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

Journal: Nature communications
Published Date:

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.

Authors

  • Haseong Kim
    Korea Biofoundry, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea.
  • Nathan J Hillson
    Joint BioEnergy Institute (JBEI) , Emeryville , California 94608 , United States.
  • Byung-Kwan Cho
    Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.
  • Bong Hyun Sung
    Korea Biofoundry, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea.
  • Dae-Hee Lee
    Korea Biofoundry, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea.
  • Dong-Myung Kim
    Department of Chemical Engineering and Applied Chemistry, Chungnam National University, Daejeon, Republic of Korea.
  • Min-Kyu Oh
    Department of Chemical and Biological Engineering, Korea University, Seoul, Republic of Korea.
  • Matthew Wook Chang
    NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore. bchcmw@nus.edu.sg.
  • Yong-Su Jin
    Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
  • Susan J Rosser
    School of Biological Sciences, University of Edinburgh, Edinburgh, UK.
  • Peter Vegh
    School of Biological Sciences, University of Edinburgh, Edinburgh, UK.
  • Rennos Fragkoudis
    School of Biological Sciences, University of Edinburgh, Edinburgh, UK.
  • Rosalind Le Feuvre
    Manchester Institute of Biotechnology, University of Manchester (UoM), Manchester, UK.
  • Nigel S Scrutton
    Manchester Synthetic Biology Research Centre for Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology and School of Chemistry , University of Manchester , Manchester M1 7DN , United Kingdom.
  • Marko Storch
    Department of Infectious Disease, Imperial College London, London, UK.
  • Wonjae Seong
    Korea Biofoundry, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea.
  • Paul S Freemont
    Department of Infectious Disease, Imperial College London, London, UK. p.freemont@imperial.ac.uk.
  • Seung-Goo Lee
    Korea Biofoundry, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea. sglee@kribb.re.kr.