ArticleNature communications2022
The automated Galaxy-SynBioCAD pipeline for synthetic biology design and engineering.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed, 40 citations in OpenAlex.
- Accelerating natural product discovery, characterization and engineering by biofoundries.Natural product reports · 2026Review
- Co-Directional Chromosomal Clustering of Metabolic Pathway Genes as a Layout Prior for Synthetic Construct Design.Biotech (Basel (Switzerland)) · 2026Article
- Autocatalytic selection of gene functions in synthetic cells.Communications biology · 2026Article
- Advances in natural product discovery: strategies, technologies, and insights.Natural products and bioprospecting · 2026Review
- RetroRules 2026: an expanded database combining biochemical and organic reaction templates for pathway discovery.Nucleic acids research · 2026Article
- StreptoCAD: An Open-Source Software Toolbox Automating Genome Engineering Workflows in Streptomycetes.ACS synthetic biology · 2025Article
- An AI-driven workflow for the accelerated optimization of cell-free protein synthesis.iScience · 2025Article
- Fungal Innovations-Advancing Sustainable Materials, Genetics, and Applications for Industry.Journal of fungi (Basel, Switzerland) · 2025Review
- Abstraction hierarchy to define biofoundry workflows and operations for interoperable synthetic biology research and applications.Nature communications · 2025Review
- Biosynthesis of Edible Terpenoids: Hosts and Applications.Foods (Basel, Switzerland) · 2025Review
- An inhibitor-free, versatile, fast, and cheap precipitation-based DNA purification method.PloS one · 2025Article
- Engineering biology and automation-Replicability as a design principle.Engineering biology · 2024Review
- Genetic Engineering Approaches for the Microbial Production of Vanillin.Biomolecules · 2024Review
- EnzChemRED, a rich enzyme chemistry relation extraction dataset.Scientific data · 2024Article
- Substitution Attacks: A Catalyst to Reframe the DNA Manufacturing Cyberbiosecurity Landscape in the Age of Benchtop Synthesizers.Applied biosafety : journal of the American Biological Safety Association · 2024Article
- Artificial Intelligence Methods and Models for Retro-Biosynthesis: A Scoping Review.ACS synthetic biology · 2024Article
- DetSpace: a web server for engineering detectable pathways for bio-based chemical production.Nucleic acids research · 2024Article
- teemi: An open-source literate programming approach for iterative design-build-test-learn cycles in bioengineering.PLoS computational biology · 2024Article
- High-throughput prediction of enzyme promiscuity based on substrate-product pairs.Briefings in bioinformatics · 2024Article
- The Laboratory Automation Protocol (LAP) Format and Repository: A Platform for Enhancing Workflow Efficiency in Synthetic Biology.ACS synthetic biology · 2023Article
Corrections and comments
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Authors and funding
14 authors at 6 institutions in 4 countries.
Funding
Abstract
Here we introduce the Galaxy-SynBioCAD portal, a toolshed for synthetic biology, metabolic engineering, and industrial biotechnology. The tools and workflows currently shared on the portal enables one to build libraries of strains producing desired chemical targets covering an end-to-end metabolic pathway design and engineering process from the selection of strains and targets, the design of DNA parts to be assembled, to the generation of scripts driving liquid handlers for plasmid assembly and strain transformations. Standard formats like SBML and SBOL are used throughout to enforce the compatibility of the tools. In a study carried out at four different sites, we illustrate the link between pathway design and engineering with the building of a library of E. coli lycopene-producing strains. We also benchmark our workflows on literature and expert validated pathways. Overall, we find an 83% success rate in retrieving the validated pathways among the top 10 pathways generated by the workflows.
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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.