Standard Formats
Displaying: 3 Found: 18 Total: 18
SBOL v2.0
Synthetic Biology Open Language Version 2.0
Synopsis
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
Authors
Organizations
Biological Scales
Scale | molecular | cellular | tissue | organ | organism | ecosystem |
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Support | intrinsic | unknown | unknown | unknown | unknown | unknown |
Spatial Representation
Spatial Representation Level | Compartment | Dimensions | Gradients | Spatial Structures |
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Support | potential | unknown | unknown | unknown |
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
Biological
Application
Format
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SBOL v2.0 |
Webpage
Specification
Software Repository
Output
Input
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SBOL v2.0 |
iBioSim |
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SBML L3V1 Core |
iBioSim |
Synthetic Biology Open Language (SBOL)
Description
SBOL is a language to describe synthetic biology constructs.
Publication date
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 FoundationLinks
SBOL Visual v1.0.0
Synthetic Biology Open Language Visual Version 1.0.0
Synopsis
Description
The Synthetic Biology Open Language Visual (SBOL Visual) project is an effort to create an open-source graphical notation to support the description and specification of genetic designs. SBOL Visual is intended for use by biological engineers in forward engineering projects. It aims to encourage and support model-driven engineering by establishing a common set of symbols.*
*(Specification (SBOL Visual) - Jacqueline Quinn, et al.: http://sbolstandard.org/downloads/specification-sbol-visual/ (date: 01.10.2015))
Publication Date
Authors
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 | unknown | unknown | unknown | unknown |
Advantage
- Standardized graphical layout of a model
Modularity: no
Components Relation
Flat Network:
no
Supported Math
Unit Support
Unit Required: no
Support: no support
Annotation Support
Biological
Application
Format
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SBOL Visual v1.0.0 |
Webpage
Software Repository
Synthetic Biology Open Language (SBOL)
Description
SBOL is a language to describe synthetic biology constructs.
Publication date
Organizations
Links
Webpage
All formats for this class
Custom License
Description
Copyright © The BioBricks Foundation (2013). All Rights Reserved.
Owner
The BioBricks FoundationLinks
SED-ML L1 V2
Simulation Experiment Description Markup Language Level 1 Version 2
Synopsis
Description
The Simulation Experiment Description Markup Language (SED-ML). SED-ML encodes in a computer-readable exchange format the information required by MIASE to enable reproduction of simulation experiments. It has been developed as a community project and it is defined in a detailed technical specification and additionally provides an XML schema. [ ... ] It covers the description of the most frequent type of simulation experiments in the area, namely time course simulations. SED-ML documents specify which models to use in an experiment, modifications to apply on the models before using them, which simulation procedures to run on each model, what analysis results to output, and how the results should be presented. These descriptions are independent of the underlying model implementation. SED-ML is a software-independent format for encoding the description of simulation experiments; it is not specific to particular simulation tools. Here, we demonstrate that with the growing software support for SED-ML we can effectively exchange executable simulation descriptions.*
SED-ML is a format describing how a simulation experiment is carried out. The simulation itself is described in the interfaced format. Biological application is therefore viewed as a property of the interfaced standard.
*(Waltemath D et al.. BMC Systems Biology. 2011; 5:198.)
Publication Date
Authors
Organizations
Biological Scales
Scale | molecular | cellular | tissue | organ | organism | ecosystem |
---|---|---|---|---|---|---|
Support | potential | potential | potential | potential | potential | potential |
Spatial Representation
Spatial Representation Level | Compartment | Dimensions | Gradients | Spatial Structures |
---|---|---|---|---|
Support | unknown | unknown | unknown | unknown |
Modularity: yes
Components Relation
Flat Network:
no
Supported Math
MathML Support: yes
Full MathML Support: no
Description
Unit Support
Unit Required: no
Support: undefined
Description
Annotation Support
Miriram Support: yes
identifiers.org Support: yes
Simulation Experiment Description Markup Language (SED-ML)
Description
SBGN describes the procedures and conditions under which a particular model is used in a unambiguous way.
Derived from
Publication date
Organizations
Links
Webpage
All formats for this class
Free and Open
Description
Not closely defiened license allowing for free use and open participation. The product is viewed as community effort.