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Activity tmp

The following table both summarizes the different packages being developed for SBML Level 3, and serves as a jumping-off point for other pages where the efforts are discussed in more detail. There is a draft procedure for proposing packages on a separate page.

Shown is the name of the package, the keyword used to refer to it in Level 3 package descriptions, a summary of the purpose of the package, the status of the package or proposal, and notes about any known implementations or work in progress. The implementations often refer to libSBML, but can also refer to any other software system that provides support for a package independent of libSBML.

Name Keyword Purpose of package Status Implementations
Core core The core portion of SBML Level 3. All other packages are layered on top of the Core. • Public draft specification released 22 Aug. 09.
• Presently in community discussion and review.
• Release candidate expected in Nov. 09.
libSBML (in progress)
Layout layout One of two packages together comprising a method for storing diagrams inside a model. The Layout package is concerned with topology; the Rendering package is concerned with glyphs and symbols. • Well-tested as annotations for Level 2.
• Specification needs minor adjustments to become formal package for Level 3.
Level 2 annotations-based implementation for libSBML provided by Ralph Gauges, incorporated in libSBML distribution.
Rendering render One of two packages together comprising a method for storing diagrams inside a model. The Layout package is concerned with topology; the Rendering package is concerned with glyphs and symbols. Proposed; awaiting implementation.
Hierarchical Model Composition comp A means for defining how a model is composed from other models. Rough draft proposed; awaiting formal Level 3 proposal.
Groups groups General mechanism for grouping SBML entities. This partially replaces the Level 2 SpeciesType and CompartmentType constructs. 1st draft proposed; awaiting revision based on public feedback.
Multistate/ multicomponent species multi Object structures for representing entity pools with multiple states and/or composed of multiple components, and reaction rules involving them. Multiple iterations made on draft proposal; awaiting formal Level 3 proposal
Qualitative Models qual Object structures for representing models in which the entity pools represent discrete levels of activities rather than amounts of matter. The processes involving them cannot be described as reactions per se (i.e., not events-per-time) but rather as transitions between states. Boolean networks, logical models and some petri-nets are examples of this type of model. Rough draft proposal made; awaiting formal Level 3 proposal.
Distribution & ranges distrib Support for expressing the idea that a given value is not known precisely but falls within some defined distribution or range. No proposals made yet.
Spatial diffusion spatial Support for describing processes that involve a spatial component.
Geometry geom Object structures for describing one-, two- and three-dimensional characteristics of SBML entities. Example: the shape of a three-dimensional compartment.
Arrays & sets arrays Support for expressing arrays or sets of things. Example: an array of identical compartments.
Dynamic structures dyn Support for creating and destroying entities during a simulation.
Steady-state models steady Support for models quantitatively representing steady-state(s) of a system. An example of such an approach is the class of models known as flux-balance analysis.
Conversion between levels convert Support for specifying a conversion between levels/versions of SBML, within SBML itself.

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This page was last modified 22:46, 22 October 2009.



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