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...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2025-07-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-025-61263-6 |
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| author | 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 Le Feuvre Nigel S. Scrutton Marko Storch Wonjae Seong Paul S. Freemont Seung-Goo Lee |
| author_facet | 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 Le Feuvre Nigel S. Scrutton Marko Storch Wonjae Seong Paul S. Freemont Seung-Goo Lee |
| author_sort | Haseong Kim |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-44dc6fc00cec4dbe87e7dfe72f4dcae9 |
| institution | Kabale University |
| issn | 2041-1723 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj-art-44dc6fc00cec4dbe87e7dfe72f4dcae92025-08-20T04:01:35ZengNature PortfolioNature Communications2041-17232025-07-011611610.1038/s41467-025-61263-6Abstraction hierarchy to define biofoundry workflows and operations for interoperable synthetic biology research and applicationsHaseong Kim0Nathan J. Hillson1Byung-Kwan Cho2Bong Hyun Sung3Dae-Hee Lee4Dong-Myung Kim5Min-Kyu Oh6Matthew Wook Chang7Yong-Su Jin8Susan J. Rosser9Peter Vegh10Rennos Fragkoudis11Rosalind Le Feuvre12Nigel S. Scrutton13Marko Storch14Wonjae Seong15Paul S. Freemont16Seung-Goo Lee17Korea Biofoundry, Korea Research Institute of Bioscience and Biotechnology (KRIBB)Department of Energy Agile BioFoundryGraduate School of Engineering Biology, Korea Advanced Institute of Science and Technology (KAIST)Korea Biofoundry, Korea Research Institute of Bioscience and Biotechnology (KRIBB)Korea Biofoundry, Korea Research Institute of Bioscience and Biotechnology (KRIBB)Department of Chemical Engineering and Applied Chemistry, Chungnam National UniversityDepartment of Chemical and Biological Engineering, Korea UniversityNUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of SingaporeDepartment of Food Science and Human Nutrition, University of Illinois at Urbana-ChampaignSchool of Biological Sciences, University of EdinburghSchool of Biological Sciences, University of EdinburghSchool of Biological Sciences, University of EdinburghManchester Institute of Biotechnology, University of Manchester (UoM)Manchester Institute of Biotechnology, University of Manchester (UoM)Department of Infectious Disease, Imperial College LondonKorea Biofoundry, Korea Research Institute of Bioscience and Biotechnology (KRIBB)Department of Infectious Disease, Imperial College LondonKorea Biofoundry, Korea Research Institute of Bioscience and Biotechnology (KRIBB)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.https://doi.org/10.1038/s41467-025-61263-6 |
| spellingShingle | 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 Le Feuvre Nigel S. Scrutton Marko Storch Wonjae Seong Paul S. Freemont Seung-Goo Lee Abstraction hierarchy to define biofoundry workflows and operations for interoperable synthetic biology research and applications Nature Communications |
| title | Abstraction hierarchy to define biofoundry workflows and operations for interoperable synthetic biology research and applications |
| title_full | Abstraction hierarchy to define biofoundry workflows and operations for interoperable synthetic biology research and applications |
| title_fullStr | Abstraction hierarchy to define biofoundry workflows and operations for interoperable synthetic biology research and applications |
| title_full_unstemmed | Abstraction hierarchy to define biofoundry workflows and operations for interoperable synthetic biology research and applications |
| title_short | Abstraction hierarchy to define biofoundry workflows and operations for interoperable synthetic biology research and applications |
| title_sort | abstraction hierarchy to define biofoundry workflows and operations for interoperable synthetic biology research and applications |
| url | https://doi.org/10.1038/s41467-025-61263-6 |
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