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

Michal Galdzicki; Kevin P. Clancy; Ernst Oberortner; Matthew Pocock; Jacqueline Y. Quinn; Cesar A. Rodriguez; Nicholas Roehner; Mandy L. Wilson; Laura Adam; J. Christopher Anderson; Bryan A. Bartley; Jacob Beal; Deepak Chandran; Joanna Chen; Douglas Densmore; Drew Endy; Raik Grünberg; Jennifer Hallinan; Nathan J. Hillson; Jeffrey D. Johnson; Allan Kuchinsky; Matthew Lux; Goksel Misirli; Jean Peccoud; Hector A. Plahar; Evren Sirin; Guy Bart Stan; Alan Villalobos; Anil Wipat; John H. Gennari; Chris J. Myers; Herbert M. Sauro

doi:10.1038/nbt.2891

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

Michal Galdzicki, Kevin P. Clancy, Ernst Oberortner, Matthew Pocock, Jacqueline Y. Quinn, Cesar A. Rodriguez, Nicholas Roehner, Mandy L. Wilson, Laura Adam, J. Christopher Anderson, Bryan A. Bartley, Jacob Beal, Deepak Chandran, Joanna Chen, Douglas Densmore, Drew Endy, Raik Grünberg, Jennifer Hallinan, Nathan J. Hillson, Jeffrey D. JohnsonAllan Kuchinsky, Matthew Lux, Goksel Misirli, Jean Peccoud, Hector A. Plahar, Evren Sirin, Guy Bart Stan, Alan Villalobos, Anil Wipat, John H. Gennari, Chris J. Myers, Herbert M. Sauro^*

^*Corresponding author for this work

Research output: Contribution to journal › Review article › peer-review

204 Citations (Scopus)

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.

Original language	English
Pages (from-to)	545-550
Number of pages	6
Journal	Nature Biotechnology
Volume	32
Issue number	6
DOIs	https://doi.org/10.1038/nbt.2891
Publication status	Published - Jun 2014
Externally published	Yes

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Galdzicki, M., Clancy, K. P., Oberortner, E., Pocock, M., Quinn, J. Y., Rodriguez, C. A., Roehner, N., Wilson, M. L., Adam, L., Anderson, J. C., Bartley, B. A., Beal, J., Chandran, D., Chen, J., Densmore, D., Endy, D., Grünberg, R., Hallinan, J., Hillson, N. J., ... Sauro, H. M. (2014). The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology. Nature Biotechnology, 32(6), 545-550. https://doi.org/10.1038/nbt.2891

@article{861198610d134daa90fe4d9f1a4cf348,

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

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.",

author = "Michal Galdzicki and Clancy, {Kevin P.} and Ernst Oberortner and Matthew Pocock and Quinn, {Jacqueline Y.} and Rodriguez, {Cesar A.} and Nicholas Roehner and Wilson, {Mandy L.} and Laura Adam and Anderson, {J. Christopher} and Bartley, {Bryan A.} and Jacob Beal and Deepak Chandran and Joanna Chen and Douglas Densmore and Drew Endy and Raik Gr{\"u}nberg and Jennifer Hallinan and Hillson, {Nathan J.} and Johnson, {Jeffrey D.} and Allan Kuchinsky and Matthew Lux and Goksel Misirli and Jean Peccoud and Plahar, {Hector A.} and Evren Sirin and Stan, {Guy Bart} and Alan Villalobos and Anil Wipat and Gennari, {John H.} and Myers, {Chris J.} and Sauro, {Herbert M.}",

year = "2014",

month = jun,

doi = "10.1038/nbt.2891",

language = "English",

volume = "32",

pages = "545--550",

journal = "Nature Biotechnology",

issn = "1087-0156",

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Galdzicki, M, Clancy, KP, Oberortner, E, Pocock, M, Quinn, JY, Rodriguez, CA, Roehner, N, Wilson, ML, Adam, L, Anderson, JC, Bartley, BA, Beal, J, Chandran, D, Chen, J, Densmore, D, Endy, D, Grünberg, R, Hallinan, J, Hillson, NJ, Johnson, JD, Kuchinsky, A, Lux, M, Misirli, G, Peccoud, J, Plahar, HA, Sirin, E, Stan, GB, Villalobos, A, Wipat, A, Gennari, JH, Myers, CJ & Sauro, HM 2014, 'The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology', Nature Biotechnology, vol. 32, no. 6, pp. 545-550. https://doi.org/10.1038/nbt.2891

TY - JOUR

T1 - The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology

AU - Galdzicki, Michal

AU - Clancy, Kevin P.

AU - Oberortner, Ernst

AU - Pocock, Matthew

AU - Quinn, Jacqueline Y.

AU - Rodriguez, Cesar A.

AU - Roehner, Nicholas

AU - Wilson, Mandy L.

AU - Adam, Laura

AU - Anderson, J. Christopher

AU - Bartley, Bryan A.

AU - Beal, Jacob

AU - Chandran, Deepak

AU - Chen, Joanna

AU - Densmore, Douglas

AU - Endy, Drew

AU - Grünberg, Raik

AU - Hallinan, Jennifer

AU - Hillson, Nathan J.

AU - Johnson, Jeffrey D.

AU - Kuchinsky, Allan

AU - Lux, Matthew

AU - Misirli, Goksel

AU - Peccoud, Jean

AU - Plahar, Hector A.

AU - Sirin, Evren

AU - Stan, Guy Bart

AU - Villalobos, Alan

AU - Wipat, Anil

AU - Gennari, John H.

AU - Myers, Chris J.

AU - Sauro, Herbert M.

PY - 2014/6

Y1 - 2014/6

N2 - 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.

AB - 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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U2 - 10.1038/nbt.2891

DO - 10.1038/nbt.2891

M3 - Review article

C2 - 24911500

AN - SCOPUS:84902159136

SN - 1087-0156

VL - 32

SP - 545

EP - 550

JO - Nature Biotechnology

JF - Nature Biotechnology

IS - 6

ER -

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

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