Synthetic Biology Open Language Visual (SBOL Visual) Version 2.1

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...

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Bibliographic Details
Published in:Journal of Integrative Bioinformatics Vol. 16; no. 2
Main Authors: Madsen, Curtis, Goni Moreno, Angel, Palchick, Zachary, P, Umesh, Roehner, Nicholas, Bartley, Bryan, Bhatia, Swapnil, Bhakta, Shyam, Bissell, Mike, Clancy, Kevin, Cox, Robert Sidney, Gorochowski, Thomas, Grunberg, Raik, Luna, Augustin, McLaughlin, James, Nguyen, Tramy, Le Novere, Nicolas, Pocock, Matthew, Sauro, Herbert, Scott-Brown, James, Sexton, John T, Stan, Guy-Bart, Tabor, Jeffrey J, Voigt, Christopher A, Zundel, Zach, Myers, Chris, Beal, Jacob, Wipat, Anil
Format: Journal Article
Language:English
Published: Germany Walter de Gruyter GmbH 13.06.2019
De Gruyter
Subjects:
Biotechnology
BrisSynBio
Bristol BioDesign Institute
diagrams
dk/atira/pure/core/keywords/biodesign_SRI
dk/atira/pure/core/keywords/biodesign_SRI; name=Bristol BioDesign Institute
dk/atira/pure/core/keywords/brissynbio
dk/atira/pure/core/keywords/brissynbio; name=BrisSynBio
Life Sciences & Biomedicine
Mathematical & Computational Biology
Models, Biological
Programming Languages
sbol visual
Science & Technology
Synthetic Biology
TP248.13-248.65
Visualisation
Diagrams
SBOL Visual
Standards
ISSN:1613-4516, 1613-4516
Online Access:Get full text
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Description
Summary: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.
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ISSN:1613-4516
1613-4516
DOI:10.1515/jib-2018-0101