Engineering biological systems using automated biofoundries

- Various Design tools at parts-, pathway-, and network-levels and for DNA assembly have been developed.
- Both bottom-up and top-down automated strategies are used for the Build step.
- Test automation should be implemented over a range of system scales including genetic constructs and genome, transcriptome, proteome, and metabolome.
- Learning through DBT cycles is crucial for both fundamental science and practical applications.
- As more enabling tools emerge for Design, Build, and Test, it has become important to integrate these steps to form industrialized pipelines.

Engineered biological systems such as genetic circuits and microbial cell factories have promised to solve many challenges in the modern society. However, the artisanal processes of research and development are slow, expensive, and inconsistent, representing a major obstacle in biotechnology and bioengineering. In recent years, biological foundries or biofoundries have been developed to automate design-build-test engineering cycles in an effort to accelerate these processes. This review summarizes the enabling technologies for such biofoundries as well as their early successes and remaining challenges.