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COMBINE standards in modelspec

combine

To illustrate the utility of modelspec, and to create a uniform, compatible set of APIs across a diverse range of model specification formats, we are investigating the COMBINE set of standards in computational biology, and attempting to express these formats in modelspec.

NeuroML

neuroml

A preliminary version of an API for NeuroML2 can be found here. This allows generation of NeuroML2 models using the modelspec based API, saving as valid XML, as well as JSON, YAML and BSON equivalents. See neuroml2_spec.py.

NeuroMLlite already uses modelspec as its primary specification format. See here.

SBML

combine

Work towards an API for SBML can be found here.

An example of an SBML file generated from this is here.

CellML

TODO...

SED-ML

TODO...