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

Haseong Kim, Nathan J. Hillson, Byung-Kwan Cho, Bong Hyun Sung, Dae-Hee Lee, Dong-Myung Kim, Min-Kyu Oh, Matthew Wook Chang, Yong-Su Jin, Susan J. Rosser, Peter Vegh, Rennos Fragkoudis, Rosalind Feuvre, Nigel S. Scrutton, Marko Storch, Wonjae Seong, Paul S. Freemont () and Seung-Goo Lee ()
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Haseong Kim: Korea Research Institute of Bioscience and Biotechnology (KRIBB)
Nathan J. Hillson: Department of Energy Agile BioFoundry
Byung-Kwan Cho: Korea Advanced Institute of Science and Technology (KAIST)
Bong Hyun Sung: Korea Research Institute of Bioscience and Biotechnology (KRIBB)
Dae-Hee Lee: Korea Research Institute of Bioscience and Biotechnology (KRIBB)
Dong-Myung Kim: Chungnam National University
Min-Kyu Oh: Korea University
Matthew Wook Chang: National University of Singapore
Yong-Su Jin: University of Illinois at Urbana-Champaign
Susan J. Rosser: University of Edinburgh
Peter Vegh: University of Edinburgh
Rennos Fragkoudis: University of Edinburgh
Rosalind Feuvre: University of Manchester (UoM)
Nigel S. Scrutton: University of Manchester (UoM)
Marko Storch: Imperial College London
Wonjae Seong: Korea Research Institute of Bioscience and Biotechnology (KRIBB)
Paul S. Freemont: Imperial College London
Seung-Goo Lee: Korea Research Institute of Bioscience and Biotechnology (KRIBB)

Nature Communications, 2025, vol. 16, issue 1, 1-6

Abstract: Abstract 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.

Date: 2025
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DOI: 10.1038/s41467-025-61263-6

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