SBOL Visual Examples

2020 (Visual Examples)

Synthetic biology open language visual (SBOL visual) version 2.2

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 2.2 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.

2019 (Visual Examples)

2015 (Visual Examples)

Examples to demonstrate the usage of SBOL Visual glyphs is given below.

Example1: A SBOL visual design of the circuit that contains a promoter, RBS, CDS, and terminator. The promoter is stimulated by CDS that it regulates.

Example 1: Promoter stimulated by CDS

Example2: Phosphorylation of an inactive transcription factor (produced by two different CDSs) by a kinase to form an active transcriptional activator, which then stimulates a promoter.

Example 2: Phosphorylation of an inactive transcription factor