SBOL Visual statistics

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Citations per year

Number of citations per year for the bioinformatics software tool SBOL Visual
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Tool usage distribution map

This map represents all the scientific publications referring to SBOL Visual per scientific context
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SBOL Visual specifications

Information


Unique identifier OMICS_30512
Name SBOL Visual
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Herbert Sauro

Publication for SBOL Visual

SBOL Visual citations

 (6)
library_books

GB3.0: a platform for plant bio design that connects functional DNA elements with associated biological data

2017
Nucleic Acids Res
PMCID: 5389719
PMID: 28053117
DOI: 10.1093/nar/gkw1326

[…] n section.This part is flanked by GGAG and AATG sequences and, consistently with the GB specifications and PSS, comprises basic parts A1-A2-A3-B1-B2 (see Figure ). The datasheet includes, next to the SBOL Visual symbol representative of its standard position, sequence-related information, the plasmid backbone, the presence of internal sites, selection marker and a link to the complete DNA sequence […]

library_books

Bioinformatics for the synthetic biology of natural products: integrating across the Design–Build–Test cycle

2016
PMCID: 5063057
PMID: 27185383
DOI: 10.1039/c6np00018e

[…] g standards such as the Systems Biology Markup Language (SBML), providing a link between computational modelling (DESIGN) and wet-lab assembly (BUILD). SBOL is augmented with a visual representation, SBOL Visual which has the goal of standardising the visual representation of synthetic gene constructs, analogous to the standard representation of electronic circuits that enables electronic engineer […]

library_books

Annotation of rule based models with formal semantics to enable creation, analysis, reuse and visualization

2015
Bioinformatics
PMCID: 4803388
PMID: 26559508
DOI: 10.1093/bioinformatics/btv660

[…] other visual formats such as SBGN or genetic circuit diagrams (). Models annotated with SBOL terms can be read for subsequent analyses, for example to produce genetic circuit diagrams using standard SBOL Visual icons.Model annotations are designed for machine readability and ideally should be produced computationally, for example by model repositories. The authors are currently developing APIs an […]

library_books

Metabolomics, Standards, and Metabolic Modeling for Synthetic Biology in Plants

2015
Front Bioeng Biotechnol
PMCID: 4617106
PMID: 26557642
DOI: 10.3389/fbioe.2015.00167

[…] ierarchical and fully annotated form with the goal to improve designing, building, testing, and dissemination of synthetic biology designs. For the visualization of synthetic biology designs in SBOL, SBOL Visual (Synthetic Biology Open Language Visual) has been developed. It is a graphical notation allowing depiction of the structure of a design using glyphs to specify genetic parts, devices, modu […]

library_books

Developments in the Tools and Methodologies of Synthetic Biology

2014
Front Bioeng Biotechnol
PMCID: 4244866
PMID: 25505788
DOI: 10.3389/fbioe.2014.00060

[…] at that is platform independent. Crucially, the format is designed to be extendable to include additional parameters as new characterization technologies and methodologies emerge. In combination with SBOL visual (SBOLv), which defines a standardized way to visually denote bioparts through symbols, the SBOL standard is set to enable the seamless sharing of genetic designs. Several bioinformatics an […]

library_books

A survey of enabling technologies in synthetic biology

2013
J Biol Eng
PMCID: 3684516
PMID: 23663447
DOI: 10.1186/1754-1611-7-13

[…] , relative mammalian promoter unit (RMPU) [], functional composition tools included the expression operating unit (EOU) [], and data exchange tools included Synthetic Biology Open Language (SBOL) [], SBOL Visual (SBOLv) [,], and visual or electronic data sheets for biological parts and devices [,]. […]


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SBOL Visual institution(s)
Autodesk Research, Autodesk Inc., San Francisco, CA, USA; Chemical Science and Engineering, Kobe University, Kobe, Japan; [etc.]
SBOL Visual funding source(s)
Supported by Autodesk, Inc., Stanford University, Brunel University, by the National Science Foundation Synthetic Biology Engineering Research Center and Grant EF-0850100, by the Office of Science, Office of Biological and Environmental Research, of the US Department of Energy (Contract No. DE-AC02-05CH11231), by the National Library of Medicine (R41 LM010745), the National Human Genome Research Institute (R42 HG006737) and NSF awards: Theoretical Biology 0827592, Molecular and Cellular Biosciences 1158573, by the UK Engineering and Physical Sciences Research Council (Flowers Consortium, Grant No. EP/J02175X/1), by the UK Biotechnology and Biosciences Research Council (Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM; BB/M017702/1), by a Chancellor's Fellowship and BBSRC grant (Building national hardware and software infrastructure for UK DNA Foundries; BB/M025640/1), and by the National Science Foundation under Grant Nos. DBI-1356041, and DBI-1355909.

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