Open Access Published by De Gruyter June 8, 2021

Synthetic biology open language visual (SBOL Visual) version 2.3

Hasan Baig , Pedro Fontanarossa , Vishwesh Kulkarni , James McLaughlin , Prashant Vaidyanathan , Bryan Bartley , Shyam Bhakta , Swapnil Bhatia , Mike Bissell , Kevin Clancy , Robert Sidney Cox , Angel Goñi Moreno , Thomas Gorochowski , Raik Grunberg , Jihwan Lee , Augustin Luna , Curtis Madsen , Goksel Misirli , Tramy Nguyen , Nicolas Le Novere , Zachary Palchick , Matthew Pocock , Nicholas Roehner , Herbert Sauro , James Scott-Brown , John T. Sexton , Guy-Bart Stan , Jeffrey J. Tabor , Logan Terry , Marta Vazquez Vilar , Christopher A. Voigt , Anil Wipat , David Zong , Zach Zundel , Jacob Beal and Chris Myers

From the journal Journal of Integrative Bioinformatics

https://doi.org/10.1515/jib-2020-0045

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 2.3 of SBOL Visual, which builds on the prior SBOL Visual 2.2 in several ways. First, the specification now includes higher-level “interactions with interactions,” such as an inducer molecule stimulating a repression interaction. Second, binding with a nucleic acid backbone can be shown by overlapping glyphs, as with other molecular complexes. Finally, a new “unspecified interaction” glyph is added for visualizing interactions whose nature is unknown, the “insulator” glyph is deprecated in favor of a new “inert DNA spacer” glyph, and the polypeptide region glyph is recommended for showing 2A sequences.

Keywords: diagrams; SBOL Visual; standards

Corresponding author: Jacob Beal, Raytheon BBN Technologies, Cambridge, USA, E-mail: editors@sbolstandard.org

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.

Received: 2020-12-10

Accepted: 2021-01-11

Published Online: 2021-06-08

This work is licensed under the Creative Commons Attribution 4.0 International License.

Synthetic biology open language visual (SBOL Visual) version 2.3

Abstract

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