Synthetic Biology Open Language (SBOL) Version 2.2.0

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

doi:10.1515/jib-2018-0001

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Synthetic Biology Open Language (SBOL) Version 2.2.0

Journal article

Open access

Peer reviewed

Synthetic Biology Open Language (SBOL) Version 2.2.0

Robert Sidney Cox, Curtis Madsen, James Alastair McLaughlin, Tramy Nguyen, Nicholas Roehner, Bryan Bartley, Jacob Beal, Michael Bissell, Kiri Choi, Kevin Clancy, …

Journal of integrative bioinformatics, Vol.15(1), 20180001

04/02/2018

DOI: 10.1515/jib-2018-0001

PMCID: PMC6167039

PMID: 29605823

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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.

Signal Transduction

Software

Animals

Guidelines as Topic

Humans

Models, Biological

Programming Languages

Synthetic Biology - standards

Details

Title: Subtitle: Synthetic Biology Open Language (SBOL) Version 2.2.0
Creators: Robert Sidney Cox
Curtis Madsen - Boston University
James Alastair McLaughlin - Newcastle University
Tramy Nguyen - University of Utah
Nicholas Roehner - RTX
Bryan Bartley - University of Washington
Jacob Beal - RTX
Michael Bissell - Amyris
Kiri Choi - University of Washington
Kevin Clancy - Thermo Fisher Scientific
Raik Grünberg - King Abdullah University of Science and Technology
Chris Macklin - Amyris
Goksel Misirli - Keele University
Ernst Oberortner - Joint Genome Institute
Matthew Pocock - Turing Institute
Meher Samineni - University of Utah
Michael Zhang - University of Utah
Zhen Zhang - Utah State University
Zach Zundel - University of Utah
Chris Myers - University of Utah
John H Gennari - University of Washington
Herbert Sauro - University of Washington
Anil Wipat - Newcastle University
Resource Type: Journal article
Publication Details: Journal of integrative bioinformatics, Vol.15(1), 20180001
DOI: 10.1515/jib-2018-0001
PMID: 29605823
PMCID: PMC6167039
NLM abbreviation: J Integr Bioinform
ISSN: 1613-4516
eISSN: 1613-4516
Language: English
Date published: 04/02/2018
Academic Unit: Electrical and Computer Engineering
Record Identifier: 9984627319402771

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