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SBML Level 3

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 Level 3 Version 1 Core

The current stable release of SBML Level 3 Version 1 Core is Release 2.

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core (Release 2)

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 2 of the specification, dated 28 Dec. 2016.

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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 Level 3 package effort has its own detailed status page. Please follow the links below for more information, including any 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.

Package name
& link to info page
Label Description Status
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 Processes dyn Support for creating and destroying entities during a simulation Draft available
Flux Balance Constraints fbc Support for constraint-based (a.k.a. steady-state) models Released
Groups groups A means for grouping elements Released
Layout layout Support for storing the spatial topology of a network diagram; adjunct to the render package Released
Extended Math math A suite of packages that collectively allow MathML beyond the subset allowed in SBML core. Not started
Multistate and Multicomponent Species multi Object structures for representing entity pools with multiple states and composed of multiple components, and reaction rules involving them Released
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
Spatial Processes spatial Support for describing processes that involve a spatial component, and describing the geometries involved Draft available
Retired packages
Annotations annot Support for richer annotation syntax than the regular annotations in SBML Level 3 Core Superceded by COMBINE annotations effort
Required Elements req Support for fine-grained indication of SBML elements that have been changed by the presence of another package Retired due to decreased demand

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.

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