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At the moment, a model written in SBML is monolithic. A model is entirely
described in an element "model",
located in a given file. This has several unpleasant consequences.
Firstly, while initialy the size of the models was on the human scale, this
is no longer the case. The largest models of the curated branch of
BioModels Database reach several hundreds reactions, and in the uncurated
branch we reach thousands (FBA models). This results in very large files,
that are slow to load and to process. In addition the structure of a model
is not easely retrieved. We need to analyse all the reactions to understand
what is going on. Finally, the unit problem is getting worse with the size.

Maybe we should create modules. A module is an SBML construct that looks
like an SBML Level2 model, but with the constraint that the units are
consistent. All the species in a module would have the same unit. All the
compartments as well. And all the time related constructs as well.

Modules could be stored in different files and an SBML file could contain
several modules. An "import" element must be created.

Modules do not contain their own namespaces.

A module could contain only one definition (such as a species), or a whole
mini-model.

A module could not contain other modules. We are not talking about model
composition here.

There is not unit conversion implied. If a symbol is defined in a module
with a given unit, it is always u
sed with this unit, even in another module. It is up to the modeller to
take care of the proper conversion
within e.g. the kineticLaw's math.

Modules are not equivalent to CellML's components. Again we are not talking
about model composition.

All that is a bit naive and fuzzy at the moment. But providing something
along these lines in the core would maybe make the model composition
extension easier.

[Alternatively, let's all have a good look at CellML and reuse their good
ideas ...]

--
Nicolas LE NOVERE, Computational Neurobiology,
EMBL-EBI, Wellcome-Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
Tel: +44(0)1223494521, Fax: 468, Mob: +44(0)7833147074 Skype:n.lenovere
http://www.ebi.ac.uk/~lenov, AIM: nlenovere, MSN: nlenovere@hotmail.com
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