omex export in vcml format should use different model references

virtualcell / vcell

Virtual Cell Framework

http://vcell.org/

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omex export in vcml format should use different model references #288

Closed moraru closed 1 year ago

moraru commented 2 years ago

we point all model references to the single instance of a vcml-encoded biomodel this is semantically incorrect while on an unmodified just-exported archive it is practically resulting in correct results upon import/execution, it will fail upon any reasonable further edits of the sedml

moraru commented 2 years ago

resolution:

primary model pointer should be URI within vcml xml to simcontext
sims with overrides should use the model change semantics

moraru commented 1 year ago

resolution:

primary model pointer should be URI within vcml xml to simcontext

sims with overrides should use the model change semantics

In addition, we should strip the biomodel of simulations upon export and let them be reconstructed upon import according to the simulations/tasks/models/changes specified by SEDML