NetPyNE simulation results for 9 biophys cell network

[salvadord]

• Raster plot generated by netpyne for the 9_cells SONATA example
  

• Soma voltage traces generated by netpyne for the 9_cells SONATA example
  

• Simulation run output log:
  Running simulation for 3000.0 ms...
  Done; run time = 3.03 s; real-time ratio: 0.99.

Gathering data...
Done; gather time = 0.17 s.

Analyzing...
Cells: 29
Connections: 180 (6.21 per cell)
Synaptic contacts: 755 (26.03 per cell)
Spikes: 735 (8.45 Hz)
Simulated time: 3.0 s; 1 workers
Run time: 3.03 s

[wvangeit]

Would you mind showing the 'expected' bmtk traces in the same plots ?

[salvadord]

trying to find where differences coming from

I did fix an issue that was preventing v_init from being set, but the results were similar as above.

[salvadord]

9_cell network just with IClamps -- seems like issue must be in reading cell params

[salvadord]

Checked:

• cell biophysics -- netpyne matches neuroml file description; need to compare directly with BioNet network params
• num secs and nseg per sec -- matches BioNet
• axon -- matches BioNet (biophys + geom; order of secs different but shouldn't affect ICLamp)
• v_init -- matches BioNet
• ICLamp params -- match BioNet

[salvadord]

Would be good to have a SONATA example with simpler cells (eg. just soma or soma+dend) to check the morphology+biophysics more in detail.

[wvangeit]

Could you change the y-scale of the plots a bit, so that we can see the voltage before the stimulus ?

There is already a soma-only cell in here:
#64
(the run bmtk with this example, this first has to be solved AllenInstitute/bmtk#50)

[salvadord]

Updated y-scale:

[wvangeit]

Did you check the temperature of the simulation ?

[salvadord]

Yes:
In [6]: h.celsius
Out[6]: 34.0

[wvangeit]

Maybe reversal of sodium / potassium ?

[salvadord]

they match the .nml values:

In [12]: sim.net.cells[0].secs['soma_0']'hObj'.ena
Out[12]: 53.0

In [13]: sim.net.cells[0].secs['soma_0']'hObj'.ek
Out[13]: -107.0

[wvangeit]

The last thing I can think of atm are the calcium dynamics. (e.g. the calcium concentration at the beginning of the simulation)

[salvadord]

@kaeldai - any update converting the cell biophys params from json to neuroml?

Also in bmtk how would I access the h.Section() objects? I wanna try to inspect them manually (from python terminal) using the new sec.psection() command which gives you detailed info, and compare to the sections in netpyne.

thanks

[kaeldai]

@salvadord - I just did a merge so that the 5_cell_iclamp example uses NeuroML files instead of json. Now every example should use NeuroML.

By default the bmtk (calls the function NMLLoad)[https://github.com/AllenInstitute/bmtk/blob/develop/bmtk/simulator/bionet/default_setters/cell_models.py#L401)] for every cell. Probably the best way to inspect it is to iterate through all the hobj sections before the function returns

for sec in hobj.all:
     # check sec properties here

One thing I noticed is that if I don't cut the axon, ie call aibs_periosomatic, it looks like the bmtk traces match closer to your results (at least gid 6 now has 2 spikes at the end). I want to investigate this further, could you attach (or email me) your voltage traces? If we can get them to line up I think it should be fine to ignore axon-cutting in this example.