AI Article Synopsis
- The Galaxy-SynBioCAD portal is a comprehensive platform designed for synthetic biology, metabolic engineering, and industrial biotech, enabling users to create strain libraries for specific chemical targets.
- It offers a complete process from strain selection and DNA design to generating automated scripts for plasmid assembly and strain transformations, utilizing standard formats like SBML and SBOL for compatibility.
- In a validation study, the portal successfully linked pathway design with practical applications, achieving an 83% success rate in retrieving expert-validated pathways from the top 10 generated by their workflows.
Article 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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|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9424320 | PMC |
| http://dx.doi.org/10.1038/s41467-022-32661-x | DOI Listing |
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