An End-to-End Workflow for Engineering of Biological Networks from High-Level Specifications

We present a workflow for the design and production of
biological
networks from high-level program specifications. The workflow is based
on a sequence of intermediate models that incrementally translate
high-level specifications into DNA samples that implement them. We
identify algorithms for translating between adjacent models and implement
them as a set of software tools, organized into a four-stage toolchain: Specification, Compilation, Part
Assignment, and Assembly. The specification
stage begins with a Boolean logic computation specified in the Proto
programming language. The compilation stage uses a library of network
motifs and cellular platforms, also specified in Proto, to transform
the program into an optimized Abstract Genetic Regulatory Network
(AGRN) that implements the programmed behavior. The part assignment
stage assigns DNA parts to the AGRN, drawing the parts from a database
for the target cellular platform, to create a DNA sequence implementing
the AGRN. Finally, the assembly stage computes an optimized assembly
plan to create the DNA sequence from available part samples, yielding
a protocol for producing a sample of engineered plasmids with robotics
assistance. Our workflow is the first to automate the production of
biological networks from a high-level program specification. Furthermore,
the workflow’s modular design allows the same program to be
realized on different cellular platforms simply by swapping workflow
configurations. We validated our workflow by specifying a small-molecule
sensor-reporter program and verifying the resulting plasmids in both
HEK 293 mammalian cells and in E. coli bacterial
cells.