academic and commercial use, while enabling simple hierarchical assemblies through an idempotent format. These attributes facilitate various applications including pathway engineering, ribosome binding site tuning, fusion protein synthesis and multiplex gRNA expression. In this work we present basicsynbio, an open-source software encompassing a Web App (https://basicsynbio.web.app/) and Python Package (https://github.com/LondonBiofoundry/basicsynbio). With basicsynbio, users can access commonly used BASIC parts and linkers while robustly designing new parts and assemblies with exception handling for common design errors. Furthermore, users can export sequence data and create build instructions for manual or automated workflows. The generation of build instructions relies on the BasicBuild Open Standard which is easily parsed for bespoke workflows and is serialised in Java Script Object Notation for transfer and storage. We demonstrate basicsynbio by assembling a collection of 30 BASIC-compatible vectors using various sequences including modules from the Standard European Vector Architecture (SEVA). The BASIC SEVA collection encompasses plasmids containing six antibiotic resistance markers and five origins of replication from different compatibility groups, including a temperature-sensitive variant. We deposit the collection on Addgene under an OpenMTA agreement, making them available. Furthermore, these sequences are accessible from within the basicsynbio application programming interface along with other collections of parts and linkers, providing an ideal environment to design BASIC DNA assemblies for bioengineering applications.

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Section: Basic Compares Favourably With Modular Methods Based On Goldenmentioning

confidence: 99%

basicsynbio and the BASIC SEVA collection: Software and vectors for an established DNA assembly method

Haines

Carling

Marshall

et al. 2022

Preprint

View full text Add to dashboard Cite

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Research progress of engineering microbial cell factories for pigment production

Gao

2023

Biotechnology Advances

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Engineering biology and automation–Replicability as a design principle

Bultelle,

Casas,

Kitney

2024

Engineering Biology

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Applications in engineering biology increasingly share the need to run operations on very large numbers of biological samples. This is a direct consequence of the application of good engineering practices, the limited predictive power of current computational models and the desire to investigate very large design spaces in order to solve the hard, important problems the discipline promises to solve. Automation has been proposed as a key component for running large numbers of operations on biological samples. This is because it is strongly associated with higher throughput, and with higher replicability (thanks to the reduction of human input). The authors focus on replicability and make the point that, far from being an additional burden for automation efforts, replicability should be considered central to the design of the automated pipelines processing biological samples at scale—as trialled in biofoundries. There cannot be successful automation without effective error control. Design principles for an IT infrastructure that supports replicability are presented. Finally, the authors conclude with some perspectives regarding the evolution of automation in engineering biology. In particular, they speculate that the integration of hardware and software will show rapid progress, and offer users a degree of control and abstraction of the robotic infrastructure on a level significantly greater than experienced today.

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PASIV: A Pooled Approach-Based Workflow to Overcome Toxicity-Induced Design of Experiments Failures and Inefficiencies

Cited by 4 publications

References 58 publications

basicsynbio and the BASIC SEVA collection: Software and vectors for an established DNA assembly method

basicsynbio and the BASIC SEVA collection: Software and vectors for an established DNA assembly method

Research progress of engineering microbial cell factories for pigment production

Engineering biology and automation–Replicability as a design principle

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