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 Beal; Anil Wipat

doi:10.1515/jib-2018-0101

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Synthetic Biology Open Language Visual (SBOL Visual) Version 2.1

Journal article

Open access

Peer reviewed

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, …

Journal of integrative bioinformatics, Vol.16(2), 20180101

06/13/2019

DOI: 10.1515/jib-2018-0101

PMCID: PMC6798824

PMID: 31199768

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https://doi.org/10.1515/jib-2018-0101View

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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.

Models, Biological

Programming Languages

Synthetic Biology

Details

Title: Subtitle: Synthetic Biology Open Language Visual (SBOL Visual) Version 2.1
Creators: Curtis Madsen - Boston University
Angel Goni Moreno - Newcastle University
Zachary Palchick - Zogenix
Umesh P - A P J Abdul Kalam Technological University
Nicholas Roehner - RTX
Bryan Bartley - RTX
Swapnil Bhatia - Boston University
Shyam Bhakta - Rice University
Mike Bissell - Amyris
Kevin Clancy - Thermo Fisher Scientific
Robert Sidney Cox - Kobe University
Thomas Gorochowski - University of Bristol
Raik Grunberg - King Abdullah University of Science and Technology
Augustin Luna - Harvard University
James McLaughlin - Newcastle University
Tramy Nguyen - University of Utah
Nicolas Le Novere - Babraham Institute
Matthew Pocock - Turing Institute
Herbert Sauro - University of Washington
James Scott-Brown - Imperial College London
John T Sexton - Rice University
Guy-Bart Stan - Imperial College London
Jeffrey J Tabor - Rice University
Christopher A Voigt - IIT@MIT
Zach Zundel - University of Utah
Chris Myers - University of Utah
Jacob Beal - RTX
Anil Wipat - Newcastle University
Resource Type: Journal article
Publication Details: Journal of integrative bioinformatics, Vol.16(2), 20180101
DOI: 10.1515/jib-2018-0101
PMID: 31199768
PMCID: PMC6798824
ISSN: 1613-4516
eISSN: 1613-4516
Grant note: BB/L01386X/1 / Biotechnology and Biological Sciences Research Council
Language: English
Date published: 06/13/2019
Academic Unit: Electrical and Computer Engineering
Record Identifier: 9984627204802771

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