Wiki

This is the top page for the SBML wiki area on SBML.org. It serves as a community-maintained resource. The wiki is suitable for long explanations, documents, proposals, etc., while the forums are more suitable for rapid discussion and exchange.

Much of the information on this page may not make sense without some knowledge of the SBML specification. Some other questions may be answered in the SBML FAQ. If you have any suggestions or questions, please don't hesitate to mention them on one of the mailing lists or by contacting sbml-team@caltech.edu.

SBML Level 3

SBML Level 3 is modular, in the sense of having a defined core set of features and optional packages adding features on top of the core. This modular approach means that models can declare which feature-sets they use, and likewise, software tools can inform users about the packages they support.

SBML Level 3 Status Summary Table

2011-08-09

The following table summarizes the different packages being developed for SBML Level 3 and serves as a jumping-off point for other pages where these efforts are discussed in more detail. The legend below the table explains the symbols used; you can also hover your pointing device over the icons to view a summary. The procedure for proposing new packages is explained on a separate page.

				Prop.	Spec.
Name	Label	Description	PWG list	Stat.	Stat.	libSBML
Level 3 Core	core	The core portion of SBML Level 3.	sbml-discuss
Layout	layout	Support for storing the spatial topology of a model's network diagram. Adjunct to the render package, below.	sbml-layout
Flux Balance Constraints	fbc	Support for constraint-based (a.k.a. steady-state) models.	sbml-flux
Rendering	render	Support for defining the graphical symbols and glyphs used in a diagram of the model. Adjunct to the layout package above.	sbml-render
Hierarchical Model Composition	comp	A means for defining how a model is composed from other models.	sbml-comp
Multistate multicomponent species	multi	Object structures for representing entity pools with multiple states and composed of multiple components, and reaction rules involving them.	sbml-multi
Qualitative Models	qual	Support for models wherein species don't represent quantity of matter & processes are not reactions per se. (E.g.: Boolean nets.)	sbml-qual
Annotations	annot	Support for richer annotation syntax than the regular annotations in SBML Level 3 Core.	sbml-annot
Spatial Processes	spatial	Support for describing processes that involve a spatial component, and describing the geometries involved.	sbml-spatial
Groups	groups	Support for groups of SBML entities. This partially replaces the Level 2 SpeciesType and CompartmentType constructs with a more general mechanism.	sbml-groups
Required Elements	req	Support for fine-grained indication of SBML elements that have been changed by the presence of another package.	sbml-required
Distribution & ranges	distrib	Support for expressing the idea that a given value is not known precisely but falls within some defined distribution or range.	sbml-distrib
Arrays & sets	arrays	Support for expressing arrays or sets of things. Example: an array of identical compartments.	sbml-arrays
Dynamic structures	dyn	Support for creating and destroying entities during a simulation.	sbml-dynamic

Table legend:

• Name: the name of the SBML Level 3 package.

• Label: the short-form label for the package. The label is often used in discussions about the package and in software examples; it is also suggested for use as the XML Namespace prefix for a package.

• Description: a short summary of the purpose of the package.

• PWG: the Package Working Group, described in the development process for SBML Level 3. The PWG name is linked to the mailing list for the group.

• Prop. Stat: proposal status. The following are the possible symbols and their meanings:

• Spec. stat.: specification status. The following are the possible symbols and their meanings:

• libSBML: state of support for the package in libSBML. The following are the possible symbols and their meanings:

SBML Level 3 Package Votes

During June 2011, we are holding up-down votes on all past Level 3 package proposals, as part of following through on the SBML Level 3 Development Process. Here is a quick list of the ongoing votes:

Topic & voting page link	Deadline	Status	Result
Proposal for 'comp'	June 3, 2011		Results page
Proposals for 'qual', 'fbc', 'annot' and 'dyn'	June 6, 2011		Results page
Proposals for 'layout' and 'render'	June 13, 2011		Results page
Proposal for 'multi'	October 3, 2011		Results page
Proposal for 'spatial'	December 1, 2011		Results page
Proposal for 'distrib'	TBA	TBA	TBA
Proposal for 'groups'	TBA	TBA	TBA

("TBA" = to be announced.) More proposal votes are still forthcoming. They will be announced on sbml-discuss and added to this table when they are ready.

Miscellaneous

The following content came from older versions of the SBML.org website, with some modifications and updates done more recently as people have had time and noticed things. Some of the content is not relevant anymore thanks to more recent versions of SBML, but they're kept around for nostalgia and historical reference.

• Catalog of known annotation schemes circa 2009
• Ad-hoc features requested pre-2004