From Bench to Breakthrough: A Findable, Accessible, Interoperable, Reusable (FAIR)-Compliant Toolkit for Synthetic Biology Automation

Author(s):

Jeanet V. Mante, Randi M. Pullen, and Randall A. Hughes

Abstract:

Automation is transforming synthetic biology, but without interoperable tools and standardized metadata, its benefits are undermined by fragmented workflows and irreproducible data. This work introduces a comprehensive suite of modular software tools that embed Findable, Accessible, Interoperable, Reusable (FAIR) principles into everyday laboratory operations. The toolkit supports sequence domestication and annotation, generates validated combinatorial part assembly instructions for acoustic liquid handlers like the Echo 525, automates liquid handling tasks across systems such as the Tecan Fluent and Formulatrix Mantis, and integrates high-throughput colony picking with the Singer Instruments PIXL. It also includes design-of-experiments modules for both binary and continuous variables, analytical workflows for expression factor importance, clustering algorithms for promoter classification, and gene identification tools for ribonucleic acid expression analysis. Together, these tools convert conceptual designs into executable robotic protocols while capturing machine-readable metadata at every step. Laboratories that fail to adopt such systems risk becoming bottlenecks in the scientific process, where data is trapped in proprietary formats, collaboration is stifled, and critical insights are lost in translation. In contrast, this framework enables rapid iteration, reproducibility, and cross-platform compatibility, making it not just a technical upgrade but a safeguard against stagnation in modern biological research.