Synthetic Biology Open Language (SBOL) Version 2.2.0

Cox, Robert Sidney; Madsen, Curtis; McLaughlin, James Alastair; Nguyen, Tramy; Roehner, Nicholas; Bartley, Bryan; Beal, Jacob; Bissell, Michael; Choi, Kiri; Clancy, Kevin; Grünberg, Raik; Macklin, Chris; Misirli, Goksel; Oberortner, Ernst; Pocock, Matthew; Samineni, Meher; Zhang, Michael; Zhang, Zhen; Zundel, Zach; Gennari, John H.; Myers, Chris; Sauro, Herbert; Wipat, Anil

doi:10.1515/jib-2018-0001

Title: Synthetic Biology Open Language (SBOL) Version 2.2.0

Abstract

Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. One method to ameliorate these problems would be to improve the exchange of information about designed systems between laboratories. The synthetic biology open language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology, filling a need not satisfied by other pre-existing standards. This document details version 2.2.0 of SBOL that builds upon version 2.1.0 published in last year’s JIB special issue. In particular, SBOL 2.2.0 includes improved description and validation rules for genetic design provenance, an extension to support combinatorial genetic designs, a new class to add non-SBOL data as attachments, a new class for genetic design implementations, and a description of a methodology to describe the entire design-build-test-learn cycle within the SBOL data model.

Authors:

Cox, Robert Sidney ^[1]; Madsen, Curtis ^[2]; McLaughlin, James Alastair ^[3]; Nguyen, Tramy ^[4]; Roehner, Nicholas ^[5]; Bartley, Bryan ^[6]; Beal, Jacob ^[5]; Bissell, Michael ^[7]; Choi, Kiri ^[6]; Clancy, Kevin ^[8]; Grünberg, Raik ^[9]; Macklin, Chris ^[7]; Misirli, Goksel ^[10]; Oberortner, Ernst ^[11]; Pocock, Matthew ^[12]; Samineni, Meher ^[4]; Zhang, Michael ^[4]; Zhang, Zhen ^[13]; Zundel, Zach ^[4]; Gennari, John H. ^[6] more »

Prospect Bio, Brisbane, CA (United States)
Boston Univ., Boston, MA (United States)
Newcastle Univ., Newcastle upon Tyne (United Kingdom)
Univ. of Utah, Salt Lake City, UT (United States)
Raytheon BBN Technologies, Cambridge, MA (United States)
Univ. of Washington, Seattle, WA (United States)
Amyris, Inc., Emeryville, CA (United States)
ThermoFisher Scientific, San Diego, CA (United States)
King Abdullah Univ. for Science and Technology, Thuwal (Saudi Arabia)
Keele Univ. (United Kingdom)
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
Turing Ate My Hamster LTD, Newcastle (United Kingdom)
Utah State Univ., Logan, UT (United States)

Publication Date:: Mon Apr 02 00:00:00 EDT 2018

Research Org.:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC)

Sponsoring Org.:: USDOE Office of Science (SC)

OSTI Identifier:: 1544297

Resource Type:: Accepted Manuscript

Journal Name:: Journal of Integrative Bioinformatics

Additional Journal Information:: Journal Volume: 15; Journal Issue: 1; Journal ID: ISSN 1613-4516

Publisher:: Walter de Gruyter GmbH

Country of Publication:: United States

Language:: English

Subject:: 59 BASIC BIOLOGICAL SCIENCES; Synthetic Biology; Synthetic Biology Open Language; Standards

Citation Formats


                    Cox, Robert Sidney, Madsen, Curtis, McLaughlin, James Alastair, Nguyen, Tramy, Roehner, Nicholas, Bartley, Bryan, Beal, Jacob, Bissell, Michael, Choi, Kiri, Clancy, Kevin, Grünberg, Raik, Macklin, Chris, Misirli, Goksel, Oberortner, Ernst, Pocock, Matthew, Samineni, Meher, Zhang, Michael, Zhang, Zhen, Zundel, Zach, Gennari, John H., Myers, Chris, Sauro, Herbert, and Wipat, Anil. Synthetic Biology Open Language (SBOL) Version 2.2.0.  United States: N. p., 2018. 
Web.  doi:10.1515/jib-2018-0001.

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                    Cox, Robert Sidney, Madsen, Curtis, McLaughlin, James Alastair, Nguyen, Tramy, Roehner, Nicholas, Bartley, Bryan, Beal, Jacob, Bissell, Michael, Choi, Kiri, Clancy, Kevin, Grünberg, Raik, Macklin, Chris, Misirli, Goksel, Oberortner, Ernst, Pocock, Matthew, Samineni, Meher, Zhang, Michael, Zhang, Zhen, Zundel, Zach, Gennari, John H., Myers, Chris, Sauro, Herbert, & Wipat, Anil. Synthetic Biology Open Language (SBOL) Version 2.2.0.  United States.  https://doi.org/10.1515/jib-2018-0001

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                    Cox, Robert Sidney, Madsen, Curtis, McLaughlin, James Alastair, Nguyen, Tramy, Roehner, Nicholas, Bartley, Bryan, Beal, Jacob, Bissell, Michael, Choi, Kiri, Clancy, Kevin, Grünberg, Raik, Macklin, Chris, Misirli, Goksel, Oberortner, Ernst, Pocock, Matthew, Samineni, Meher, Zhang, Michael, Zhang, Zhen, Zundel, Zach, Gennari, John H., Myers, Chris, Sauro, Herbert, and Wipat, Anil. Mon .  
"Synthetic Biology Open Language (SBOL) Version 2.2.0".  United States.  https://doi.org/10.1515/jib-2018-0001.  https://www.osti.gov/servlets/purl/1544297.

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@article{osti_1544297,

  title        = {Synthetic Biology Open Language (SBOL) Version 2.2.0},

  author       = {Cox, Robert Sidney and Madsen, Curtis and McLaughlin, James Alastair and Nguyen, Tramy and Roehner, Nicholas and Bartley, Bryan and Beal, Jacob and Bissell, Michael and Choi, Kiri and Clancy, Kevin and Grünberg, Raik and Macklin, Chris and Misirli, Goksel and Oberortner, Ernst and Pocock, Matthew and Samineni, Meher and Zhang, Michael and Zhang, Zhen and Zundel, Zach and Gennari, John H. and Myers, Chris and Sauro, Herbert and Wipat, Anil},

  abstractNote = {Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. One method to ameliorate these problems would be to improve the exchange of information about designed systems between laboratories. The synthetic biology open language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology, filling a need not satisfied by other pre-existing standards. This document details version 2.2.0 of SBOL that builds upon version 2.1.0 published in last year’s JIB special issue. In particular, SBOL 2.2.0 includes improved description and validation rules for genetic design provenance, an extension to support combinatorial genetic designs, a new class to add non-SBOL data as attachments, a new class for genetic design implementations, and a description of a methodology to describe the entire design-build-test-learn cycle within the SBOL data model.},

  doi          = {10.1515/jib-2018-0001},

  journal      = {Journal of Integrative Bioinformatics},

  number       = 1,

  volume       = 15,

  place        = {United States},

  year         = {Mon Apr 02 00:00:00 EDT 2018},

  month        = {Mon Apr 02 00:00:00 EDT 2018}

}

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Works referencing / citing this record:

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BpForms and BcForms: a toolkit for concretely describing non-canonical polymers and complexes to facilitate global biochemical networks
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Genome Biology, Vol. 21, Issue 1
DOI: 10.1186/s13059-020-02025-z

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Title: Synthetic Biology Open Language (SBOL) Version 2.2.0

Abstract

Citation Formats

Scaling up genetic circuit design for cellular computing: advances and prospects journal, October 2018

Utilising datasheets for the informed automated design and build of a synthetic metabolic pathway journal, January 2019

BpForms and BcForms: a toolkit for concretely describing non-canonical polymers and complexes to facilitate global biochemical networks journal, May 2020

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journal, October 2018

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journal, January 2019

BpForms and BcForms: a toolkit for concretely describing non-canonical polymers and complexes to facilitate global biochemical networks
journal, May 2020