300 cell example in NetPyNE not working

[pgleeson]

@salvadord I've added your script from https://github.com/Neurosim-lab/netpyne/tree/development/examples/sonata_300_cells here: https://github.com/pgleeson/sonata/blob/master/examples/300_cells/run_netpyne.py to facilitate running with the sonata original files. It does run now, but the spikes only last for ~100ms. Can you have a look? You'll need the latest bmtk and my sonata fork to run the latest example in BMTK for comparison.

[pgleeson]

Not sure if it's the direct cause but I'm getting warnings like:

Cell 0/100 (gid=300) of pop external_virtual_100, on node 0, 

Error: VecStim requires interval, rate or spkTimes
Cell 1/100 (gid=301) of pop external_virtual_100, on node 0, 

Error: VecStim requires interval, rate or spkTimes
Cell 2/100 (gid=302) of pop external_virtual_100, on node 0, 
...

Error: VecStim requires interval, rate or spkTimes
Cell 98/100 (gid=398) of pop external_virtual_100, on node 0, 

Error: VecStim requires interval, rate or spkTimes
Cell 99/100 (gid=399) of pop external_virtual_100, on node 0, 
  Number of stims on node 0: 0 
  Done; cell stims creation time = 0.00 s.

[pgleeson]

Fix above seems to have resolved it:

[pgleeson]

Close once suny-downstate-medical-center/netpyne#457 merged...

[salvadord]

@pgleeson I'm running the run_netpyne.py vs run_bionet.py from your sonata fork (https://github.com/pgleeson/sonata/blob/master/examples/300_cells/run_netpyne.py) using the 'development' branch of netpyne (40dfb0a2f392a) and both v0.0.7 and the 'develop' branch of bmtk and I'm getting the same result as we had before (Python 2.7 on Mac OS).

Note: I had to make some changes to the plotting scripts (in run_netpyne.py) to make them work with bmtk 'develop' branch.

SONATA Padraig fork + NetPyNE 'development' + BMTK 'v0.0.7':

SONATA Padraig fork + NetPyNE 'development' + BMTK 'develop':

@pgleeson @kaeldai - what am I missing? why did the raster plots change from the previous figs we had? do I need to update anything else?