Synthetic biology open language visual (SBOL Visual) version 2.3
<jats:title>Abstract</jats:title> <jats:p>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...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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| Other Authors: | |
| Format: | Article |
| Language: | English |
| Published: |
Walter de Gruyter GmbH
2021
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| Online Access: | https://hdl.handle.net/1721.1/135615.2 |
| _version_ | 1811077170612666368 |
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| author | Baig, Hasan Fontanarossa, Pedro Kulkarni, Vishwesh McLaughlin, James Vaidyanathan, Prashant Bartley, Bryan Bhakta, Shyam Bhatia, Swapnil Bissell, Mike Clancy, Kevin Cox, Robert Sidney Goñi Moreno, Angel Gorochowski, Thomas Grunberg, Raik Lee, Jihwan Luna, Augustin Madsen, Curtis Misirli, Goksel Nguyen, Tramy Le Novere, Nicolas Palchick, Zachary Pocock, Matthew Roehner, Nicholas Sauro, Herbert Scott-Brown, James Sexton, John T. Stan, Guy-Bart Tabor, Jeffrey J. Terry, Logan Vazquez Vilar, Marta Voigt, Christopher A. Wipat, Anil Zong, David Zundel, Zach Beal, Jacob Myers, Chris |
| author2 | Massachusetts Institute of Technology. Department of Biological Engineering |
| author_facet | Massachusetts Institute of Technology. Department of Biological Engineering Baig, Hasan Fontanarossa, Pedro Kulkarni, Vishwesh McLaughlin, James Vaidyanathan, Prashant Bartley, Bryan Bhakta, Shyam Bhatia, Swapnil Bissell, Mike Clancy, Kevin Cox, Robert Sidney Goñi Moreno, Angel Gorochowski, Thomas Grunberg, Raik Lee, Jihwan Luna, Augustin Madsen, Curtis Misirli, Goksel Nguyen, Tramy Le Novere, Nicolas Palchick, Zachary Pocock, Matthew Roehner, Nicholas Sauro, Herbert Scott-Brown, James Sexton, John T. Stan, Guy-Bart Tabor, Jeffrey J. Terry, Logan Vazquez Vilar, Marta Voigt, Christopher A. Wipat, Anil Zong, David Zundel, Zach Beal, Jacob Myers, Chris |
| author_sort | Baig, Hasan |
| collection | MIT |
| description | <jats:title>Abstract</jats:title>
<jats:p>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.</jats:p> |
| first_indexed | 2024-09-23T10:38:58Z |
| format | Article |
| id | mit-1721.1/135615.2 |
| institution | Massachusetts Institute of Technology |
| language | English |
| last_indexed | 2024-09-23T10:38:58Z |
| publishDate | 2021 |
| publisher | Walter de Gruyter GmbH |
| record_format | dspace |
| spelling | mit-1721.1/135615.22021-11-10T21:15:26Z Synthetic biology open language visual (SBOL Visual) version 2.3 Baig, Hasan Fontanarossa, Pedro Kulkarni, Vishwesh McLaughlin, James Vaidyanathan, Prashant Bartley, Bryan Bhakta, Shyam Bhatia, Swapnil Bissell, Mike Clancy, Kevin Cox, Robert Sidney Goñi Moreno, Angel Gorochowski, Thomas Grunberg, Raik Lee, Jihwan Luna, Augustin Madsen, Curtis Misirli, Goksel Nguyen, Tramy Le Novere, Nicolas Palchick, Zachary Pocock, Matthew Roehner, Nicholas Sauro, Herbert Scott-Brown, James Sexton, John T. Stan, Guy-Bart Tabor, Jeffrey J. Terry, Logan Vazquez Vilar, Marta Voigt, Christopher A. Wipat, Anil Zong, David Zundel, Zach Beal, Jacob Myers, Chris Massachusetts Institute of Technology. Department of Biological Engineering <jats:title>Abstract</jats:title> <jats:p>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.</jats:p> 2021-11-10T21:15:25Z 2021-10-27T20:24:16Z 2021-11-10T21:15:25Z 2021-06 2021-09-10T17:18:21Z Article http://purl.org/eprint/type/JournalArticle 1613-4516 https://hdl.handle.net/1721.1/135615.2 en 10.1515/jib-2020-0045 Journal of Integrative Bioinformatics Creative Commons Attribution 4.0 International license https://creativecommons.org/licenses/by/4.0/ application/octet-stream Walter de Gruyter GmbH De Gruyter |
| spellingShingle | Baig, Hasan Fontanarossa, Pedro Kulkarni, Vishwesh McLaughlin, James Vaidyanathan, Prashant Bartley, Bryan Bhakta, Shyam Bhatia, Swapnil Bissell, Mike Clancy, Kevin Cox, Robert Sidney Goñi Moreno, Angel Gorochowski, Thomas Grunberg, Raik Lee, Jihwan Luna, Augustin Madsen, Curtis Misirli, Goksel Nguyen, Tramy Le Novere, Nicolas Palchick, Zachary Pocock, Matthew Roehner, Nicholas Sauro, Herbert Scott-Brown, James Sexton, John T. Stan, Guy-Bart Tabor, Jeffrey J. Terry, Logan Vazquez Vilar, Marta Voigt, Christopher A. Wipat, Anil Zong, David Zundel, Zach Beal, Jacob Myers, Chris Synthetic biology open language visual (SBOL Visual) version 2.3 |
| title | Synthetic biology open language visual (SBOL Visual) version 2.3 |
| title_full | Synthetic biology open language visual (SBOL Visual) version 2.3 |
| title_fullStr | Synthetic biology open language visual (SBOL Visual) version 2.3 |
| title_full_unstemmed | Synthetic biology open language visual (SBOL Visual) version 2.3 |
| title_short | Synthetic biology open language visual (SBOL Visual) version 2.3 |
| title_sort | synthetic biology open language visual sbol visual version 2 3 |
| url | https://hdl.handle.net/1721.1/135615.2 |
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