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Standardization in synthetic biology : an engineering discipline coming of age

Thomas Decoene (UGent) , Brecht De Paepe (UGent) , Jo Maertens (UGent) , Pieter Coussement (UGent) , Gert Peters (UGent) , Sofie De Maeseneire (UGent) and Marjan De Mey (UGent)
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Abstract
Background: Leaping DNA read-and-write technologies, and extensive automation and miniaturization are radically transforming the field of biological experimentation by providing the tools that enable the cost-effective high-throughput required to address the enormous complexity of biological systems. However, standardization of the synthetic biology workflow has not kept abreast with dwindling technical and resource constraints, leading, for example, to the collection of multi-level and multi-omics large data sets that end up disconnected or remain under- or even unexploited. Purpose: In this contribution, we critically evaluate the various efforts, and the (limited) success thereof, in order to introduce standards for defining, designing, assembling, characterizing, and sharing synthetic biology parts. The causes for this success or the lack thereof, as well as possible solutions to overcome these, are discussed. Conclusion: Akin to other engineering disciplines, extensive standardization will undoubtedly speed-up and reduce the cost of bioprocess development. In this respect, further implementation of synthetic biology standards will be crucial for the field in order to redeem its promise, i.e. to enable predictable forward engineering.
Keywords
Standardization, biological parts, part characterization, synthetic biology, data management, forward engineering, HETEROLOGOUS GENE-EXPRESSION, ESCHERICHIA-COLI PROMOTERS, GREEN FLUORESCENT PROTEIN, RIBOSOME BINDING-SITES, SACCHAROMYCES-CEREVISIAE, BACTERIAL PROMOTERS, MINIMUM INFORMATION, AUTOMATED DESIGN, ASSEMBLY METHOD, DNA-SEQUENCES

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MLA
Decoene, Thomas, Brecht De Paepe, Jo Maertens, et al. “Standardization in Synthetic Biology : an Engineering Discipline Coming of Age.” CRITICAL REVIEWS IN BIOTECHNOLOGY 38.5 (2018): 647–656. Print.
APA
Decoene, T., De Paepe, B., Maertens, J., Coussement, P., Peters, G., De Maeseneire, S., & De Mey, M. (2018). Standardization in synthetic biology : an engineering discipline coming of age. CRITICAL REVIEWS IN BIOTECHNOLOGY, 38(5), 647–656.
Chicago author-date
Decoene, Thomas, Brecht De Paepe, Jo Maertens, Pieter Coussement, Gert Peters, Sofie De Maeseneire, and Marjan De Mey. 2018. “Standardization in Synthetic Biology : an Engineering Discipline Coming of Age.” Critical Reviews in Biotechnology 38 (5): 647–656.
Chicago author-date (all authors)
Decoene, Thomas, Brecht De Paepe, Jo Maertens, Pieter Coussement, Gert Peters, Sofie De Maeseneire, and Marjan De Mey. 2018. “Standardization in Synthetic Biology : an Engineering Discipline Coming of Age.” Critical Reviews in Biotechnology 38 (5): 647–656.
Vancouver
1.
Decoene T, De Paepe B, Maertens J, Coussement P, Peters G, De Maeseneire S, et al. Standardization in synthetic biology : an engineering discipline coming of age. CRITICAL REVIEWS IN BIOTECHNOLOGY. 2018;38(5):647–56.
IEEE
[1]
T. Decoene et al., “Standardization in synthetic biology : an engineering discipline coming of age,” CRITICAL REVIEWS IN BIOTECHNOLOGY, vol. 38, no. 5, pp. 647–656, 2018.
@article{8539033,
  abstract     = {Background: Leaping DNA read-and-write technologies, and extensive automation and miniaturization are radically transforming the field of biological experimentation by providing the tools that enable the cost-effective high-throughput required to address the enormous complexity of biological systems. However, standardization of the synthetic biology workflow has not kept abreast with dwindling technical and resource constraints, leading, for example, to the collection of multi-level and multi-omics large data sets that end up disconnected or remain under- or even unexploited.
Purpose: In this contribution, we critically evaluate the various efforts, and the (limited) success thereof, in order to introduce standards for defining, designing, assembling, characterizing, and sharing synthetic biology parts. The causes for this success or the lack thereof, as well as possible solutions to overcome these, are discussed.
Conclusion: Akin to other engineering disciplines, extensive standardization will undoubtedly speed-up and reduce the cost of bioprocess development. In this respect, further implementation of synthetic biology standards will be crucial for the field in order to redeem its promise, i.e. to enable predictable forward engineering.},
  author       = {Decoene, Thomas and De Paepe, Brecht and Maertens, Jo and Coussement, Pieter and Peters, Gert and De Maeseneire, Sofie and De Mey, Marjan},
  issn         = {0738-8551},
  journal      = {CRITICAL REVIEWS IN BIOTECHNOLOGY},
  keywords     = {Standardization,biological parts,part characterization,synthetic biology,data management,forward engineering,HETEROLOGOUS GENE-EXPRESSION,ESCHERICHIA-COLI PROMOTERS,GREEN FLUORESCENT PROTEIN,RIBOSOME BINDING-SITES,SACCHAROMYCES-CEREVISIAE,BACTERIAL PROMOTERS,MINIMUM INFORMATION,AUTOMATED DESIGN,ASSEMBLY METHOD,DNA-SEQUENCES},
  language     = {eng},
  number       = {5},
  pages        = {647--656},
  title        = {Standardization in synthetic biology : an engineering discipline coming of age},
  url          = {http://dx.doi.org/10.1080/07388551.2017.1380600},
  volume       = {38},
  year         = {2018},
}

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