Abstract
A synthetic biology workflow covers the roadmap from conceptualization of a genetic device to its construction and measurement. It is composed of databases that provide DNA parts/plasmids, wet-lab methods , software tools to design circuits, simulation packages , and tools to analyze circuit performance. The interdisciplinary nature of such a workflow requires that experimental results and their in-silico counterparts proceed alongside, with constant feedback between them. We present an end-to-end use case for engineering a simple synthetic device, where information standards maintain coherence throughout the workflow. These are the Standard European Vector Architecture (SEVA), the Synthetic Biology Open Language (SBOL), and the Systems Biology Markup Language (SBML).
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Goni-Moreno A, Carcajona M, Kim J, Martínez-García E, Amos M, de Lorenzo V (2016) An implementation-focused bio/algorithmic workflow for synthetic biology. ACS Synth Biol 5(10):1127–1135
Beal J, Weiss R, Densmore D, Adler A, Appleton E, Babb J, Bhatia S, Davidsohn N, Haddock T, Loyall J (2012) An end-to-end workflow for engineering of biological networks from high-level specifications. ACS Synth Biol 1(8):317–331
Peccoud J, Anderson JC, Chandran D, Densmore D, Galdzicki M, Lux MW, Rodriguez CA, Stan G-B, Sauro HM (2011) Essential information for synthetic DNA sequences. Nat Biotechnol 29(1):22–22
Andrianantoandro E, Basu S, Karig DK, Weiss R (2006) Synthetic biology: new engineering rules for an emerging discipline. Mol Syst Biol 2(1):2006.0028
Nielsen AA, Der BS, Shin J, Vaidyanathan P, Paralanov V, Strychalski EA, Ross D, Densmore D, Voigt CA (2016) Genetic circuit design automation. Science 352(6281):aac7341
Martínez-García E, Aparicio T, Goñi-Moreno A, Fraile S, de Lorenzo V (2014) SEVA 2.0: an update of the standard European vector architecture for de−/re-construction of bacterial functionalities. Nucleic Acids Res 43(D1):D1183–D1189
Galdzicki M, Clancy KP, Oberortner E, Pocock M, Quinn JY, Rodriguez CA, Roehner N, Wilson ML, Adam L, Anderson JC (2014) The synthetic biology open language (SBOL) provides a community standard for communicating designs in synthetic biology. Nat Biotechnol 32(6):545–550
Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H, Arkin AP, Bornstein BJ, Bray D, Cornish-Bowden A (2003) The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 19(4):524–531
Goni-Moreno A, Amos M (2015) DiSCUS: a simulation platform for conjugation computing. In: Lecture notes in computer science, vol 9252. Springer, Cham
Young JW, Locke JC, Altinok A, Rosenfeld N, Bacarian T, Swain PS, Mjolsness E, Elowitz MB (2012) Measuring single-cell gene expression dynamics in bacteria using fluorescence time-lapse microscopy. Nat Protoc 7(1):80–88
GoñiMoreno Á, Kim J, de Lorenzo V (2017) CellShape: a user friendly image analysis tool for quantitative visualization of bacterial cell factories inside. Biotechnol J 12(2). https://doi.org/10.1002/biot.201600323
Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual, Ed. 2 edn. Cold spring harbor laboratory press, Cold Spring Harbor, N.Y.
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Goñi-Moreno, A., de Lorenzo, V. (2018). Bio-Algorithmic Workflows for Standardized Synthetic Biology Constructs. In: Braman, J. (eds) Synthetic Biology. Methods in Molecular Biology, vol 1772. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7795-6_20
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DOI: https://doi.org/10.1007/978-1-4939-7795-6_20
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