The automated Galaxy-SynBioCAD pipeline for synthetic biology design and engineering

Hérisson, Joan; Duigou, Thomas; du, Melchior; Bazi-Kabbaj, Kenza; Azad, Mahnaz Sabeti; Buldum, Gizem; Telle, Olivier; Moubayed, Yorgo El; Carbonell, Pablo; Swainston, Neil; Zulkower, Valentin; Kushwaha, Manish; Baldwin, Geoff; Faulon, Jean‐Loup

doi:10.1038/s41467-022-32661-x

Cited by 16 publications

(16 citation statements)

References 60 publications

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“…The rise in tools for specific tasks has led to their integration into pipelines and repositories like SynBioHub, Galaxy SynBioCAD, and Infobiotics . SynBioHub is a platform that facilitates the integration of software and data for synthetic biological designs so that users can easily share and reproduce system designs in a standardized format.…”

Section: Introductionmentioning

confidence: 99%

Characterization of Integrase and Excisionase Activity in a Cell-Free Protein Expression System Using a Modeling and Analysis Pipeline

Pandey

Rodriguez

Poole³

et al. 2023

ACS Synth. Biol.

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We present a full-stack modeling, analysis, and parameter identification pipeline to guide the modeling and design of biological systems starting from specifications to circuit implementations and parametrizations. We demonstrate this pipeline by characterizing the integrase and excisionase activity in a cell-free protein expression system. We build on existing Python tools� BioCRNpyler, AutoReduce, and Bioscrape�to create this pipeline. For enzyme-mediated DNA recombination in a cell-free system, we create detailed chemical reaction network models from simple highlevel descriptions of the biological circuits and their context using BioCRNpyler. We use Bioscrape to show that the output of the detailed model is sensitive to many parameters. However, parameter identification is infeasible for this high-dimensional model; hence, we use AutoReduce to automatically obtain reduced models that have fewer parameters. This results in a hierarchy of reduced models under different assumptions to finally arrive at a minimal ODE model for each circuit. Then, we run sensitivity analysis-guided Bayesian inference using Bioscrape for each circuit to identify the model parameters. This process allows us to quantify integrase and excisionase activity in cell extracts enabling complex-circuit designs that depend on accurate control over protein expression levels through DNA recombination. The automated pipeline presented in this paper opens up a new approach to complex circuit design, modeling, reduction, and parametrization.

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Section: Introductionmentioning

confidence: 99%

Characterization of Integrase and Excisionase Activity in a Cell-Free Protein Expression System Using a Modeling and Analysis Pipeline

Pandey

Rodriguez

Poole³

et al. 2023

ACS Synth. Biol.

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“…Although a flexible, open-source build automation platform would be a good alternative, few exist ( 14 , 15 ), particularly those that make use of liquid handling robotics. Many of the build platforms that do exist are fairly inaccessible, difficult to find and not interoperable ( 2 , 16 ). This hampers the efficiency of DBTL cycles by preventing remote design implementation and automatic data feedback for optimized in silico redesign ( 17 ).…”

Section: Introductionmentioning

confidence: 99%

AssemblyTron: flexible automation of DNA assembly with Opentrons OT-2 lab robots

et al. 2022

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As one of the newest fields of engineering, synthetic biology relies upon a trial-and-error Design-Build-Test-Learn approach to simultaneously learn how function is encoded in biology and attempt to engineer it. Many software and hardware platforms have been developed to automate, optimize, and algorithmically perform each step of the Design-Build-Test-Learn cycle. However, there are many fewer options for automating the Build step. Build typically involves DNA assembly, which remains manual, low throughput, and unreliable in most cases and limits our ability to advance the science and engineering of biology. Here, we present AssemblyTron: an open-source python package to integrate j5 DNA assembly design software outputs with build implementation in Opentrons liquid handling robotics with minimal human intervention. We demonstrate the versatility of AssemblyTron through several scarless, multipart DNA assemblies beginning from fragment amplification. We show that AssemblyTron can perform PCRs across a range of fragment lengths and annealing temperatures by using an optimal annealing temperature gradient calculation algorithm. We then demonstrate that AssemblyTron can perform Golden Gate and homology-dependent in vivo assemblies with comparable fidelity to manual assemblies by simultaneously building four four-fragment assemblies of chromoprotein reporter expression plasmids. Finally, we used AssemblyTron to perform site-directed mutagenesis reactions via homology-dependent in vivo assembly also achieving comparable fidelity to manual assemblies as assessed by sequencing. AssemblyTron can reduce the time, training, costs, and wastes associated with synthetic biology, which along with open-source and affordable automation, will further foster the accessibility of synthetic biology and accelerate biological research and engineering.

show abstract

“…Though a flexible, open-source build automation platform would be a good alternative, few exist (14,15), particularly those which make use of liquid handling robotics. Many of the build platforms that do exist are fairly inaccessible, difficult to find, and not interoperable (2,16).…”

Section: Introductionmentioning

confidence: 99%

“…Many of the build platforms that do exist are fairly inaccessible, difficult to find, and not interoperable (2,16).…”

Section: Introductionmentioning

confidence: 99%

AssemblyTron: Flexible automation of DNA assembly with Opentrons OT-2 lab robots

Bryant

Kellinger

Longmire

et al. 2022

Preprint

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As one of the newest fields of engineering, synthetic biology relies upon a trial-and-error Design-Build-Test-Learn approach to simultaneously learn how function is encoded in biology and attempt to engineer it. Many software and hardware platforms have been developed to automate, optimize, and algorithmically perform each step of the Design-Build-Test-Learn cycle. However, there are many fewer options for automating the Build step. Build typically involves DNA assembly, which remains manual, low throughput, and unreliable in most cases, limiting our ability to advance the science and engineering of biology. Here, we present AssemblyTron: an open-source python package to integrate j5 DNA assembly design software outputs with build implementation in Opentrons liquid handling robotics with minimal human intervention. We demonstrate the versatility of AssemblyTron through several scarless, multipart DNA assemblies beginning from fragment amplification. We show that AssemblyTron can perform PCRs across a range of fragment lengths and annealing temperatures by using an optimal annealing temperature gradient calculation algorithm. We then demonstrate that AssemblyTron can perform Golden Gate and homology-dependent in vivo assemblies with comparable fidelity to manual assemblies by simultaneously building four four-fragment assemblies of chromoprotein reporter expression plasmids. Finally, we used AssemblyTron to perform site-directed mutagenesis reactions via homology-dependent in vivo assembly also achieving comparable fidelity to manual assemblies as assessed by sequencing. AssemblyTron can reduce the time, training, costs, and wastes associated with synthetic biology, which along with open-source and affordable automation, will further foster the accessibility of synthetic biology and accelerate biological research and engineering.

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The automated Galaxy-SynBioCAD pipeline for synthetic biology design and engineering

Cited by 16 publications

References 60 publications

Characterization of Integrase and Excisionase Activity in a Cell-Free Protein Expression System Using a Modeling and Analysis Pipeline

Characterization of Integrase and Excisionase Activity in a Cell-Free Protein Expression System Using a Modeling and Analysis Pipeline

AssemblyTron: flexible automation of DNA assembly with Opentrons OT-2 lab robots

AssemblyTron: Flexible automation of DNA assembly with Opentrons OT-2 lab robots

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