Wiki
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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.
General status notes
24 June 2010, by M. Hucka
From June 24 to July 9, the SBML Editors are running three surveys to determine whether certain aspects of SBML Events should be corrected before Level 3 Version 1 Core is finalized. The survey announcements were posted to sbml-discuss; for convenience, the links are also included here:
- Topic 1: adding priorities to events
- Topic 2: initial trigger values
- Topic 3: disabling events
Important: the SBML Development Process mandates that only the votes of subscribers to the sbml-discuss mailing list are counted. If you do not have a subscription to the actual list (e.g., if you read it using the web interface) but you want to vote, please register for the actual mailing list. During the vote counting, only votes from registered list members are counted.
15 January 2010, by M. Hucka
Release 1 candidate of the SBML Level 3 Version 1 Core specification is now available. The SBML Editors very much welcome feedback. Please use the short, dedicated form to report anything you find. Please direct longer discussion-type questions to the sbml-discuss mailing list.
This specification document is labeled a candidate until two independent software implementations are reported by the SBML-using community. At that time, if no significant errors or issues are reported, the specification will be considered final. The use of the term "candidate" should not discourage implemention of support for this specification. This definition of SBML Level 3 Version 1 Core Release 1 will not be modified unless errors are found.
Some characteristics of SBML Level 3 preclude producing a complete XML Schema. Consequently, the specification document no longer contains an XML Schema. Instead, we are working on creating RELAX NG and Schematron schemas for SBML. The base L3V1Core specification document is purposefully titled "The Systems Biology Markup Language (SBML): Language Speciļ¬cation for Level 3 Version 1 Core", because the intention is to issue additional companion documents with titles along the lines of "The Systems Biology Markup Language (SBML): RELAX NG Schema for Level 3 Version 1 Core", etc.
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 aboutĀ the packages they support.
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
|
All of the Level 3 work has a long history. We keep a short list of proposals on a separate page for historical reference.
SBML Annotations in Use
5 May 2009. "Annotations" are a mechanism in SBML for adding information to defined locations in an SBML model using an approach detailed in the SBML specification. Each object in SBML can have an annotation element whose contents can be essentially anything written in proper XML. Typically, annotations are used by software packages to add private or application-specific information to a model.
A separate page provides a catalog of known annotation schemes. Please help us keep it up-to-date by notifying us of annotations that are not listed in the catalog.
Miscellaneous
The following content came from the SBML.org website prior to 2007, 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 and the upcoming SBML Level 3 plans, but they're kept around for nostalgia.