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

Author

Listed:
  • Haseong Kim

    (Korea Research Institute of Bioscience and Biotechnology (KRIBB)
    Korea Research Institute of Bioscience and Biotechnology (KRIBB)
    University of Science and Technology (UST)
    Korea Advanced Institute of Science and Technology (KAIST))

  • Nathan J. Hillson

    (Department of Energy Agile BioFoundry
    Lawrence Berkeley National Lab)

  • Byung-Kwan Cho

    (Korea Advanced Institute of Science and Technology (KAIST)
    Korea Advanced Institute of Science and Technology (KAIST))

  • Bong Hyun Sung

    (Korea Research Institute of Bioscience and Biotechnology (KRIBB)
    Korea Research Institute of Bioscience and Biotechnology (KRIBB)
    University of Science and Technology (UST)
    Korea Advanced Institute of Science and Technology (KAIST))

  • Dae-Hee Lee

    (Korea Research Institute of Bioscience and Biotechnology (KRIBB)
    Korea Research Institute of Bioscience and Biotechnology (KRIBB)
    University of Science and Technology (UST)
    Korea Advanced Institute of Science and Technology (KAIST))

  • Dong-Myung Kim

    (Chungnam National University)

  • Min-Kyu Oh

    (Korea University)

  • Matthew Wook Chang

    (National University of Singapore
    National University of Singapore
    National University of Singapore
    National Centre for Engineering Biology (NCEB))

  • Yong-Su Jin

    (University of Illinois at Urbana-Champaign
    University of Illinois at Urbana-Champaign)

  • Susan J. Rosser

    (University of Edinburgh
    University of Edinburgh)

  • Peter Vegh

    (University of Edinburgh
    University of Edinburgh)

  • Rennos Fragkoudis

    (University of Edinburgh
    University of Edinburgh)

  • Rosalind Feuvre

    (University of Manchester (UoM))

  • Nigel S. Scrutton

    (University of Manchester (UoM))

  • Marko Storch

    (Imperial College London
    Imperial College London)

  • Wonjae Seong

    (Korea Research Institute of Bioscience and Biotechnology (KRIBB)
    Korea Research Institute of Bioscience and Biotechnology (KRIBB))

  • Paul S. Freemont

    (Imperial College London
    Imperial College London
    UK Dementia Research Institute)

  • Seung-Goo Lee

    (Korea Research Institute of Bioscience and Biotechnology (KRIBB)
    Korea Research Institute of Bioscience and Biotechnology (KRIBB)
    University of Science and Technology (UST)
    Korea Advanced Institute of Science and Technology (KAIST))

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.

Suggested Citation

  • 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 & Ro, 2025. "Abstraction hierarchy to define biofoundry workflows and operations for interoperable synthetic biology research and applications," Nature Communications, Nature, vol. 16(1), pages 1-6, December.
    • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-61263-6
    DOI: 10.1038/s41467-025-61263-6
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    References listed on IDEAS

    as
    1. Michael A. Crone & Miles Priestman & Marta Ciechonska & Kirsten Jensen & David J. Sharp & Arthi Anand & Paul Randell & Marko Storch & Paul S. Freemont, 2020. "Author Correction: A role for Biofoundries in rapid development and validation of automated SARS-CoV-2 clinical diagnostics," Nature Communications, Nature, vol. 11(1), pages 1-1, December.
    2. Claudia E. Vickers & Paul S. Freemont, 2022. "Pandemic preparedness: synthetic biology and publicly funded biofoundries can rapidly accelerate response time," Nature Communications, Nature, vol. 13(1), pages 1-4, December.
    3. Michael A. Crone & Miles Priestman & Marta Ciechonska & Kirsten Jensen & David J. Sharp & Arthi Anand & Paul Randell & Marko Storch & Paul S. Freemont, 2020. "A role for Biofoundries in rapid development and validation of automated SARS-CoV-2 clinical diagnostics," Nature Communications, Nature, vol. 11(1), pages 1-11, December.
    4. Joseph L. Watson & David Juergens & Nathaniel R. Bennett & Brian L. Trippe & Jason Yim & Helen E. Eisenach & Woody Ahern & Andrew J. Borst & Robert J. Ragotte & Lukas F. Milles & Basile I. M. Wicky & , 2023. "De novo design of protein structure and function with RFdiffusion," Nature, Nature, vol. 620(7976), pages 1089-1100, August.
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