Hierarchical Model Composition
SBML Level 3 Package Activity Status Page
Contents |
Package objectives
Model composition refers to the ability to include models as submodels inside other models. This requires defining the interfaces between the models and rules for connecting parts of models together. The motivation is to enable the creation of standard, vetted models and use them as library components when creating larger models, much as is done in software development, electronics design, and other engineering fields.
The short label for this package is comp.
Draft specifications
Work is currently progressing on formalising the specification.
| Specification name or identification | Date | Comments |
|---|---|---|
| "comp" draft specification 04 April 2012 | 2012-04-04 | (3) |
Legend for editorial comments:
(1) Proposal has not yet been structured according to the recommended format for SBML Level 3 package specification.
(2) Proposal needs to be updated for SBML Level 3.
(3) Work in progress—the authors have not finalized this specification.
Proposals
The proposal was accepted by community vote and has now entered the specification phase.
The SBML Development Process for SBML Level 3 defines two stages: a proposal stage, and a specification development stage. The following is a list of the active proposals for Hierarchical Model Composition in SBML Level 3:
| Proposal name or identification | Date | Comments |
|---|---|---|
| Hierarchical Model Composition proposal by Smith and Hucka | 2011-04-25 | (3) |
Package Working Group
After a vote by the SBML community to accept the above proposal as addressing a valid need and taking a reasonable approach towards addressing this need, a working group was formed to help complete the proposal and work on any implementation issues that may arise. Membership of this group is open to anyone by signing up for the mailing list at:https://lists.sourceforge.net/lists/listinfo/sbml-comp
Working Topics
As the above proposal is being developed and implemented, certain topics have come up for which we are soliciting community input. These pages serve as a place to discuss these topics, and as a reference for future implementers of the specification:
Combining Glycolysis: An example comp model that takes three related models and combines them.
Recipe to Cake: Because the comp package is rule-based (a 'recipe'), you must follow those rules in your own software to create an object model where each object corresponds to a single SBML element (the 'cake'). How do you do that?
Flattening and other packages: The easiest way to transfer a hierarchical model to software that doesn't know about this package is to 'flatten' it to no longer use 'comp' constructs. How can this be accomplished? What are the complications that arise when flattening a model with information from a different package?
Adding Ports: Suppose you had an existing Level 3 model, and wanted to add ports to it. How could this be done?
Proposal for 'Replaced By': If you want a submodel element to be the 'canonical' form, but you want to attach things to it in the containing model, is there a way we can allow this without literally copying and pasting the model?
Previous proposals
The following is a list of previous proposals for Hierarchical Model Composition in SBML Level 3:
| Proposal name or identification | Date | Comments |
|---|---|---|
| Hierarchical Model Composition proposal by Hoops et al. | 2007-09-11 | (3) |
Legend for editorial comments:
(1) Proposal has not yet been structured according to the recommended format for SBML Level 3 package proposals.
(2) Proposal needs to be updated for SBML Level 3.
(3) Work in progress—the authors have not finalized this proposal.
Active specifications
There are no active specifications for the SBML Level 3 Hierarchical Model Composition package at this time.