Abstract
SummarySynthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. One method to ameliorate these problems would be to improve the exchange of information about designed systems between laboratories. The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology, filling a need not satisfied by other pre-existing standards. This document details version 2.1 of SBOL that builds upon version 2.0 published in last year’s JIB special issue. In particular, SBOL 2.1 includes improved rules for what constitutes a valid SBOL document, new role fields to simplify the expression of sequence features and how components are used in context, and new best practices descriptions to improve the exchange of basic sequence topology information and the description of genetic design provenance, as well as miscellaneous other minor improvements.
Highlights
Synthetic biology builds upon genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems
Synthetic Biology Open Language (SBOL) 3.0.0, (1) separates sequence features from part/sub-part relationships, (2) renames Component Definition/Component to Component/SubComponent, (3) merges Component and Module classes, (4) ensures consistency between data model and ontology terms, (5) extends the means to define and reference Sub-Components, (6) refines requirements on object Uniform Resource Identifiers (URIs), (7) enables graph-based serialization, (8) moves Systems Biology Ontology (SBO) for Component types, (9) makes all sequence associations explicit, (10) makes interfaces explicit, (11) generalizes Sequence Constraints into a general structural Constraint class, and (12) expands the set of allowed constraints
Synthetic biology builds upon genetics, molecular biology, and metabolic engineering by applying engineering 2 principles to the design of biological systems
Summary
Synthetic biology builds upon genetics, molecular biology, and metabolic engineering by applying engineering 2 principles to the design of biological systems. There are often multiple aspects to a design such as a specified nucleic 5 acid sequence (e.g., a sequence that encodes an enzyme or transcription factor), the molecular interactions that 6 a designer intends to result from the introduction of this sequence (e.g., chemical modification of metabolites or 7 regulation of gene expression), and the experiments and data associated with the system All these perspectives 8 need to be connected together to facilitate the engineering of biological systems. SBOL 2 enabled the description and exchange of hierarchical, modular representations of both the intended structure and function of designed biological systems, as well as providing support for representing provenance, combinatorial designs, genetic design implementations, external file attachments, experimental data, and numerical measurements.
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
