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biosimulators / Biosimulators_pyNeuroML

pyNeuroML simulation program via BioSimulators-compliant command-line interface and Docker container
https://docs.biosimulators.org/Biosimulators_pyNeuroML
MIT License
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Align support for SED-ML with SED-ML files exported by pyNeuroML #1

Closed jonrkarr closed 2 years ago

jonrkarr commented 3 years ago

PyNeuroML can convert LEMS files to SED-ML L1V1

Example:

pip install pyneuroml
pynml tests/fixtures/LEMS_NML2_Ex5_DetCell.xml -sedml

This creates a file in the same folder as the LEMs file with the .sedml extension (tests/fixtures/LEMS_NML2_Ex5_DetCell.sedml).

I don't think PyNeuroML can read these files.

We should try to align our usage of NeuroML/SED-ML with this (specifically targets for model elements).

jonrkarr commented 3 years ago

This package is aligned with the SED-ML exported by pyNeuroML with the one exception that pyNeuroML uses urn:sedml:language:neuroml2 rather than a URN for LEMS. See also NeuroML/org.neuroml.export#113.

urn:sedml:language:neuroml2 doesn't make sense to me because the direct model file is a LEMS file. Also the URN for NeuroML 2 should be urn:sedml:language:neuroml.version-2_1.

jonrkarr commented 2 years ago

Reported as NeuroML/org.neuroml.export#76