title: An Implementation-Focused Bio/Algorithmic Workflow for Synthetic Biology.
abstract: As synthetic biology moves away from trial and error and embraces more formal processes, workflows have emerged that cover the roadmap from conceptualization of a genetic device to its construction and measurement. This latter aspect (i.e., characterization and measurement of synthetic genetic constructs) has received relatively little attention to date, but it is crucial for their outcome. An end-to-end use case for engineering a simple synthetic device is presented, which is supported by information standards and computational methods and focuses on such characterization/measurement. This workflow captures the main stages of genetic device design and description and offers standardized tools for both population-based measurement and single-cell analysis. To this end, three separate aspects are addressed. First, the specific vector features are discussed. Although device/circuit design has been successfully automated, important structural information is usually overlooked, as in the case of plasmid vectors. The use of the Standard European Vector Architecture (SEVA) is advocated for selecting the optimal carrier of a design and its thorough description in order to unequivocally correlate digital definitions and molecular devices. A digital version of this plasmid format was developed with the Synthetic Biology Open Language (SBOL) along with a software tool that allows users to embed genetic parts in vector cargoes. This enables annotation of a mathematical model of the device's kinetic reactions formatted with the Systems Biology Markup Language (SBML). From that point onward, the experimental results and their in silico counterparts proceed alongside, with constant feedback to preserve consistency between them. A second aspect involves a framework for the calibration of fluorescence-based measurements. One of the most challenging endeavors in standardization, metrology, is tackled by reinterpreting the experimental output in light of simulation results, allowing us to turn arbitrary fluorescence units into relative measurements. Finally, integration of single-cell methods into a framework for multicellular simulation and measurement is addressed, allowing standardized inspection of the interplay between the carrier chassis and the culture conditions.
authors.affiliation: Systems Biology Program, Centro Nacional de Biotecnología , Cantoblanco, 28049 Madrid, Spain.
authors.forename: Angel
authors.initials: A
authors.lastname: Goñi-Moreno
authors.affiliation: Systems Biology Program, Centro Nacional de Biotecnología , Cantoblanco, 28049 Madrid, Spain.
authors.forename: Marta
authors.initials: M
authors.lastname: Carcajona
authors.affiliation: Systems Biology Program, Centro Nacional de Biotecnología , Cantoblanco, 28049 Madrid, Spain.
authors.forename: Juhyun
authors.initials: J
authors.lastname: Kim
authors.affiliation: Systems Biology Program, Centro Nacional de Biotecnología , Cantoblanco, 28049 Madrid, Spain.
authors.forename: Esteban
authors.initials: E
authors.lastname: Martínez-García
authors.affiliation: Informatics Research Centre, Manchester Metropolitan University , Manchester M1 5GD, United Kingdom.
authors.forename: Martyn
authors.initials: M
authors.lastname: Amos
authors.affiliation: Systems Biology Program, Centro Nacional de Biotecnología , Cantoblanco, 28049 Madrid, Spain.
authors.forename: Víctor
authors.initials: V
authors.lastname: de Lorenzo
mesh_terms: D000465:Algorithms; D003001:Cloning, Molecular; D004269:DNA, Bacterial / Q000235:genetics; D004926:Escherichia coli / Q000235:genetics; D005822:Genetic Vectors / Q000235:genetics; D008962:Models, Theoretical; D010957:Plasmids / Q000235:genetics; D011381:Programming Languages; D011401:Promoter Regions, Genetic; D059010:Single-Cell Analysis; D012984:Software; D058615:Synthetic Biology / Q000379:methods*; D057188:Workflow
chemical_list: D004269:DNA, Bacterial