An explanation is warranted about release numbering. The term Releases was introduced in SBML Level 2 Version 3; the Release approach is used to cope with minor editorial changes to specification documents. Prior to that, in Version 2, the same concept existed under the name Revision, but only one revision of Level 2 Version 2 was ever produced. In SBML Level 2 Version 1, the Release/Revision concept was not used at all; there is only “SBML Level 2 Version 1”. To make matters simpler, this page lists all previously issued specifications of SBML Level 2, regardless of whether they were Releases of Version 5, or past Versions.
Developers and modelers are strongly encouraged to support the latest Version of SBML in any new software development and modeling efforts, as well as to update actively-supported software tools they may be involved in developing or maintaining.
SBML uses a subset of MathML 2.0 to encode mathematical expressions. The XML Schema for this subset of MathML is included in the SBML specification documents themselves; it is is also provided here as a separate download for convenience:
sbml-mathml.xsd.
Although
XML Schemas are available for SBML Level 2,
the schemas only capture the basic syntax of the format. Semantics and correct usage are
not captured by the schemas and can only be understood by reading the specification documents.
SBML Level 2 Version 5
The current definition of SBML Level 2 is Version 5.
Specification
Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions
Authors:
Michael Hucka, Frank T. Bergmann, Andreas Dräger, Stefan Hoops, Sarah M. Keating, Nicolas Le Novère, Chris J. Myers, Brett G. Olivier, Sven Sahle, James C. Schaff, Lucian P. Smith, Dagmar Waltemath, and Darren J. Wilkinson.
This is Release 1 of
the specification for SBML Level 2
Version 5, made available on 2015-08-03.
How to cite the publication:
Michael Hucka, Frank T. Bergmann, Andreas Dräger, Stefan Hoops, Sarah M. Keating, Nicolas Le Novère, Chris J. Myers, Brett G. Olivier, Sven Sahle, James C. Schaff, Lucian P. Smith, Dagmar Waltemath, and Darren J. Wilkinson. (2015). Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions. Journal of Integrative Bioinformatics, 12(2), 271
BibTeX
RIS
SBML Level 2 Version 4
Release 1
Specification
Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions
Authors:
Michael Hucka, Stefan Hoops, Sarah M. Keating, Nicolas Le Novère, Sven Sahle, and Darren J. Wilkinson.
This is Release 1 of
the specification for SBML Level 2
Version 4, made available on 2008-12-22.
How to cite the publication:
Michael Hucka, Stephan Hoops, Sarah M. Keating, Nicholas Le Novère, Sven Sahle, and Darren Wilkinson. (2008). Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions. Nature Preceedings, hdl.handle.net/10101/npre.2008.2715.1
BibTeX
RIS
SBML Level 2 Version 3
Release 2
Specification
Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions
Authors:
Michael Hucka, Andrew Finney, Stefan Hoops, Sarah M. Keating and Nicolas Le Novère.
This is Release 2 of
the specification for SBML Level 2
Version 3, made available on 2007-09-26.
This specification does not have a journal publication associated with it. Suggested citation:
Michael Hucka, Andrew M. Finney, Stefan Hoops, Sarah M. Keating, Nicolas Le Novère. Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions. Retrieved from COMBINE, http://identifiers.org/combine.specifications/sbml.level-2.version-3.release-2
BibTeX
RIS
Release 1
Specification
Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions
Authors:
Michael Hucka, Andrew Finney, Stefan Hoops, Sarah M. Keating and Nicolas Le Novère.
This is Release 1 of
the specification for SBML Level 2
Version 3, made available on 2007-06-16.
How to cite the publication:
Michael Hucka, Andrew Finney, Stephan Hoops, Sarah M. Keating, and Nicholas Le Novère. (2007). Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions. Nature Preceedings, hdl.handle.net/10101/npre.2007.58.2
BibTeX
RIS
SBML Level 2 Version 2
As noted above, SBML Level 2 Version 2 existed in only one Revision.
Specification
Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions
Authors:
Andrew Finney, Michael Hucka, and Nicolas Le Novère.
This is Revision 1 of
the specification for SBML Level 2
Version 2, made available on 2006-09-26.
This specification does not have a journal publication associated with it. Suggested citation:
Andrew M. Finney, Nicolas Le Novère, and Michael Hucka. (2006). Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions. Retrieved from COMBINE, http://identifiers.org/combine.specifications/sbml.level-2.version-2
BibTeX
RIS
SBML Level 2 Version 1
As noted above, the use of Releases/Revisions was introduced after Level 2 Version 1 was developed; consequently, for Level 2 Version 1, there is no “Release” or “Revision” designation.
Note that Version 1 has significant limitations and conceptual gaps. The SBML Editors strongly encourage developers to update existing Version 1-supporting tools to support a later version of SBML Level 2 or SBML Level 3;. Similarly, we courage modelers who have models in Version 1 format to update their models to a later Version.
Specification
Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions
Authors:
Andrew Finney and Michael Hucka.
This is
the specification for SBML Level 2
Version 1, made available on 2003-06-28.
This specification does not have a journal publication associated with it. Suggested citation:
Andrew M. Finney and Michael Hucka. (2003). Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions. Retrieved from COMBINE, http://identifiers.org/combine.specifications/sbml.level-2.version-1
BibTeX
RIS