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Synthetic Biology Open Language Visual (SBOL Visual) version 2.1

Title: Synthetic Biology Open Language Visual (SBOL Visual) version 2.1
Authors: Madsen, C
Goni Moreno, A
Palchick, Z
P, U
Roehner, N
Bartley, B
Bhatia, S
Bhakta, S
Bissell, M
Clancy, K
Cox, RS
Gorochowski, T
Grunberg, R
Luna, A
McLaughlin, J
Nguyen, T
Le Novere, N
Pocock, M
Sauro, H
Scott-Brown, J
Sexton, JT
Stan, G-B
Tabor, JJ
Voigt, CA
Zundel, Z
Myers, C
Beal, J
Wipat, A
Item Type: Journal Article
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.
Issue Date: 13-Jun-2019
Date of Acceptance: 20-May-2019
URI: http://hdl.handle.net/10044/1/70645
DOI: 10.1515/jib-2018-0101
ISSN: 1613-4516
Publisher: IMBio e.V.
Start Page: 1
End Page: 78
Journal / Book Title: Journal of Integrative Bioinformatics
Volume: 16
Issue: 2
Copyright Statement: © 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. CC BY 4.0 (https://creativecommons.org/licenses/by/4.0/)
Sponsor/Funder: Engineering & Physical Science Research Council (EPSRC)
Royal Academy Of Engineering
Funder's Grant Number: EP/M002187/1
CiET1819\5 (CiET1819\TUA\20)
Keywords: Science & Technology
Life Sciences & Biomedicine
Mathematical & Computational Biology
SBOL Visual
Standards
Diagrams
Diagrams
SBOL Visual
Standards
Diagrams
SBOL Visual
Standards
Publication Status: Published
Conference Place: Germany
Open Access location: https://www.degruyter.com/view/j/jib.ahead-of-print/jib-2018-0101/jib-2018-0101.xml
Online Publication Date: 2019-06-13
Appears in Collections:Bioengineering
Faculty of Engineering