Abstraction hierarchy to define biofoundry workflows and operations for interoperable synthetic biology research and applications

Journal Article · Wed Jan 01 00:00:00 UTC 2025 · Nature Communications

DOI: https://doi.org/10.1038/s41467-025-61263-6 · OSTI ID:2583659

Kim, Haseong; Hillson, Nathan J; Cho, Byung-Kwan; Sung, Bong Hyun; Lee, Dae-Hee; Kim, Dong-Myung; Oh, Min-Kyu; Chang, Matthew Wook; Jin, Yong-Su; Rosser, Susan J; Vegh, Peter; Fragkoudis, Rennos; Le Feuvre, Rosalind; Scrutton, Nigel S; Storch, Marko; Seong, Wonjae; Freemont, Paul S; Lee, Seung-Goo

Lack of standardization in biofoundries limits the scalability and efficiency of synthetic biology research. Here, we propose an abstraction hierarchy that organizes biofoundry activities into four interoperable levels: Project, Service/Capability, Workflow, and Unit Operation, effectively streamlining the Design‑Build‑Test‑Learn (DBTL) cycle. This framework enables more modular, flexible, and automated experimental workflows. It improves communication between researchers and systems, supports reproducibility, and facilitates better integration of software tools and artificial intelligence. Our approach lays the foundation for a globally interoperable biofoundry network, advancing collaborative synthetic biology and accelerating innovation in response to scientific and societal challenges.

• Research Organization: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
• Sponsoring Organization: US Department of Energy; USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23), Biological Systems Science Division (SC-23.2 )
• Grant/Contract Number: AC02-05CH11231
• OSTI ID: 2583659
• Journal Information: Nature Communications, Journal Name: Nature Communications Journal Issue: 1 Vol. 16
• Country of Publication: United States
• Language: English