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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.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8560346 | PMC |
http://dx.doi.org/10.1515/jib-2021-0013 | DOI Listing |
Methods Mol Biol
March 2024
Interdisciplinary Computing and Complex Biosystems, School of Computing, Newcastle University, Newcastle upon Tyne, UK.
Flapjack presents a valuable solution for addressing challenges in the Design, Build, Test, Learn (DBTL) cycle of engineering synthetic genetic circuits. This platform provides a comprehensive suite of features for managing, analyzing, and visualizing kinetic gene expression data and associated metadata. By utilizing the Flapjack platform, researchers can effectively integrate the test phase with the build and learn phases, facilitating the characterization and optimization of genetic circuits.
View Article and Find Full Text PDFMethods Mol Biol
March 2024
Interdisciplinary Computing and Complex Biosystems, School of Computing, Newcastle University, Newcastle upon Tyne, UK.
Genetic design automation (GDA) is the use of computer-aided design (CAD) in designing genetic networks. GDA tools are necessary to create more complex synthetic genetic networks in a high-throughput fashion. At the core of these tools is the abstraction of a hierarchy of standardized components.
View Article and Find Full Text PDFACS Synth Biol
December 2023
Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Madrid 28223, Spain.
GENETTA is a software tool that transforms synthetic biology designs into networks using graph theory for analysis and manipulation. By representing complex data as interconnected points, GENETTA allows dynamic customization of visualizations, including interaction networks and parts hierarchies. It can also merge design data from multiple databases, providing a unified perspective.
View Article and Find Full Text PDFSynth Biol (Oxf)
August 2021
School of Biological Sciences, University of Bristol, Bristol, UK.
J Integr Bioinform
October 2021
University of Colorado Boulder, Boulder, USA.
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.
View Article and Find Full Text PDFEnter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!