The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology

Michal Galdzicki¹, Kevin P Clancy², Ernst Oberortner³, Matthew Pocock⁴, Jacqueline Y Quinn⁵, Cesar A Rodriguez⁵, Nicholas Roehner⁶, Mandy L Wilson⁷, Laura Adam⁷, J Christopher Anderson⁸, Bryan A Bartley⁹, Jacob Beal¹⁰, Deepak Chandran⁵, Joanna Chen¹¹, Douglas Densmore³, Drew Endy¹², Raik Grünberg¹³, Jennifer Hallinan⁴, Nathan J Hillson¹¹, Jeffrey D Johnson¹⁴, Allan Kuchinsky¹⁵, Matthew Lux⁷, Goksel Misirli⁴, Jean Peccoud⁷, Hector A Plahar¹¹, Evren Sirin¹⁶, Guy-Bart Stan¹⁷, Alan Villalobos¹⁸, Anil Wipat⁴, John H Gennari¹, Chris J Myers¹⁹, Herbert M Sauro⁹

Affiliations

¹ Biomedical and Health Informatics, University of Washington, Seattle, Washington, USA.
² Synthetic Biology Unit, Life Technologies, Carlsbad, California, USA.
³ Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts, USA.
⁴ School of Computing Science, Newcastle University, Newcastle upon Tyne, UK.
⁵ Autodesk Research, Autodesk, San Francisco, California, USA.
⁶ Bioengineering, University of Utah, Salt Lake City, Utah, USA.
⁷ Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia, USA.
⁸ Department of Bioengineering, University of California, Berkeley, Berkeley, California, USA.
⁹ Department of Bioengineering, University of Washington, Seattle, Washington, USA.
¹⁰ Raytheon BBN Technologies, Cambridge, Massachusetts, USA.
¹¹ Fuels Synthesis Division, Joint Bioenergy Institute (JBEI), Berkeley, California, USA.
¹² Department of Bioengineering, Stanford University, Stanford, California, USA.
¹³ IRIC, University of Montreal, Montreal, Quebec, Canada.
¹⁴ Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA.
¹⁵ Molecular Tools Laboratory, Agilent Technologies, Santa Clara, California, USA.
¹⁶ Clark & Parsia, Arlington, Massachusetts, USA.
¹⁷ Bioengineering, Imperial College London, London, UK.
¹⁸ DNA2.0, Menlo Park, California, USA.
¹⁹ Department of Electrical and Computer Engineering, University of Utah, Salt Lake City, Utah, USA.

PMID: 24911500
DOI: 10.1038/nbt.2891

The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology

Michal Galdzicki et al. Nat Biotechnol. 2014 Jun.

. 2014 Jun;32(6):545-50.

doi: 10.1038/nbt.2891. Epub 2014 Jun 6.

Authors

Affiliations

¹ Biomedical and Health Informatics, University of Washington, Seattle, Washington, USA.
² Synthetic Biology Unit, Life Technologies, Carlsbad, California, USA.
³ Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts, USA.
⁴ School of Computing Science, Newcastle University, Newcastle upon Tyne, UK.
⁵ Autodesk Research, Autodesk, San Francisco, California, USA.
⁶ Bioengineering, University of Utah, Salt Lake City, Utah, USA.
⁷ Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia, USA.
⁸ Department of Bioengineering, University of California, Berkeley, Berkeley, California, USA.
⁹ Department of Bioengineering, University of Washington, Seattle, Washington, USA.
¹⁰ Raytheon BBN Technologies, Cambridge, Massachusetts, USA.
¹¹ Fuels Synthesis Division, Joint Bioenergy Institute (JBEI), Berkeley, California, USA.
¹² Department of Bioengineering, Stanford University, Stanford, California, USA.
¹³ IRIC, University of Montreal, Montreal, Quebec, Canada.
¹⁴ Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA.
¹⁵ Molecular Tools Laboratory, Agilent Technologies, Santa Clara, California, USA.
¹⁶ Clark & Parsia, Arlington, Massachusetts, USA.
¹⁷ Bioengineering, Imperial College London, London, UK.
¹⁸ DNA2.0, Menlo Park, California, USA.
¹⁹ Department of Electrical and Computer Engineering, University of Utah, Salt Lake City, Utah, USA.

PMID: 24911500
DOI: 10.1038/nbt.2891

Abstract

The re-use of previously validated designs is critical to the evolution of synthetic biology from a research discipline to an engineering practice. Here we describe the Synthetic Biology Open Language (SBOL), a proposed data standard for exchanging designs within the synthetic biology community. SBOL represents synthetic biology designs in a community-driven, formalized format for exchange between software tools, research groups and commercial service providers. The SBOL Developers Group has implemented SBOL as an XML/RDF serialization and provides software libraries and specification documentation to help developers implement SBOL in their own software. We describe early successes, including a demonstration of the utility of SBOL for information exchange between several different software tools and repositories from both academic and industrial partners. As a community-driven standard, SBOL will be updated as synthetic biology evolves to provide specific capabilities for different aspects of the synthetic biology workflow.

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Comment in

Intellectual property issues and synthetic biology standards.
Contreras JL, Rai AK, Torrance AW. Contreras JL, et al. Nat Biotechnol. 2015 Jan;33(1):24-5. doi: 10.1038/nbt.3107. Nat Biotechnol. 2015. PMID: 25574630 No abstract available.
Reply to Intellectual property issues and synthetic biology standards.
Galdzicki M, Kahl LJ, Endy D, Sauro HM. Galdzicki M, et al. Nat Biotechnol. 2015 Jan;33(1):25. doi: 10.1038/nbt.3114. Nat Biotechnol. 2015. PMID: 25574632 No abstract available.

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The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology

Affiliations

The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology

Authors

Affiliations

Abstract

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References

Publication types

MeSH terms

Grants and funding

LinkOut - more resources

Full Text Sources

Other Literature Sources

Research Materials