Cargando…
The automated Galaxy-SynBioCAD pipeline for synthetic biology design and engineering
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 p...
Autores principales: | , , , , , , , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2022
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9424320/ https://www.ncbi.nlm.nih.gov/pubmed/36038542 http://dx.doi.org/10.1038/s41467-022-32661-x |
_version_ | 1784778215156350976 |
---|---|
author | Hérisson, Joan Duigou, Thomas du Lac, Melchior Bazi-Kabbaj, Kenza Sabeti Azad, Mahnaz Buldum, Gizem Telle, Olivier El Moubayed, Yorgo Carbonell, Pablo Swainston, Neil Zulkower, Valentin Kushwaha, Manish Baldwin, Geoff S. Faulon, Jean-Loup |
author_facet | Hérisson, Joan Duigou, Thomas du Lac, Melchior Bazi-Kabbaj, Kenza Sabeti Azad, Mahnaz Buldum, Gizem Telle, Olivier El Moubayed, Yorgo Carbonell, Pablo Swainston, Neil Zulkower, Valentin Kushwaha, Manish Baldwin, Geoff S. Faulon, Jean-Loup |
author_sort | Hérisson, Joan |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-9424320 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-94243202022-08-31 The automated Galaxy-SynBioCAD pipeline for synthetic biology design and engineering Hérisson, Joan Duigou, Thomas du Lac, Melchior Bazi-Kabbaj, Kenza Sabeti Azad, Mahnaz Buldum, Gizem Telle, Olivier El Moubayed, Yorgo Carbonell, Pablo Swainston, Neil Zulkower, Valentin Kushwaha, Manish Baldwin, Geoff S. Faulon, Jean-Loup Nat Commun Article 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. Nature Publishing Group UK 2022-08-29 /pmc/articles/PMC9424320/ /pubmed/36038542 http://dx.doi.org/10.1038/s41467-022-32661-x Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . |
spellingShingle | Article Hérisson, Joan Duigou, Thomas du Lac, Melchior Bazi-Kabbaj, Kenza Sabeti Azad, Mahnaz Buldum, Gizem Telle, Olivier El Moubayed, Yorgo Carbonell, Pablo Swainston, Neil Zulkower, Valentin Kushwaha, Manish Baldwin, Geoff S. Faulon, Jean-Loup The automated Galaxy-SynBioCAD pipeline for synthetic biology design and engineering |
title | The automated Galaxy-SynBioCAD pipeline for synthetic biology design and engineering |
title_full | The automated Galaxy-SynBioCAD pipeline for synthetic biology design and engineering |
title_fullStr | The automated Galaxy-SynBioCAD pipeline for synthetic biology design and engineering |
title_full_unstemmed | The automated Galaxy-SynBioCAD pipeline for synthetic biology design and engineering |
title_short | The automated Galaxy-SynBioCAD pipeline for synthetic biology design and engineering |
title_sort | automated galaxy-synbiocad pipeline for synthetic biology design and engineering |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9424320/ https://www.ncbi.nlm.nih.gov/pubmed/36038542 http://dx.doi.org/10.1038/s41467-022-32661-x |
work_keys_str_mv | AT herissonjoan theautomatedgalaxysynbiocadpipelineforsyntheticbiologydesignandengineering AT duigouthomas theautomatedgalaxysynbiocadpipelineforsyntheticbiologydesignandengineering AT dulacmelchior theautomatedgalaxysynbiocadpipelineforsyntheticbiologydesignandengineering AT bazikabbajkenza theautomatedgalaxysynbiocadpipelineforsyntheticbiologydesignandengineering AT sabetiazadmahnaz theautomatedgalaxysynbiocadpipelineforsyntheticbiologydesignandengineering AT buldumgizem theautomatedgalaxysynbiocadpipelineforsyntheticbiologydesignandengineering AT telleolivier theautomatedgalaxysynbiocadpipelineforsyntheticbiologydesignandengineering AT elmoubayedyorgo theautomatedgalaxysynbiocadpipelineforsyntheticbiologydesignandengineering AT carbonellpablo theautomatedgalaxysynbiocadpipelineforsyntheticbiologydesignandengineering AT swainstonneil theautomatedgalaxysynbiocadpipelineforsyntheticbiologydesignandengineering AT zulkowervalentin theautomatedgalaxysynbiocadpipelineforsyntheticbiologydesignandengineering AT kushwahamanish theautomatedgalaxysynbiocadpipelineforsyntheticbiologydesignandengineering AT baldwingeoffs theautomatedgalaxysynbiocadpipelineforsyntheticbiologydesignandengineering AT faulonjeanloup theautomatedgalaxysynbiocadpipelineforsyntheticbiologydesignandengineering AT herissonjoan automatedgalaxysynbiocadpipelineforsyntheticbiologydesignandengineering AT duigouthomas automatedgalaxysynbiocadpipelineforsyntheticbiologydesignandengineering AT dulacmelchior automatedgalaxysynbiocadpipelineforsyntheticbiologydesignandengineering AT bazikabbajkenza automatedgalaxysynbiocadpipelineforsyntheticbiologydesignandengineering AT sabetiazadmahnaz automatedgalaxysynbiocadpipelineforsyntheticbiologydesignandengineering AT buldumgizem automatedgalaxysynbiocadpipelineforsyntheticbiologydesignandengineering AT telleolivier automatedgalaxysynbiocadpipelineforsyntheticbiologydesignandengineering AT elmoubayedyorgo automatedgalaxysynbiocadpipelineforsyntheticbiologydesignandengineering AT carbonellpablo automatedgalaxysynbiocadpipelineforsyntheticbiologydesignandengineering AT swainstonneil automatedgalaxysynbiocadpipelineforsyntheticbiologydesignandengineering AT zulkowervalentin automatedgalaxysynbiocadpipelineforsyntheticbiologydesignandengineering AT kushwahamanish automatedgalaxysynbiocadpipelineforsyntheticbiologydesignandengineering AT baldwingeoffs automatedgalaxysynbiocadpipelineforsyntheticbiologydesignandengineering AT faulonjeanloup automatedgalaxysynbiocadpipelineforsyntheticbiologydesignandengineering |