News, Recent papers, RetroPath, Tools

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

We believe that the synthetic biology and metabolic engineering communities need to be provided with easily acessible and usable computational tools enabling them to apply their creativity, and simulate their unique ideas regardless of their informatics expertise.

Galaxy SynBioCAD is an open access Galaxy workflow environment to design and build different metabolic routes for the production of a compound of interest. Galaxy-SynBioCAD combines (1) the proven efficiency of RetroPath2.0 – an automated open-source retrosynthesis software based on generalized reaction rules that generates networks linking the target compound(s)  to the metabolites of the chassis strain (2) a downstream analysis method which encompasses flux analysis and (3) Design of Experiments to determine the DNA parts to be assemble to build pathway libraries, and (4) automated script generator to drive robotized workstations for vector assembly and strain transformation.

The intuitive, user-friendly platform of the Galaxy SynBioCAD Portal: 

  • offers a versatile one-stop destination to access multiple, connected tools in one place.
  • enables to construct customized workflows for generating and analyzing pathways, pathway ranking, designing genetic parts, etc that can be seamlessly integrated with your data files.
  • provides a graphical user interface allows for rapid test and prototyping, even for users with little to no knowledge in programing.

These features make this tool a valuable addition to a biological engineer’s bench desk, thus accelerating development of synthetic biology and metabolic engineering technology.

Visit the SynBioCAD Portal

Galaxy SynBioCAD publications

  • Hérisson J, Duigou T, et al. The automated Galaxy-SynBioCAD pipeline for synthetic biology design and engineering, Nat Commun. 2022 Aug 29;13(1):5082. | doi: 10.1038/s41467-022-32661-x
  • Faulon, JL, du Lac, M, Duigou, T., Carbonell, P., Herisson, J. Design Automation Workflows for Synthetic Biology and Metabolic Engineering: The Galaxy SynBioCAD portal, of 12th IWBDA-2020, 25-26, 2020.

Galaxy SynBioCAD tools publications

  • Koch M, Duigou T, Faulon JL. Reinforcement Learning for Bioretrosynthesis. ACS Synthetic Biology, 9(1): 15, 2020. | doi: 10.1021/acssynbio.9b00447 | PMID: 31841626
  • Storch M, Haines MC, Baldwin GS. DNA-BOT: a low-cost, automated DNA assembly platform for synthetic biology. Synth Biol (Oxf). 2020 Jul 9;5(1):ysaa010. doi: 10.1093/synbio/ysaa010. PMID: 32995552; PMCID: PMC7476404.
  • Carbonell, P. Faulon JL, Breitling, R. Efficient learning in metabolic designs through optimal assembling. IFAC-PapersOnLine, 52(26): 7-22 , 2019. | doi: 10.1016/j.ifacol.2019.12.228
  • Duigou T, du Lac M, Carbonell P, Faulon JL*. RetroRules: a database of reaction rules for engineering biology. Nucleic Acids Research, 47(D1): D1229-1235, 2019. | doi: 10.1093/nar/gky940 | PMID: 30321422
  • Carbonell P*, Wong J, Swainston N, Takano E, Turner NJ, Scrutton NS, Kell DB, Breitling R, Faulon JL*. Selenzyme: enzyme selection tool for pathway design. Bioinformatics, 34(12): 2153-2154, 2018. | doi: 10.1093/bioinformatics/bty065
  • Delépine B, Duigou T, Carbonell P, Faulon JL*. RetroPath2.0: A retrosynthesis workflow for metabolic engineers. Metabolic Engineering, 45: 158-170, 2018. | doi: 10.1016/j.ymben.2017.12.002 | PMID: 29233745
  • Swainston N, Dunstan M, Jervis AJ, Robinson CJ, Carbonell P, Williams AR, Faulon JL, Scrutton NS, Kell DB. PartsGenie: an integrated tool for optimising and sharing synthetic biology parts. Bioinformatics, 34(13): 2327-2329, 2018. | doi: 10.1093/bioinformatics/bty105
  • Koch M, Duigou T, Carbonell P, Faulon JL*. Molecular structures enumeration and virtual screening in the chemical space with RetroPath2.0. Journal of Cheminformatics, 9(1): 64, 2017. | doi: 10.1186/s13321-017-0252-9
  • Fehér T, Planson AG, Carbonell P, Fernández-Castané A, Grigoras I, Dariy E, Perret A, Faulon JL*. Validation of RetroPath, a computer-aided design tool for metabolic pathway engineering. Biotechnology Journal, 9(11): 1446-1457, 2014. | doi: 10.1002/biot.201400055 | PMID: 25224453
  • Carbonell P, Parutto P, Baudier C, Junot C, Faulon JL*. Retropath: automated pipeline for embedded metabolic circuits. ACS Synthetic Biology, 3(8): 565-577, 2014. | doi: 10.1021/sb4001273 | PMID: 24131345
  • Carbonell P, Parutto P, Herisson J, Pandit S, Faulon JL*. XTMS: pathway design in an eXTended metabolic space. Nucleic Acids Research, 42: W389-394, 2014. | doi: 10.1093/nar/gku362 | PMID: 24792156
  • Carbonell P, Fichera D, Pandit SB, Faulon JL*. Enumerating metabolic pathways for the production of heterologous target chemicals in chassis organisms. BMC Systems Biology, 6: 10, 2012. | doi: 10.1186/1752-0509-6-10 | PMID: 22309974
  • Carbonell P, Planson AG, Fichera D, Faulon JL*. A retrosynthetic biology approach to metabolic pathway design for therapeutic production. BMC Systems Biology, 5: 122, 2011. | doi: 10.1186/1752-0509-5-122 | PMID: 21819595