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Activity Table Lucian

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.

The following chart shows the name of the package, when it was first proposed, its current status (proposed, specified, accepted, and implemented), how complex it is (simple, moderate, or complex), its implementation status in libSBML (either 'done' or who (if anyone) is working on its implementation, and an ETA), and its implementation status in any non-libSBML parsers.

Name Proposed Status Complexity libSBML? Other?
Level 3 Core (core) 2003 Accepted; awaiting implementation Moderate (similar to L2v4) libSBML dev team; ETA Oct '09 <none (?)>
The core portion of SBML Level 3. Expected to be roughly SBML Level 2 Version 4, plus some technical modifications to support SBML Level 3 packages and its implications.
Layout (layout) (present in L2) Awaiting implementation Simple (present in L2v4) libSBML dev team; ETA Nov '09 <none>
A means for representing the way that a diagram of the model is meant to be organized spatially on a printed page or a computer monitor. The "SBML Level 3 Layout" package is concerned with the topology of the diagram, while the SBML Level 3 Rendering package is concerned with the glyphs and symbols that are used in the diagram.
Flux Balance Analysis (fba) Sept '09 Specified and implemented as L2 annotation Simple <none> SBW Flux Balance; PySCeS FBA; COBRA SBML/FBA coverter
Support for storing flux balance analysis constraints, objectives, and fluxes inside an SBML model
Groups (groups) Sept '09 Proposed, awaiting final specification Simple libSBML dev team; ETA unknown <none?>
Support for groups of SBML entities. This partially replaces the Level 2 SpeciesType and CompartmentType constructs with a more general mechanism.
Rendering (render) 2005 Proposed, specified (?), and awaiting approval/implementation Simple <none> <none>
A means for defining the graphical shapes and symbols that are meant to be used in a diagram of the model. It is an adjunct to the SBML Level 3 Layout package.
Multistate multicomponent species (multi) Sept '09 Proposed, largely specified, generally accepted, awaiting implementation Complex <none> EBI (ETA ??)
Object structures for representing entity pools with multiple states and composed of multiple components, and reaction rules involving them.
Hierarchical Model Composition (comp) Sept '07 Proposed, largely specified, generally accepted, awaiting implementation Complex <none> <none>
A means for defining how a model is composed from other models.
Qualitative Models (qual) Sept '07 Proposed  ? <none> <none>
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.
Distribution & ranges (distrib) July '05 Proposed  ? <none?> <none?>
Support for expressing the idea that a given value is not known precisely but falls within some defined distribution or range.
Spatial diffusion (spatial) ?? Proposed  ? <none?> <none?>
Support for describing processes that involve a spatial component.
Geometry (geom) 2005 (?) Proposed  ? <none?> <none?>
Object structures for describing one-, two- and three-dimensional characteristics of SBML entities. Example: the shape of a three-dimensional compartment.
Arrays & sets (arrays) Dec '04 Proposed  ? <none?> <none?>
Support for expressing arrays or sets of things. Example: an array of identical compartments.
Dynamic structures (dyn) Dec. '08 Proposed  ? <none?> <none?>
Support for creating and destroying entities during a simulation.
Steady-state models (steady) ?? Proposed  ? <none?> <none?>
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) Sept '09 Proposed  ? <none?> <none?>
Support for specifying a conversion between levels/versions of SBML, within SBML itself.

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This page was last modified 06:51, 22 October 2009.



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