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SBML Level 3 is the most recent specification of SBML. It is a modular language, with a core comprising a complete format that can be used alone. Additional Level 3 packages are layered on this core to provide additional, optional features.

SBML Levels are intended to coexist. For example, SBML Level 3 does not render Level 2 obsolete, and Level 2-compatible models and software tools still continue to be used. (For more information about the notion of "SBML Levels", please see the description in the FAQ.)

Please notify the SBML Editors of problems and other issues in the documents, or any topics, using the issue trackers indicated below for each specification.

SBML Level 3

At this time, only Version 1 Core of SBML Level 3 has been released. Definitions of packages to go with Version 1 Core are expected in the very near future. When the specifications become available, they will be listed below. For now, you can find information about the ongoing activities in the community wiki.

SBML Level 3 Version 1 Core

The most recent release of SBML Level 3 Version 1 Core is Release 1.

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core

Authors: Michael Hucka, Frank Bergmann, Stefan Hoops, Sarah Keating, Sven Sahle, James Schaff, Lucian Smith, and Darren Wilkinson

This is the final Release 1 specification of 6 Oct. 2010.

The document link refers to the file on SourceForge.net. If you have any problems accessing the PDF file from there, a backup copy of the document is also available locally from this server.

Specification →
Errata →
Submit issue →
Schemas →

Issues with the specification are tracked on the issue tracker whose link is indicated above. Accepted issues are periodically collected and listed on the Errata page indicated above. Once a general consensus emerges that the known errata warrant a new release of the SBML specification, a new Release is made.

SBML Level 3 Packages

Each individual SBML Level 3 package effort has its own separate status page. Please follow the relevant links in the table below to find out more about a given package, including any draft specifications that may be available. This list is in alphabetical order by package label. The information in this table is drawn from the master table for Level 3 package statuses maintained as a Google Docs spreadsheet.

Package name
& link to info page
Label Description Status
Annotations

annot Support for richer annotation syntax than the regular annotations in SBML Level 3 Core Stalled
Arrays

arrays Support for expressing arrays of things Draft available
Hierarchical Model Composition

comp A means for defining how a model is composed from other models Released
Distributions

distrib Support for encoding models that sample values from statistical distributions Draft available
Dynamic Structures

dyn Support for creating and destroying entities during a simulation Stalled
Flux Balance Constraints

fbc Support for constraint-based (a.k.a. steady-state) models Released
Groups

groups A means for grouping elements Draft available
Layout

layout Support for storing the spatial topology of a network diagram; adjunct to the render package Released
Multistate and Multicomponent Species

multi Object structures for representing entity pools with multiple states and composed of multiple components, and reaction rules involving them Draft available
Qualitative Models

qual Support for models wherein species do not represent quantity of matter & processes are not reactions per se Released
Rendering

render Support for defining the graphical symbols and glyphs used in a diagram of the model; adjunct to the layout package Draft available
Required Elements

req Support for fine-grained indication of SBML elements that have been changed by the presence of another package Draft available
Spatial Processes

spatial Support for describing processes that involve a spatial component, and describing the geometries involved Draft available


SBML Level 3 package specification documents are written using a standardized LaTeX template developed by the SBML Team for this purpose. The template is freely available for use by other efforts.

SBML Level 2

Within a given SBML Level, minor revisions to SBML are termed Versions and constitute changes within a Level to correct, adjust and refine language features. Additionally, to cope with occasional minor editorial changes that may be needed, SBML specification come with Release numbers within Versions.

Developers and modelers are strongly encouraged to support the latest Version 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 Level 2 Version 4

The most recent release of SBML Level 2 Version 4 is Release 1.

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 the SBML Level 2 Version 4 specification, Release 1. It was made publicly available on 22 December 2008.

The document link refers to the file on SourceForge.net If you have any problems accessing the PDF file from there, a backup copy of the document is also available locally from this server.

Specification:
Errata:
Issue tracker:
SBML XML Schema:
MathML Schema:

Issues with the specification are tracked on the issue tracker whose link is indicated above. Accepted issues are periodically collected and listed on the Errata page indicated above. Once a general consensus emerges that the known errata warrant a new release of the SBML specification, a new Release is made.

Past Releases and Versions of SBML Level 2

Past Releases of SBML Level 2 Version 4 and past Versions of SBML Level 2 (i.e., Versions 1–3) are available from a separate page.

SBML Level 1

Level 1 is simpler (but less powerful) than Level 2. The separate levels are intended to coexist; SBML Level 2 does not render Level 1 obsolete. Software tools that cannot support higher levels can go on using lower levels; tools that can read higher levels are assured of also being able to interpret models defined in the lower levels.

Developers and modelers are strongly encouraged to support the latest Version 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 Level 1 Version 2

The current definition of SBML Level 1 is Version 2.

Systems Biology Markup Language (SBML) Level 1: Structures and Facilities for Basic Model Definitions

Authors: Michael Hucka, Andrew Finney, Herbert Sauro, and
Hamid Bolouri.

This is the SBML Level 1 Version 2 specification, made publicly available on 28 August 2003. It supercedes the Level 1 Version 1 specification.

Note that SBML Level 1 currently does not have release numbers because the release numbering system was introduced after the last version of Level 1 was produced. Future versions of SBML Level 1 may introduce a similar number scheme to that used for Level 2.

The document links refer to the files on SourceForge.net. If you have any problems accessing the files from there, local backup copies of the PDF and PS files are also available from this server.

Specification:
Errata:
Issue tracker:
SBML XML Schema:

Past Versions of SBML Level 1

Past Releases of SBML Level 1 are available from a separate page.

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This page was last modified 03:28, 15 August 2012.



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