The meaning of each symbol is established by association with terms in the Sequence Ontology ( S1 and S2 Tables). In its current form, SBOL Visual is a set of symbols that correspond to sequence features encoded by a DNA molecule. Synthetic Biology Open Language (SBOL) Visual is the product of an ongoing community effort to develop and standardize a graphical language for synthetic biology and biological engineering, focusing initially on symbols for commonly used sequence features. SBOL Visual aims to have a similar salutary effect for the engineering of biological systems. Standard symbols simplify figures and user interfaces, enhance familiarity, and streamline the design process. Standards are enabling technologies for communication: standard symbols have had a profound impact in other engineering disciplines, such as the Institute of Electrical and Electronics Engineers (IEEE) standards for representing electronic components and circuits, or computer-aided design (CAD) standards for representing architecture and mechanical engineering. This is especially true for genetic designs expressed heterologously and when a system is engineered first in one organism (e.g., ), then moved to a different host (e.g., ). These properties become relevant as genetic designs become more complex, with multiple promoters, CDSs, etc. A visual representation of genetic sequence elements and their arrangement can quickly communicate adjacency, contiguity, repetition, and uniqueness. This has increased the need for consistent terminology and representations of genetic designs. This effort helped unify annotation efforts during the rise of high-throughput genome sequencing in the last decade.Īcross that same decade, synthetic biology has advanced capabilities for forward engineering of complex genetic systems with multiple sequence features. To address such concerns, the Sequence Ontology maintains a standard set of terms for describing different genetic features. A protein-coding DNA sequence might be called a coding sequence (CDS), an open reading frame, an exon, or simply a gene, depending on the organism and method of study. ![]() Therefore, SBOL Visual symbols can represent Activity Flow nodes, with arcs representing the regulation logic.īy the 1970s, molecular biologists had already developed many variations in the language used to describe functional regions of DNA, or genetic sequence features, with different terms used to describe similar features in different organisms. In Activity Flow, nodes represent “activities” (e.g., gene activity) while arcs represent the effect of one activity on another. SBGN is particularly compatible with SBOL Visual, and the vast majority of regulation maps in synthetic biology publications can be described using the SBGN Activity Flow language. In such combined diagrams, SBOL Visual depicts the genetic parts while SBGN depicts the network of interactions between biological components. This is formally described by SBGN Activity Flow as an inhibitory arc. For example, “ repressor tetR represses promoter Ptet”is represented by a line linking the tetR CDS symbol with the Ptet promoter symbol. Parts (A) and (B) demonstrate depiction of regulation alongside SBOL Visual. ![]() led to the inclusion of the symbol in Pigeon, and the symbol is currently going through the new symbol adoption process. Use of the circle around an “x” for spacer by Temme et al. ![]() Also illustrated here is how symbol use influences the development of the standard. For example, (A) and (B) include regulation arcs while the figure in the original manuscript includes origin of replication and resistance markers. These illustrate how different stages of the design process use the symbols differently. ![]() is shown: (A) informally sketched on a whiteboard, as might be done in design brainstorming, and (B) generated using Pigeon. A gene regulatory network for production of T7 RNA Polymerase as an output to isopropyl-beta-D-thiogalactopyranoside(IPTG) AND aTc logic as presented by Temme et al. S1 Fig: SBOL Visual diagrams can be created by multiple methods for various use cases and levels of formality.
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