Standard Formats

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SBOL v2.0


Synthetic Biology Open Language Version 2.0

Synopsis

Representation of genetic designs.

Description

The re-use of previously validated designs is critical to the evolution of synthetic biology from a research discipline to an engineering practice. Here we describe the Synthetic Biology Open Language (SBOL), a proposed data standard for exchanging designs within the synthetic biology community. SBOL represents synthetic biology designs in a community-driven, formalized format for exchange between software tools, research groups and commercial service providers. The SBOL Developers Group has implemented SBOL as an XML/RDF serialization and provides software libraries and specification documentation to help developers implement SBOL in their own software. We describe early successes, including a demonstration of the utility of SBOL for information exchange between several different software tools and repositories from both academic and industrial partners. As a community-driven standard, SBOL will be updated as synthetic biology evolves to provide specific capabilities for different aspects of the synthetic biology workflow.*

*(Michal Galdzicki et al. Nature Biotechnology 32, 545-550 (2014))

Publication Date

07/2015

Authors

Bartley, Bryan
Beal, Jacob
Clancy, Kevin
Misirli, Goksel
Roehner, Nicholas
Sauro, Herbert
Oberortner, Ernst
Madsen, Curtis
Pocock, Matthew
Wipat, Anil
Nguyen, Tramy
Zhang, Zhen
Myers, Chris
H. Gennari, John
Bissell, Michael

Organizations


Biological Scales

Scale molecular cellular tissue organ organism ecosystem
Support intrinsic unknown unknown unknown unknown unknown

Spatial Representation

Spatial Representation Level Compartment Dimensions Gradients Spatial Structures
Support potential unknown unknown unknown

Modeling Formalisms for this format

Software support for this format

Examples for this format


Modularity: yes


Components Relation
Flat Network: no


Supported Math

MathML Support: no

Full MathML Support: no

Description

Link to mathematical models written in other standards


Unit Support


Annotation Support

Miriram Support: no

identifiers.org Support: yes


libSBOLj


Programming language

Java

Links

API

sboljs


Programming language

Javascript

Links

API

libSBOL


Programming language

C++

Links

API

pySBOL


Programming language

Python

Links

API

libSBOLj


SBOL Validator/Converter


Validation Portal

Synthetic Biology Open Language (SBOL)


Description

SBOL is a language to describe synthetic biology constructs.


Publication date

03/2012

Organizations

Links

Webpage

All formats for this class

Creative Commons Attribution 4.0 International Public License - The BioBricks Foundation


Description

Copyright (C) The BioBricks Foundation and all authors listed on this BBF RFC. This work is made available 2 under the Creative Commons Attribution 4.0 International Public License. To view a copy of this license visit 3 https://creativecommons.org/licenses/by/4.0/. 4 In addition to the listed authors, the following people are specifically recognized as additional contributors sharing 5 in the copyright (alphabetically by institution): Douglas Densmore (Boston University, USA), Jacqueline Quinn 6 (Google, USA), and Guy-Bart Stan (Imperial College London, UK).

Owner

The BioBricks Foundation

Links