Wiki
Contents |
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
2012-12-21
The status of package efforts is now listed in a new set of packages oriented to the specifications rather than the proposals.
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 3 Package Votes
We continue to hold 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 status of different package 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 'groups' | July 13, 2012 |
| Results page |
| Proposal for 'arrays' | December 14, 2012 |
| Results page |
| Proposal for 'distrib' | December 17, 2012 |
| Results page |
| Proposal for 'req' | December 19, 2012 |
| Results page |
("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.