Journal article
Synthetic biology open language visual (SBOL Visual) version 2.3
Journal of integrative bioinformatics, Vol.18(3), 20200045
06/08/2021
DOI: 10.1515/jib-2020-0045
PMCID: PMC8560345
PMID: 34098590
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.
Details
- Title: Subtitle
- Synthetic biology open language visual (SBOL Visual) version 2.3
- Creators
- Hasan Baig - University of ConnecticutPedro Fontanarossa - University of UtahVishwesh Kulkarni - University of WarwickJames McLaughlin - University of Newcastle AustraliaPrashant Vaidyanathan - Microsoft ResearchBryan Bartley - RTXShyam Bhakta - Rice UniversitySwapnil Bhatia - Boston UniversityMike Bissell - Shipyard Toolchains LLC, Emeryville, USAKevin Clancy - Thermo Fisher ScientificRobert Sidney Cox - Kobe UniversityAngel Goñi Moreno - Newcastle UniversityThomas Gorochowski - University of BristolRaik Grunberg - King Abdullah University of Science and TechnologyJihwan Lee - Rice UniversityAugustin Luna - Harvard UniversityCurtis Madsen - Boston UniversityGoksel Misirli - Keele UniversityTramy Nguyen - RTXNicolas Le Novere - Babraham InstituteZachary Palchick - ZogenixMatthew Pocock - Turing InstituteNicholas Roehner - RTXHerbert Sauro - University of WashingtonJames Scott-Brown - University of OxfordJohn T. Sexton - Rice UniversityGuy-Bart Stan - Imperial College LondonJeffrey J. Tabor - Rice UniversityLogan Terry - University of UtahMarta Vazquez Vilar - Universitat Politècnica de ValènciaChristopher A. Voigt - IIT@MITAnil Wipat - Newcastle UniversityDavid Zong - Rice UniversityZach Zundel - University of UtahJacob Beal - RTXChris Myers - University of Colorado Boulder
- Resource Type
- Journal article
- Publication Details
- Journal of integrative bioinformatics, Vol.18(3), 20200045
- Publisher
- De Gruyter
- DOI
- 10.1515/jib-2020-0045
- PMID
- 34098590
- PMCID
- PMC8560345
- ISSN
- 1613-4516
- eISSN
- 1613-4516
- Number of pages
- 90
- Language
- English
- Date published
- 06/08/2021
- Academic Unit
- Electrical and Computer Engineering
- Record Identifier
- 9984627307702771
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