SBML Level 3 Proposals
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.
| Area name | Description | Label |
|---|---|---|
| Level 3 Core | The core portion of SBML Level 3. | core
|
| Layout | 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. | layout
|
| Rendering | 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. | render
|
| Multistate multicomponent species | Object structures for representing entity pools with multiple states and composed of multiple components, and reaction rules involving them. | multi
|
| Hierarchical Model Composition | A means for defining how a model is composed from other models. | comp
|
| Qualitative Models | 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. | qual
|
| Distribution & ranges | Support for expressing the idea that a given value is not known precisely but falls within some defined distribution or range. | distrib
|
| Spatial Diffusion | Support for describing processes that involve a spatial component. | spatial
|
| Geometry | Object structures for describing one-, two- and three-dimensional characteristics of SBML entities. Example: the shape of a three-dimensional compartment. | geom
|
| Arrays & sets | Support for expressing arrays or sets of things. Example: an array of identical compartments. | arrays
|
| Dynamic structures | Support for creating and destroying entities during a simulation. | dyn
|
| Steady-state models | 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. | steady
|
| Groups | Support for groups of SBML entities. This partially replaces the Level 2 SpeciesType and CompartmentType constructs with a more general mechanism. | groups
|
| Annotations | Support for more elaborate (full RDF) annotations. | annot
|