scholarly journals Capturing Multicellular System Designs Using the Synthetic Biology Open Language (SBOL)

2018 ◽  
Author(s):  
Bradley Brown ◽  
Christian Atallah ◽  
James Alastair McLaughlin ◽  
Göksel Misirli ◽  
Ángel Goñi-Moreno ◽  
...  
Keyword(s):  
Synthetic Biology ◽  
Biological Systems ◽  
Data Standard ◽  
Homogeneous Systems ◽  
System Behaviour ◽  
Synthetic Biology Open Language ◽  
And Function ◽  
Multiple Cells ◽  
System Designs ◽  
Multicellular System

AbstractSynthetic biology aims to improve the development of biological systems and in-crease their reproducibility through the use of engineering principles, such as stan-dardisation and modularisation. It is important that these systems can be represented and shared in a standard way to ensure they are easily understood, reproduced, and utilised by other researchers. The Synthetic Biology Open Language (SBOL) is a data standard for sharing biological designs and information about their implementation and characterisation. Thus far, this standard has been used to represent designs in homogeneous systems, where the same design is implemented in every cell. In recent years there has been increasing interest in multicellular systems, where biological designs are split across multiple cells to optimise the system behaviour and function. Here we show how the SBOL standard can be used to represent such multicellular systems, and hence how researchers can better share designs with the community.

scholarly journals Capturing Multicellular System Designs Using Synthetic Biology Open Language (SBOL)

2020 ◽  
Vol 9 (9) ◽  
pp. 2410-2417
Author(s):  
Bradley Brown ◽  
Bryan Bartley ◽  
Jacob Beal ◽  
Jasmine E. Bird ◽  
Ángel Goñi-Moreno ◽  
...  
Keyword(s):  
Synthetic Biology ◽  
Synthetic Biology Open Language ◽  
System Designs ◽  
Multicellular System

scholarly journals Synthetic Biology Open Language Visual (SBOL Visual) Version 2.1

2019 ◽  
Vol 16 (2) ◽  
Author(s):  
Curtis Madsen ◽  
Angel Goni Moreno ◽  
Zachary Palchick ◽  
Umesh P ◽  
Nicholas Roehner ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Synthetic Biology ◽  
Molecular Species ◽  
Chemical Process ◽  
Structure And Function ◽  
Genomic Context ◽  
Functional Relationships ◽  
Synthetic Biology Open Language ◽  
And Function ◽  
Biological Organisms

AbstractPeople 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.

scholarly journals Synthetic biology open language visual (SBOL visual) version 3.0

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Hasan Baig ◽  
Pedro Fontanarossa ◽  
James McLaughlin ◽  
James Scott-Brown ◽  
Prashant Vaidyanathan ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Synthetic Biology ◽  
Molecular Species ◽  
Data Model ◽  
Structure And Function ◽  
Sequence Features ◽  
Functional Relationships ◽  
Synthetic Biology Open Language ◽  
And Function ◽  
Biological Organisms

Abstract People who engineer biological organisms often find it useful to draw diagrams in order to communicate both the structure of the nucleic acid sequences that they are engineering and the functional relationships between sequence features and other molecular species. Some typical practices and conventions have begun to emerge for such diagrams. SBOL Visual aims to organize and systematize such conventions in order to produce a coherent language for expressing the structure and function of genetic designs. This document details version 3.0 of SBOL Visual, a new major revision of the standard. The major difference between SBOL Visual 3 and SBOL Visual 2 is that diagrams and glyphs are defined with respect to the SBOL 3 data model rather than the SBOL 2 data model. A byproduct of this change is that the use of dashed undirected lines for subsystem mappings has been removed, pending future determination on how to represent general SBOL 3 constraints; in the interim, this annotation can still be used as an annotation. Finally, deprecated material has been removed from collection of glyphs: the deprecated “insulator” glyph and “macromolecule” alternative glyphs have been removed, as have the deprecated BioPAX alternatives to SBO terms.

scholarly journals Synthetic Biology Open Language Visual (SBOL Visual) Version 2.0

2018 ◽  
Vol 15 (1) ◽  
Author(s):  
Robert Sidney Cox ◽  
Curtis Madsen ◽  
James McLaughlin ◽  
Tramy Nguyen ◽  
Nicholas Roehner ◽  
...  
Keyword(s):  
Synthetic Biology ◽  
Best Practices ◽  
Molecular Species ◽  
Data Model ◽  
Functional Relationships ◽  
Version 2.0 ◽  
Synthetic Biology Open Language ◽  
And Function ◽  
The Relationship ◽  
Biological Organisms

AbstractPeople 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 2.0 of SBOL Visual, which builds on the prior SBOL Visual 1.0 standard by expanding diagram syntax to include functional interactions and molecular species, making the relationship between diagrams and the SBOL data model explicit, supporting families of symbol variants, clarifying a number of requirements and best practices, and significantly expanding the collection of diagram glyphs.

scholarly journals Synthetic biology open language visual (SBOL visual) version 2.2

2020 ◽  
Vol 17 (2-3) ◽  
Author(s):  
Hasan Baig ◽  
Pedro Fontanarrosa ◽  
Vishwesh Kulkarni ◽  
James McLaughlin ◽  
Prashant Vaidyanathan ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Synthetic Biology ◽  
G Protein ◽  
Molecular Species ◽  
Structure And Function ◽  
Sequence Features ◽  
Functional Relationships ◽  
Synthetic Biology Open Language ◽  
And Function ◽  
Biological Organisms

AbstractPeople 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 2.2 of SBOL Visual, which builds on the prior SBOL Visual 2.1 in several ways. First, the grounding of molecular species glyphs is changed from BioPAX to SBO, aligning with the use of SBO terms for interaction glyphs. Second, new glyphs are added for proteins, introns, and polypeptide regions (e. g., protein domains), the prior recommended macromolecule glyph is deprecated in favor of its alternative, and small polygons are introduced as alternative glyphs for simple chemicals.

scholarly journals ShortBOL: A Language for Scripting Designs for Engineered Biological Systems Using Synthetic Biology Open Language (SBOL)

2020 ◽  
Vol 9 (4) ◽  
pp. 962-966 ◽  
Author(s):  
Matthew Crowther ◽  
Lewis Grozinger ◽  
Matthew Pocock ◽  
Christopher P. D. Taylor ◽  
James A. McLaughlin ◽  
...  
Keyword(s):  
Synthetic Biology ◽  
Biological Systems ◽  
Synthetic Biology Open Language

scholarly journals Synthetic biology open language visual (SBOL Visual) version 2.3

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Hasan Baig ◽  
Pedro Fontanarossa ◽  
Vishwesh Kulkarni ◽  
James McLaughlin ◽  
Prashant Vaidyanathan ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Synthetic Biology ◽  
Molecular Species ◽  
Molecular Complexes ◽  
Structure And Function ◽  
Sequence Features ◽  
Functional Relationships ◽  
Synthetic Biology Open Language ◽  
And Function ◽  
Biological Organisms

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.

Repeat proteins challenge the concept of structural domains

2015 ◽  
Vol 43 (5) ◽  
pp. 844-849 ◽  
Author(s):  
Rocío Espada ◽  
R. Gonzalo Parra ◽  
Manfred J. Sippl ◽  
Thierry Mora ◽  
Aleksandra M. Walczak ◽  
...  
Keyword(s):  
Biological Systems ◽  
Modular Structure ◽  
Structural Domains ◽  
Repeat Array ◽  
Repeat Units ◽  
Repeat Proteins ◽  
Folding Dynamics ◽  
And Function

Structural domains are believed to be modules within proteins that can fold and function independently. Some proteins show tandem repetitions of apparent modular structure that do not fold independently, but rather co-operate in stabilizing structural forms that comprise several repeat-units. For many natural repeat-proteins, it has been shown that weak energetic links between repeats lead to the breakdown of co-operativity and the appearance of folding sub-domains within an apparently regular repeat array. The quasi-1D architecture of repeat-proteins is crucial in detailing how the local energetic balances can modulate the folding dynamics of these proteins, which can be related to the physiological behaviour of these ubiquitous biological systems.

scholarly journals A standard-enabled workflow for synthetic biology

2017 ◽  
Vol 45 (3) ◽  
pp. 793-803 ◽  
Author(s):  
Chris J. Myers ◽  
Jacob Beal ◽  
Thomas E. Gorochowski ◽  
Hiroyuki Kuwahara ◽  
Curtis Madsen ◽  
...  
Keyword(s):  
Systems Biology ◽  
Synthetic Biology ◽  
Markup Language ◽  
Design Tools ◽  
Data Standards ◽  
Data Repositories ◽  
Simulation Tools ◽  
Systems Biology Markup Language ◽  
Visualization Tools ◽  
Synthetic Biology Open Language

A synthetic biology workflow is composed of data repositories that provide information about genetic parts, sequence-level design tools to compose these parts into circuits, visualization tools to depict these designs, genetic design tools to select parts to create systems, and modeling and simulation tools to evaluate alternative design choices. Data standards enable the ready exchange of information within such a workflow, allowing repositories and tools to be connected from a diversity of sources. The present paper describes one such workflow that utilizes, among others, the Synthetic Biology Open Language (SBOL) to describe genetic designs, the Systems Biology Markup Language to model these designs, and SBOL Visual to visualize these designs. We describe how a standard-enabled workflow can be used to produce types of design information, including multiple repositories and software tools exchanging information using a variety of data standards. Recently, the ACS Synthetic Biology journal has recommended the use of SBOL in their publications.

A Validator and Converter for the Synthetic Biology Open Language

2017 ◽  
Vol 6 (7) ◽  
pp. 1161-1168 ◽  
Author(s):  
Zach Zundel ◽  
Meher Samineni ◽  
Zhen Zhang ◽  
Chris J. Myers
Keyword(s):  
Synthetic Biology ◽  
Synthetic Biology Open Language
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