An Implementation-Focused Bio/Algorithmic Workflow for Synthetic Biology

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.