Simile and SBML

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Simile allows such models to be specified in terms of stocks and flows, while SBML (generally) encourages models to be expressed in terms of rate equations for biological processes.   Both approaches can be thought of as a user-friendly interface for defining differential-equation models.  Because they have this in common, it is in principle possible to convert some Simile models into SBML, and some SBML models into Simile.   One topic for this group are tools for performing these conversions.

A significant difference between Simile and SBML is that the former has a much richer set of notations for defining models with complex structure.   In contrast, SBML generally defines models in which all variables are scalars (i.e. have a single value.   The SBML community has for some time been discussing ways of extending it (e.g. through introducing arrays), but so far the specification does not include such constructs.   There is therefore potential for Simile to inform futre developments of the SBML specification.   This topic, and other related ones dealing with Simile features which may be of use to the SBML community, are also discussed here.

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