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Journal of Integrative Bioinformatics

Editor-in-Chief: Schreiber, Falk / Hofestädt, Ralf

Managing Editor: Sommer, Björn

Ed. by Baumbach, Jan / Chen, Ming / Orlov, Yuriy / Allmer, Jens

Editorial Board: Giorgetti, Alejandro / Harrison, Andrew / Kochetov, Aleksey / Krüger, Jens / Ma, Qi / Matsuno, Hiroshi / Mitra, Chanchal K. / Pauling, Josch K. / Rawlings, Chris / Fdez-Riverola, Florentino / Romano, Paolo / Röttger, Richard / Shoshi, Alban / Soares, Siomar de Castro / Taubert, Jan / Tauch, Andreas / Yousef, Malik / Weise, Stephan / Hassani-Pak, Keywan


CiteScore 2017: 0.77

SCImago Journal Rank (SJR) 2017: 0.336

Open Access
Online
ISSN
1613-4516
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Volume 16, Issue 2

Issues

Synthetic Biology Open Language (SBOL) Version 2.3

Curtis Madsen / Angel Goñi Moreno / Umesh P / Zachary Palchick / Nicholas Roehner / Christian Atallah / Bryan Bartley / Kiri Choi / Robert Sidney Cox / Thomas Gorochowski / Raik Grünberg / Chris Macklin / James McLaughlin / Xianwei Meng / Tramy Nguyen / Matthew Pocock / Meher Samineni / James Scott-Brown / Ysis Tarter / Michael Zhang / Zhen Zhang / Zach Zundel / Jacob BealORCID iD: https://orcid.org/0000-0002-1663-5102 / Michael Bissell / Kevin Clancy / John H. Gennari / Goksel Misirli / Chris Myers / Ernst Oberortner / Herbert Sauro / Anil Wipat
Published Online: 2019-06-13 | DOI: https://doi.org/10.1515/jib-2019-0025

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 is 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 2.3.0 of SBOL, which builds upon version 2.2.0 published in last year’s JIB Standards in Systems Biology special issue. In particular, SBOL 2.3.0 includes means of succinctly representing sequence modifications, such as insertion, deletion, and replacement, an extension to support organization and attachment of experimental data derived from designs, and an extension for describing numerical parameters of design elements. The new version also includes specifying types of synthetic biology activities, unambiguous locations for sequences with multiple encodings, refinement of a number of validation rules, improved figures and examples, and clarification on a number of issues related to the use of external ontology terms.

Keywords: Synthetic Biology; Synthetic Biology Open Language; Standards

About the article

Received: 2019-04-03

Accepted: 2019-05-20

Published Online: 2019-06-13


Citation Information: Journal of Integrative Bioinformatics, Volume 16, Issue 2, 20190025, ISSN (Online) 1613-4516, DOI: https://doi.org/10.1515/jib-2019-0025.

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© 2019, Curtis Madsen et al., published by Walter de Gruyter GmbH, Berlin/Boston. This work is licensed under the Creative Commons Attribution 4.0 Public License. BY 4.0

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