Synthetic biology open language visual (SBOL Visual) version 2.3

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.

Stochastic Hazard Analysis of Genetic Circuits in iBioSim and STAMINA

“…The following is a high-level description of the key features of iBioSim used in this project: Genetic Circuit Design The genetic circuits described in this paper were constructed using the sequence editor GDA tool SBOLDesigner . This tool allows for the creation and editing of hierarchical genetic designs represented using the SBOL data standard and depicted using the SBOL Visual standard. − Parts for these designs were fetched from a collection stored in the Living Computing instance of SynBioHub (). Model Generation The Virtual Parts Repository (VPR) model generator , is used to enrich the SBOL representation with non-DNA components and interactions between the components as described in ref . For example, VPR adds the proteins produced by the genetic circuits and the interactions that indicate which coding sequence they are produced from, as well as the inhibition interactions between these proteins and promoters within the design.…”

“…Genetic Circuit Design The genetic circuits described in this paper were constructed using the sequence editor GDA tool SBOLDesigner . This tool allows for the creation and editing of hierarchical genetic designs represented using the SBOL data standard and depicted using the SBOL Visual standard. − Parts for these designs were fetched from a collection stored in the Living Computing instance of SynBioHub (). …”

“…The genetic circuits described in this paper were constructed using the sequence editor GDA tool SBOLDesigner . This tool allows for the creation and editing of hierarchical genetic designs represented using the SBOL data standard and depicted using the SBOL Visual standard. − …”

The GB4.0 Platform, an All-In-One Tool for CRISPR/Cas-Based Multiplex Genome Engineering in Plants

“…All described software-tools, listed in Supplementary Table 1, were conceived to provide a centralized user-friendly gateway for the design of CRISPR/Cas constructs, both for genome editing and for other expanded applications as gene regulation. All GB-software tools provide Genbank output files next to a vSBOL-based representation of the generated construct (Baig et al, 2021) and a detailed protocol. All CRISPR/Cas constructs are assembled in destination binary plasmids ready for Agrobacterium-mediated transformation.…”

Specifications of standards in systems and synthetic biology: status and developments in 2021

“…NEW Synthetic biology open language visual (SBOL Visual) Version 2.3 [ 34 ] updates SBOL visual version 2.2 with several new features. These include higher-level “interactions with interactions”, the representation of the binding with a nucleic acid backbone using overlapping glyphs, and a new “unspecified interaction” glyph.…”