First version of sim test suite #64
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| <channelDensity id="gnabar_hh" segmentGroup="soma" ion="na" ionChannel="hh" erev="50 mV" condDensity="0.0 S_per_cm2"/> | ||
| <channelDensity id="gkbar_hh" segmentGroup="soma" ion="k" ionChannel="hh" erev="-85 mV" condDensity="0.00 S_per_cm2"/> | ||
| <channelDensity id="gl_hh" segmentGroup="soma" ion="non_specific" ionChannel="hh" erev="-80 mV" condDensity="0.005 S_per_cm2"/> | ||
| <channelDensity id="el_hh" segmentGroup="soma" ion="non_specific" ionChannel="hh" erev="-80 mV" condDensity="-80"/> |
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@pgleeson, a question. Is there a way to specifiy the el_hh (reversal potential NEURON hh mechanism) without putting -80 in the condDensity field ? It seems the erev="-80 mV" of the line above gets ignored.
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@wvangeit The reversal potential for the passive component of the hh mechanism should be covered in the gl_hh, i.e. setting erev there should be sufficient for setting this, along with the conductance of the passive component.
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Ok, then I guess I will have to check the bmtk, because as far as I could see specifying erev didn't have an effect.
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A more general question about this. How would a simulator know it has to set el_hh when erev is specified ?
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There is no el independent of gl_hh... I'm suggesting to remove the channelDensity id="el_hh", and the existing channelDensity id="gl_hh" is sufficient to set both the conductance and rev pot of the passive/leak conductance... This has worked fine for setting the passive properties in detailed cells already, e.g. https://github.com/AllenInstitute/sonata/blob/master/examples/shared_components/biophysical_neuron_templates/nml/Cell_472363762.cell.nml#L23,
https://github.com/OpenSourceBrain/BlueBrainProjectShowcase/blob/master/NMC/NeuroML2/Soma_AllNML2.cell.nml#L69
A first version of the simulator test suite as discussed here:
#59
Creating a PR, so that @pgleeson can use this branch to add his own tests according to a similar structure.
The input files for a tests are in the relevevant 'input' directory, as in:
examples/sim_tests/biophysical/one_cell/soma_cm2/input
The expected output in expected_output
The bmtk_build has the script to build the network.
In the bmtk_test there is a test_output.py file which be used in conjunction with pytest to test aspects of the output generate by the simulator (in this case bmtk).
I marked this PR as 'dontmerge' because there are still several issues that have to be solved. The most important one:
AllenInstitute/bmtk#50
In the mean time I'm running a modified version of the bmtk with this line commented out:
https://github.com/AllenInstitute/bmtk/blob/develop/bmtk/simulator/bionet/default_setters/cell_models.py#L399
There are still things that have to be fixed / completed in soma_cm2_hh
Still have to add READMEs to the relevant subdirectories.