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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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Synthetic Biology Open Language Visual (SBOL Visual) Version 2.1

Curtis Madsen / Angel Goni Moreno / Zachary Palchick / Umesh P / Nicholas Roehner / Bryan Bartley / Swapnil Bhatia / Shyam Bhakta / Mike Bissell / Kevin Clancy / Robert Sidney Cox / Thomas Gorochowski / Raik Grunberg / Augustin Luna / James McLaughlin / Tramy Nguyen / Nicolas Le Novere / Matthew Pocock / Herbert Sauro / James Scott-Brown / John T. Sexton / Guy-Bart Stan / Jeffrey J. Tabor / Christopher A. Voigt / Zach Zundel / Chris Myers / Jacob BealORCID iD: https://orcid.org/0000-0002-1663-5102 / Anil Wipat
Published Online: 2019-06-13 | DOI: https://doi.org/10.1515/jib-2018-0101

Abstract

People who are engineering biological organisms often find it useful to communicate in diagrams, both about the structure of the nucleic acid sequences that they are engineering and about the functional relationships between sequence features and other molecular species . Some typical practices and conventions have begun to emerge for such diagrams. The Synthetic Biology Open Language Visual (SBOL Visual) has been developed as a standard for organizing and systematizing such conventions in order to produce a coherent language for expressing the structure and function of genetic designs. This document details version 2.1 of SBOL Visual, which builds on the prior SBOL Visual 2.0 standard by expanding diagram syntax to include methods for showing modular structure and mappings between elements of a system, interactions arrows that can split or join (with the glyph at the split or join indicating either superposition or a chemical process), and adding new glyphs for indicating genomic context (e.g., integration into a plasmid or genome) and for stop codons.

Keywords: SBOL Visual; Standards; Diagrams

Article Note

This document does not contain technology or technical data controlled under either the U.S. International Traffic in Arms Regulations or the U.S. Export Administration Regulations.

About the article

Received: 2018-12-21

Accepted: 2019-05-20

Published Online: 2019-06-13


Citation Information: Journal of Integrative Bioinformatics, 20180101, ISSN (Online) 1613-4516, DOI: https://doi.org/10.1515/jib-2018-0101.

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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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