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Hierarchical Model Composition

SBML Level 3 Package Activity Status Page

Package name: Hierarchical Model Composition
Package label: comp
Package purpose: A means for defining how a model is composed from other models.
Package Working Group mailing list: sbml-comp

Contact address (where to ask questions): sbml-comp@lists.sourceforge.net
Specification status: Final specification approved and two independent implementations are available.
Latest specification document: Version of 14 November 2013

SBML Editor acting as liason: Lucian Smith
This table is generated automatically from the data for comp in the SBML Level 3 Package Status spreadsheet.

Status of specification and/or proposal development

Update of 2012-07-20: Editing of the specification is underway. A new release is expect prior to COMBINE 2012.

A separate page lists a number of examples, discussion points and questions about the Hierarchical Model Composition package for SBML Level 3.

Status of LibSBML support

LibSBML implementation status: A full (with respect to the specification) implementation is available.
Where can you find a distribution?: SourceForge directory

Support for an SBML Level 3 package in libSBML is realized as a compile-time, plug-in extension. This table summarizes the status of the libSBML support for comp. Source code for any given libSBML extension (if one has been developed) is available from the libsbml-packages branch of the SBML project SVN repository on SourceForge.

Currently, in the implementation of the extension for libSBML 5.5.0, all new attributes and child objects can be read, written, created, examined, and modified. Additionally, a 'flattening' routine is available that will fully translate a hierarchical model to a non-hierarchical 'flat' model with exactly the same mathematics, including all conversion factors.

Unavailable at this time is a method for validating a model according to the rules defined in the 'comp' specification, though many of these rules are implemented to prevent dynamic creation of invalid models. Additionally, no routine is available to calculate the MD5 hash of a file within libsbml. These capabilities are planned for a future release.

Status of JSBML support

JSBML implementation status: A full (with respect to the specification) implementation is available.
Where can you find a distribution?: directory

Where can you find in-progress source code?: directory

Support for an SBML Level 3 package in JSBML is realized as a dynamically-loadable Java package. This table summarizes the status of the JSBML support for comp. Source code for any given JSBML extension (if one has been developed) is available from the extensions portion of the JSBML project on GitHub.

No work is currently being done to implement comp in JSBML. Volunteers are welcome.

Status of RELAX NG schemas

RELAX NG schema status: A final schema is available.
Link to schema: comp

The RELAX NG (RNG) schemas are basic schemas for validating SBML Level 3 in any RNG schema processor. More information about the use of these RNG schemas for SBML is available in a separate page.

The existing RNG schema for comp is based on the proposed schema from 2011, and has not yet been updated to include newer constructs like the 'ReplacedBy' element, nor to incorporate validation decisions that were made at the 2012 HARMONY, such as restricting replacements to only involve the same class of element. The majority of the proposed specification is implemented, however.

Status of third-party application support

3rd-party software implementation status: Two or more implementations have been released.
This table summarizes, in a general sense, the state of support for the comp package in software applications. Implementation of support for a Level 3 package in applications is an important criterion for approving a package specification according to the SBML Development Process.

Two programs are in development that implement comp: Antimony and iBioSim.

The released Antimony v2.1-beta has partial support for comp, and can create, read, and flatten the hierarchical models it creates using these constructs. Current development work in Antimony includes better support for rule and assignment replacement, as well as for deletions.

iBioSim support for comp is still in development, but will, when released, include support for import and export of all (or nearly all) comp elements.

Package history

The proposal was accepted by community vote and has now entered the specification phase. The current public specification document is indicated above. For historical reference, the proposal put to a vote is still available in the SVN repository A full detailed history of the research and development of this specification (starting in the year 2000) is available in the 'History' section of the current proposed specification.

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This page was last modified 20:43, 20 July 2012.



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