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NeuroML / NeuroML2

This repository hosts the NeuroML 2 Schema, the ComponentType definitions in LEMS and the core documentation of NeuroML2.
https://docs.neuroml.org
GNU Lesser General Public License v3.0
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Check status of fractional gate #186

Closed pgleeson closed 2 years ago

pgleeson commented 2 years ago

@borismarin previously added an example of a channel with fractional gates here: https://github.com/NeuroML/NeuroML2/blob/master/LEMSexamples/LEMS_NML2_Ex24_FractionalConductance.xml, which was presumably required for converting this channel to NeuroML: https://github.com/OpenSourceBrain/korngreen-pyramidal/blob/79a2354c377bd405bc3467ee5bf700c4dd15b73a/NEURON/kslow.mod#L99-L103

Need to check on the status of this and whether the NeuroML form can be converted successfully back to NEURON mod file... Any idea @borismarin?

Will be needed for the conversion of this: https://github.com/OpenSourceBrain/BahlEtAl2012_ReducedL5PyrCell/blob/master/NEURON/channels/kslow.mod to NML. @shayan823

borismarin commented 2 years ago

I would need to have a detailed look at NeuronWriter (in org.neuroml.export, supposing it is still there) to be sure, but I assume that constructs that have been "promoted" to LEMSExamples have been thoroughly tested (shame on me if that is not the case). Anyways, I seem to have asked similar questions some time ago: https://github.com/OpenSourceBrain/korngreen-pyramidal/issues/2

borismarin commented 2 years ago

Notice that the kslow channel (as well as all the other channels in the model) has been converted to NeuroML2, on the nml2 branch: https://github.com/OpenSourceBrain/korngreen-pyramidal/blob/nml2/NeuroML2/kslow.channel.nml

borismarin commented 2 years ago

more archaeology: https://github.com/NeuroML/NeuroML2/pull/86 https://github.com/SilverLabUCL/osbpaper/issues/9#issuecomment-195469658

shayanshafquat commented 2 years ago

@pgleeson The kslow channel in https://github.com/OpenSourceBrain/korngreen-pyramidal/blob/nml2/NeuroML2/kslow.channel.nml is throwing the error https://paste.centos.org/view/23c7fdb9 when validated using pynml.

pgleeson commented 2 years ago

@shayan823 Check the fractional gate example here in the latest commit to development branch. It's now running fine in Neuron also after restructuring a bit.

sanjayankur31 commented 2 years ago

@shayan823 : if possible, probably better to attach the error log (or paste it as code) here because pastebins usually get rid of the paste after some limited time and that'll break the discussion thread

pgleeson commented 2 years ago

Closing as there is a working example running on jnml & jnml_nrn in the repo