Automated and Programmable Cell-Free Systems for Scalable Synthetic Biology with a Focus on Biofoundry Integration

Cell-free protein synthesis (CFPS) has been used as a transformative technology in synthetic biology, providing a programmable, scalable, and automation-compatible platform for biological engineering. Freed from the limitations of cell viability and growth, CFPS enables rapid design iteration, precise control of reaction conditions, and high-throughput experimentation. Recent integration of CFPS with biofoundries-automated, high-throughput biological engineering platforms-has dramatically accelerated the Design-Build-Test-Learn cycle, facilitating applications such as enzyme engineering, metabolic pathway prototyping, biosensor development, and remote biomanufacturing. Advances in automation technologies, including liquid-handling robotics and digital microfluidics, have further enhanced the scalability and reproducibility of CFPS workflows. Additionally, coupling CFPS with machine learning has enabled predictive optimization of genetic constructs and biosynthetic systems. This review highlights the technological innovations driving the convergence of CFPS and automated biofoundries, outlining current capabilities, challenges, and future directions toward programmable, scalable, and distributed biological engineering.