Specifications
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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 |
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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 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 |
|---|---|---|
| Annotations | annot
| Support for richer annotation syntax than the regular annotations in SBML Level 3 Core |
| Arrays and Sets | arrays
| Support for expressing arrays or sets of things |
| Hierarchical Model Composition | comp
| A means for defining how a model is composed from other models |
| Distributions | distrib
| Support for encoding models that sample values from statistical distributions |
| Dynamic Structures | dyn
| Support for creating and destroying entities during a simulation |
| Flux Balance Constraints | fbc
| Support for constraint-based (a.k.a. steady-state) models |
| Groups | groups
| A means for grouping elements |
| Layout | layout
| Support for storing the spatial topology of a network diagram; adjunct to the render package |
| Multistate and Multicomponent Species | multi
| Object structures for representing entity pools with multiple states and composed of multiple components, and reaction rules involving them |
| Qualitative Models | qual
| Support for models wherein species do not represent quantity of matter & processes are not reactions per se |
| Rendering | render
| Support for defining the graphical symbols and glyphs used in a diagram of the model; adjunct to the layout package |
| Required Elements | req
| Support for fine-grained indication of SBML elements that have been changed by the presence of another package |
| Spatial Processes | spatial
| Support for describing processes that involve a spatial component, and describing the geometries involved |
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 |
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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.
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 |
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Past Versions of SBML Level 1
Past Releases of SBML Level 1 are available from a separate page.