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Hi all,

I have had a look through the proposals at
http://sbml.org/wiki/SBML_Level_3_Efforts . I don't know if there is a
draft for the 'core' of SBML level three yet, although it seems the plan
is that it will not change much from level 2.

I think that under the current approach of splitting metadata and data
in CellML such that anything which alters the mathematical
interpretation of the model is data, and anything else is metadata,
some, but not all, of the extensions for SBML 3 would be data in CellML.

Going through each extension:
* Diagram Representation: This appears to be pure metadata information.
* Spatial Features: This also appears to be pure metadata information.
* Hierarchical Model Composition: This is similar in intent to the
import functionality already present in CellML.
* Multicomponent species: This seems to address a number of related
problems regarding the representations of reactions which act on more
than one species, where the species differ only by changes in
phosphorylation state or location, or some other property like this.
This is probably too domain specific for CellML to deal with in this way.
* Dynamic structures: This aims to allow for the structure of models to
change dynamically (e.g. to create multicellular models). The module
documentation notes that "arrays and sets are alternative proposals for
roughly the same kind of capability, and it is likely that only one will
ultimately be chosen as a supported SBML Level 3 language extension".
* Arrays / Sets: This extension aims to describe something fairly
similar to the goals of the CellML proposals to add additional data
types other than real numbers.
* Parameter Sets: This seems to be a way to split the model mathematics
away from parameter definitions. This is commonly already done in CellML
using imports.
* Alternative Reactions: This aims at being able to specify what type of
model is being expressed. It has some similarities in intent to the
simulation metadata, but it does actually alter the interpretation of
the model. I think that this only makes sense in SBML because of the
domain specific representation in SBML can be mapped to multiple
different non-domain specific mappings. In CellML, this mapping has
already been performed. However, the extension in SBML does imply the
ability to represent other types of models, such as stochastic models.
* Distributions: The representation of statistical distributions is
something which CellML does not currently provide any explicit provision
for. However, it may be something that could be fitted into CellML
without any major changes, so is something worth studying. This may be
complicated by the operators present as predifined symbols content
MathML - we may need to define some new semantics to allow for this type
of model.

Best regards,
Andrew

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• [cellml-discussion] Identifying features for CellML from the SBML level 3 proposals, Andrew Miller, 01/16/2008

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