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

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

doi:10.1038/s41467-025-61263-6

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

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

Research output: Contribution to journal › Article › peer-review

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.

Original language	English
Article number	6056
Journal	Nature Communications
Volume	16
DOIs	https://doi.org/10.1038/s41467-025-61263-6
Publication status	Published - 1 Jul 2025

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kim, H., Hillson, N., Cho, B. K., Sung, B. H., Lee, D.-H., Kim, D.-M., Oh, M.-K., Chang, M., Jin, Y.-S., Rosser, S. J., Vegh, P., Fragkoudis, R., Feuvre, R. L., Scrutton, N., Storch, M., Seong, W., Freemont, P., & Lee, S.-G. (2025). Abstraction hierarchy to define biofoundry workflows and operations for interoperable synthetic biology research and applications. Nature Communications, 16, Article 6056. https://doi.org/10.1038/s41467-025-61263-6

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title = "Abstraction hierarchy to define biofoundry workflows and operations for interoperable synthetic biology research and applications",

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.",

author = "haseong kim and Nathan Hillson and Cho, \{Byung Kwan\} and Sung, \{Bong Hyun\} and Dae-Hee Lee and Dong-Myung Kim and Min-Kyu Oh and Matthew Chang and Yong-Su Jin and Rosser, \{Susan J.\} and Peter Vegh and Rennos Fragkoudis and Feuvre, \{Rosalind Le\} and Nigel Scrutton and Marko Storch and Wonjae Seong and Paul Freemont and Seung-Goo Lee",

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month = jul,

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doi = "10.1038/s41467-025-61263-6",

language = "English",

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journal = "Nature Communications",

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kim, H, Hillson, N, Cho, BK, Sung, BH, Lee, D-H, Kim, D-M, Oh, M-K, Chang, M, Jin, Y-S, Rosser, SJ, Vegh, P, Fragkoudis, R, Feuvre, RL , Scrutton, N, Storch, M, Seong, W, Freemont, P & Lee, S-G 2025, 'Abstraction hierarchy to define biofoundry workflows and operations for interoperable synthetic biology research and applications', Nature Communications, vol. 16, 6056. https://doi.org/10.1038/s41467-025-61263-6

TY - JOUR

T1 - Abstraction hierarchy to define biofoundry workflows and operations for interoperable synthetic biology research and applications

AU - kim, haseong

AU - Hillson, Nathan

AU - Cho, Byung Kwan

AU - Sung, Bong Hyun

AU - Lee, Dae-Hee

AU - Kim, Dong-Myung

AU - Oh, Min-Kyu

AU - Chang, Matthew

AU - Jin, Yong-Su

AU - Rosser, Susan J.

AU - Vegh, Peter

AU - Fragkoudis, Rennos

AU - Feuvre, Rosalind Le

AU - Scrutton, Nigel

AU - Storch, Marko

AU - Seong, Wonjae

AU - Freemont, Paul

AU - Lee, Seung-Goo

PY - 2025/7/1

Y1 - 2025/7/1

N2 - 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.

AB - 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.

U2 - 10.1038/s41467-025-61263-6

DO - 10.1038/s41467-025-61263-6

M3 - Article

SN - 2041-1723

VL - 16

JO - Nature Communications

JF - Nature Communications

M1 - 6056

ER -

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

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