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Improved hybridsmall, valid with netpyne fomat json... #11

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merged 8 commits into from
May 2, 2024
Merged

Improved hybridsmall, valid with netpyne fomat json... #11

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564eced
Regenerated
pgleeson Mar 20, 2024
f876044
Initial test on index.npjson
pgleeson Mar 21, 2024
7839c02
Update hybridsmall to pref form
pgleeson Mar 21, 2024
47d995c
Passes validation!
pgleeson Mar 21, 2024
a2f87ef
Regenerated hybridsmall nml
pgleeson Mar 21, 2024
9b2e50a
Regenerated
pgleeson May 2, 2024
0c83616
Better hybridsmall
pgleeson May 2, 2024
7b5b4cb
Merge branch 'experimental' into development
pgleeson May 2, 2024
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32 changes: 12 additions & 20 deletions NetPyNE/HybridSmall/HybridSmall.py
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@@ -1,13 +1,3 @@
"""
params.py

netParams is a dict containing a set of network parameters using a standardized structure

simConfig is a dict containing a set of simulation configurations using a standardized structure

Contributors: [email protected]
"""

from netpyne import specs

netParams = specs.NetParams() # object of class NetParams to store the network parameters
Expand All @@ -26,13 +16,13 @@
pop_size = 3

# Population parameters
netParams.popParams['PYR_HH'] = {'cellModel': 'HH', 'cellType': 'PYR', 'numCells': pop_size} # add dict with params for this pop
netParams.popParams['PYR_Izhi'] = {'cellModel': 'Izhi', 'cellType': 'PYR', 'numCells': pop_size} # add dict with params for this pop
netParams.popParams['PYR_HH'] = {'cellType': 'PYR_HH', 'numCells': pop_size} # add dict with params for this pop
netParams.popParams['PYR_Izhi'] = {'cellType': 'PYR_Izhi', 'numCells': pop_size} # add dict with params for this pop


# Cell parameters list
## PYR cell properties (HH)
cellRule = {'conds': {'cellType': 'PYR', 'cellModel': 'HH'}, 'secs': {}}
cellRule = {'secs': {}}
cellRule['secs']['soma'] = {'geom': {}, 'topol': {}, 'mechs': {}} # soma properties
cellRule['secs']['soma']['geom'] = {'diam': 18.8, 'L': 18.8, 'Ra': 123.0, 'pt3d':[]}
cellRule['secs']['soma']['geom']['pt3d'].append((0, 0, 0, 18.8))
Expand All @@ -42,7 +32,7 @@
netParams.cellParams['PYR_HH'] = cellRule # add dict to list of cell properties

## PYR cell properties (Izhi)
cellRule = {'conds': {'cellType': 'PYR', 'cellModel': 'Izhi'}, 'secs': {}}
cellRule = {'secs': {}}
cellRule['secs']['soma'] = {'geom': {}, 'pointps':{}} # soma properties
cellRule['secs']['soma']['geom'] = {'diam': 10, 'L': 10, 'cm': 31.831}
cellRule['secs']['soma']['pointps']['Izhi'] = {'mod':'Izhi2007b',
Expand All @@ -58,15 +48,15 @@
# Stimulation parameters
netParams.stimSourceParams['bkg1'] = {'type': 'NetStim', 'rate': 20, 'noise': 0}
netParams.stimSourceParams['bkg2'] = {'type': 'NetStim', 'rate': 20, 'noise': 1}
netParams.stimTargetParams['bg->PYR_Izhi'] = {'source': 'bkg1', 'conds': {'cellType': 'PYR', 'cellModel': 'Izhi'},
'connFunc': 'fullConn','weight': 0.01, 'delay': 0, 'synMech': 'syn2'}
netParams.stimTargetParams['bg->PYR_HH'] = {'source': 'bkg2', 'conds': {'cellType': 'PYR', 'cellModel': 'HH'},
'connFunc': 'fullConn','weight': 0.005, 'synMech': 'syn1', 'sec': 'soma', 'loc': 1.0, 'delay': 0}
netParams.stimTargetParams['bg->PYR_Izhi'] = {'source': 'bkg1', 'conds': {'cellType': 'PYR_Izhi'},
'weight': 0.01, 'delay': 0, 'synMech': 'syn2'}
netParams.stimTargetParams['bg->PYR_HH'] = {'source': 'bkg2', 'conds': {'cellType': 'PYR_HH'},
'weight': 0.005, 'synMech': 'syn1', 'sec': 'soma', 'loc': 1.0, 'delay': 0}


# Connectivity parameters
netParams.connParams['PYR->PYR'] = {
'preConds': {'cellType': 'PYR'}, 'postConds': {'cellType': 'PYR'},
'preConds': {'cellType': ['PYR_HH', 'PYR_Izhi']}, 'postConds': {'cellType': ['PYR_HH', 'PYR_Izhi']},
'weight': 0.0, # weight of each connection
'delay': '0.2+normal(13.0,1.4)', # delay min=0.2, mean=13.0, var = 1.4
'threshold': 10, # threshold
Expand All @@ -75,7 +65,6 @@




###############################################################################
# SIMULATION PARAMETERS
###############################################################################
Expand Down Expand Up @@ -110,8 +99,11 @@
simConfig.saveDpk = False # save to a .dpk pickled file
simConfig.saveDat = True

simConfig.validateNetParams=True

# Analysis and plotting
simConfig.analysis['plotRaster'] = {'orderInverse': False} #True # Whether or not to plot a raster
simConfig.analysis['plotTraces'] = {'include': [1,51]} # plot recorded traces for this list of cells
#simConfig.analysis['plotRatePSD'] = {'include': ['allCells', 'PYR_HH', 'PYR_Izhi'], 'smooth': 10} # plot recorded traces for this list of cells

cfg = simConfig
6 changes: 6 additions & 0 deletions NetPyNE/HybridSmall/index.npjson
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@@ -0,0 +1,6 @@
{
"mod_folder": "../HybridSmall",
"simConfig": "HybridSmall.py",
"python_run": "init.py",
"netParams": "HybridSmall.py"
}
10 changes: 10 additions & 0 deletions NetPyNE/HybridSmall/init.py
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@@ -0,0 +1,10 @@
"""
init.py
Starting script to run NetPyNE-based model.
"""

from netpyne import sim

cfg, netParams = sim.loadFromIndexFile('index.npjson')
sim.createSimulateAnalyze(netParams, cfg)
2 changes: 1 addition & 1 deletion NetPyNE/UI/clean.sh
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@@ -1,2 +1,2 @@
rm -rf x86_64 __pycache__
rm -rf x86_64 arm64 __pycache__ *dat
mv *mod *hoc *nrn_py *netpyne.py *nrn.py *dat *spikes *props *txt NET*nml LEMS*json test*json /tmp
62 changes: 31 additions & 31 deletions NeuroML2/HybridSmall.net.nml
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Expand Up @@ -23,10 +23,10 @@
</ionChannelHH>
<expOneSynapse id="syn1" gbase="1uS" erev="0mV" tauDecay="30ms"/>
<expOneSynapse id="syn2" gbase="1uS" erev="0mV" tauDecay="4ms"/>
<cell id="CELL_HH_PYR">
<cell id="CELL_PYR_HH">
<notes>Cell exported from NetPyNE:
{'conds': {'cellType': 'PYR', 'cellModel': 'HH'}, 'secs': {'soma': {'geom': {'diam': 18.8, 'L': 18.8, 'Ra': 123.0, 'pt3d': [(0, 0, 0, 18.8), (0, 0, 18.8, 18.8)]}, 'topol': {}, 'mechs': {'hh': {'gnabar': 0.12, 'gkbar': 0.036, 'gl': 0.003, 'el': -70}}}}}</notes>
<morphology id="morph_CELL_HH_PYR">
{secs: {'soma': {'geom': {'diam': 18.8, 'L': 18.8, 'Ra': 123.0, 'pt3d': [(0, 0, 0, 18.8), (0, 0, 18.8, 18.8)]}, 'topol': {}, 'mechs': {'hh': {'gnabar': 0.12, 'gkbar': 0.036, 'gl': 0.003, 'el': -70}}}}}</notes>
<morphology id="morph_CELL_PYR_HH">
<segment id="0" name="soma">
<proximal x="0.0" y="0.0" z="0.0" diameter="18.8"/>
<distal x="0.0" y="0.0" z="18.8" diameter="18.8"/>
Expand All @@ -38,7 +38,7 @@
<include segmentGroup="soma_SECTION"/>
</segmentGroup>
</morphology>
<biophysicalProperties id="biophys_CELL_HH_PYR">
<biophysicalProperties id="biophys_CELL_PYR_HH">
<membraneProperties>
<channelDensity id="leak_soma_group" ionChannel="leak_hh" condDensity="0.003 S_per_cm2" erev="-70 mV" ion="non_specific"/>
<channelDensity id="k_soma_group" ionChannel="k_hh" condDensity="0.036 S_per_cm2" erev="-77 mV" ion="k"/>
Expand All @@ -52,11 +52,11 @@
</intracellularProperties>
</biophysicalProperties>
</cell>
<izhikevich2007Cell id="CELL_Izhi_PYR" C="100 pF" v0="-60 mV" k="0.7 nS_per_mV" vr="-60 mV" vt="-40 mV" vpeak="35 mV" a="0.03 per_ms" b="-2 nS" c="-50 mV" d="100 pA"/>
<izhikevich2007Cell id="CELL_PYR_Izhi" C="100 pF" v0="-60 mV" k="0.7 nS_per_mV" vr="-60 mV" vt="-40 mV" vpeak="35 mV" a="0.03 per_ms" b="-2 nS" c="-50 mV" d="100 pA"/>
<spikeGenerator id="NetStim_bkg1_PYR_Izhi_20_0_syn2" period="0.05s"/>
<spikeGeneratorPoisson id="NetStim_bkg2_PYR_HH_20_1_syn1" averageRate="20 Hz"/>
<network id="HybridSmall">
<population id="PYR_HH" component="CELL_HH_PYR" size="3" type="populationList">
<population id="PYR_HH" component="CELL_PYR_HH" size="3" type="populationList">
<property tag="color" value="0.41661987254534116 0.010169169457068361 0.8252065092537432"/>
<instance id="0">
<location x="29.565889544420436" y="18.528336282230836" z="13.667258291117088"/>
Expand All @@ -68,7 +68,7 @@
<location x="28.392855676730893" y="55.244638897654454" z="91.525576195790066"/>
</instance>
</population>
<population id="PYR_Izhi" component="CELL_Izhi_PYR" size="3" type="populationList">
<population id="PYR_Izhi" component="CELL_PYR_Izhi" size="3" type="populationList">
<property tag="radius" value="5"/>
<property tag="color" value="0.2986398551995928 0.3684116894884757 0.19366134904507426"/>
<instance id="0">
Expand All @@ -84,40 +84,40 @@
<population id="Pop_NetStim_bkg2_PYR_HH_20_1_syn1" component="NetStim_bkg2_PYR_HH_20_1_syn1" size="3"/>
<population id="Pop_NetStim_bkg1_PYR_Izhi_20_0_syn2" component="NetStim_bkg1_PYR_Izhi_20_0_syn2" size="3"/>
<projection id="NetConn_PYR_Izhi_PYR_HH_syn1" presynapticPopulation="PYR_Izhi" postsynapticPopulation="PYR_HH" synapse="syn1">
<connectionWD id="0" preCellId="../PYR_Izhi/0/CELL_Izhi_PYR" postCellId="../PYR_HH/0/CELL_HH_PYR" weight="0.0" delay="12.369474744944261 ms"/>
<connectionWD id="1" preCellId="../PYR_Izhi/2/CELL_Izhi_PYR" postCellId="../PYR_HH/0/CELL_HH_PYR" weight="0.0" delay="12.97146338366091 ms"/>
<connectionWD id="2" preCellId="../PYR_Izhi/0/CELL_Izhi_PYR" postCellId="../PYR_HH/1/CELL_HH_PYR" weight="0.0" delay="14.241028963278428 ms"/>
<connectionWD id="3" preCellId="../PYR_Izhi/2/CELL_Izhi_PYR" postCellId="../PYR_HH/1/CELL_HH_PYR" weight="0.0" delay="11.661004595683124 ms"/>
<connectionWD id="4" preCellId="../PYR_Izhi/1/CELL_Izhi_PYR" postCellId="../PYR_HH/2/CELL_HH_PYR" weight="0.0" delay="13.099619872130592 ms"/>
<connectionWD id="5" preCellId="../PYR_Izhi/2/CELL_Izhi_PYR" postCellId="../PYR_HH/2/CELL_HH_PYR" weight="0.0" delay="14.315653269032612 ms"/>
<connectionWD id="0" preCellId="../PYR_Izhi/0/CELL_PYR_Izhi" postCellId="../PYR_HH/0/CELL_PYR_HH" weight="0.0" delay="12.369474744944261 ms"/>
<connectionWD id="1" preCellId="../PYR_Izhi/2/CELL_PYR_Izhi" postCellId="../PYR_HH/0/CELL_PYR_HH" weight="0.0" delay="12.97146338366091 ms"/>
<connectionWD id="2" preCellId="../PYR_Izhi/0/CELL_PYR_Izhi" postCellId="../PYR_HH/1/CELL_PYR_HH" weight="0.0" delay="14.241028963278428 ms"/>
<connectionWD id="3" preCellId="../PYR_Izhi/2/CELL_PYR_Izhi" postCellId="../PYR_HH/1/CELL_PYR_HH" weight="0.0" delay="11.661004595683124 ms"/>
<connectionWD id="4" preCellId="../PYR_Izhi/1/CELL_PYR_Izhi" postCellId="../PYR_HH/2/CELL_PYR_HH" weight="0.0" delay="13.099619872130592 ms"/>
<connectionWD id="5" preCellId="../PYR_Izhi/2/CELL_PYR_Izhi" postCellId="../PYR_HH/2/CELL_PYR_HH" weight="0.0" delay="14.315653269032612 ms"/>
</projection>
<projection id="NetConn_PYR_HH_PYR_HH_syn1" presynapticPopulation="PYR_HH" postsynapticPopulation="PYR_HH" synapse="syn1">
<connectionWD id="0" preCellId="../PYR_HH/0/CELL_HH_PYR" postCellId="../PYR_HH/1/CELL_HH_PYR" weight="0.0" delay="12.882266700443374 ms"/>
<connectionWD id="1" preCellId="../PYR_HH/2/CELL_HH_PYR" postCellId="../PYR_HH/1/CELL_HH_PYR" weight="0.0" delay="14.214732391680146 ms"/>
<connectionWD id="2" preCellId="../PYR_HH/0/CELL_HH_PYR" postCellId="../PYR_HH/2/CELL_HH_PYR" weight="0.0" delay="14.602870231822557 ms"/>
<connectionWD id="3" preCellId="../PYR_HH/1/CELL_HH_PYR" postCellId="../PYR_HH/2/CELL_HH_PYR" weight="0.0" delay="11.514025612022943 ms"/>
<connectionWD id="0" preCellId="../PYR_HH/0/CELL_PYR_HH" postCellId="../PYR_HH/1/CELL_PYR_HH" weight="0.0" delay="12.882266700443374 ms"/>
<connectionWD id="1" preCellId="../PYR_HH/2/CELL_PYR_HH" postCellId="../PYR_HH/1/CELL_PYR_HH" weight="0.0" delay="14.214732391680146 ms"/>
<connectionWD id="2" preCellId="../PYR_HH/0/CELL_PYR_HH" postCellId="../PYR_HH/2/CELL_PYR_HH" weight="0.0" delay="14.602870231822557 ms"/>
<connectionWD id="3" preCellId="../PYR_HH/1/CELL_PYR_HH" postCellId="../PYR_HH/2/CELL_PYR_HH" weight="0.0" delay="11.514025612022943 ms"/>
</projection>
<projection id="NetConn_PYR_HH_PYR_Izhi_syn1" presynapticPopulation="PYR_HH" postsynapticPopulation="PYR_Izhi" synapse="syn1">
<connectionWD id="0" preCellId="../PYR_HH/0/CELL_HH_PYR" postCellId="../PYR_Izhi/0/CELL_Izhi_PYR" weight="0.0" delay="12.913412871388646 ms"/>
<connectionWD id="1" preCellId="../PYR_HH/2/CELL_HH_PYR" postCellId="../PYR_Izhi/0/CELL_Izhi_PYR" weight="0.0" delay="11.564341090342863 ms"/>
<connectionWD id="2" preCellId="../PYR_HH/0/CELL_HH_PYR" postCellId="../PYR_Izhi/2/CELL_Izhi_PYR" weight="0.0" delay="13.45455050580457 ms"/>
<connectionWD id="3" preCellId="../PYR_HH/1/CELL_HH_PYR" postCellId="../PYR_Izhi/2/CELL_Izhi_PYR" weight="0.0" delay="12.817358977569082 ms"/>
<connectionWD id="4" preCellId="../PYR_HH/2/CELL_HH_PYR" postCellId="../PYR_Izhi/2/CELL_Izhi_PYR" weight="0.0" delay="15.581628749853062 ms"/>
<connectionWD id="0" preCellId="../PYR_HH/0/CELL_PYR_HH" postCellId="../PYR_Izhi/0/CELL_PYR_Izhi" weight="0.0" delay="12.913412871388646 ms"/>
<connectionWD id="1" preCellId="../PYR_HH/2/CELL_PYR_HH" postCellId="../PYR_Izhi/0/CELL_PYR_Izhi" weight="0.0" delay="11.564341090342863 ms"/>
<connectionWD id="2" preCellId="../PYR_HH/0/CELL_PYR_HH" postCellId="../PYR_Izhi/2/CELL_PYR_Izhi" weight="0.0" delay="13.45455050580457 ms"/>
<connectionWD id="3" preCellId="../PYR_HH/1/CELL_PYR_HH" postCellId="../PYR_Izhi/2/CELL_PYR_Izhi" weight="0.0" delay="12.817358977569082 ms"/>
<connectionWD id="4" preCellId="../PYR_HH/2/CELL_PYR_HH" postCellId="../PYR_Izhi/2/CELL_PYR_Izhi" weight="0.0" delay="15.581628749853062 ms"/>
</projection>
<projection id="NetConn_PYR_Izhi_PYR_Izhi_syn1" presynapticPopulation="PYR_Izhi" postsynapticPopulation="PYR_Izhi" synapse="syn1">
<connectionWD id="0" preCellId="../PYR_Izhi/2/CELL_Izhi_PYR" postCellId="../PYR_Izhi/0/CELL_Izhi_PYR" weight="0.0" delay="15.017115573506961 ms"/>
<connectionWD id="1" preCellId="../PYR_Izhi/0/CELL_Izhi_PYR" postCellId="../PYR_Izhi/2/CELL_Izhi_PYR" weight="0.0" delay="13.643281270729352 ms"/>
<connectionWD id="2" preCellId="../PYR_Izhi/1/CELL_Izhi_PYR" postCellId="../PYR_Izhi/2/CELL_Izhi_PYR" weight="0.0" delay="11.557444650642978 ms"/>
<connectionWD id="0" preCellId="../PYR_Izhi/2/CELL_PYR_Izhi" postCellId="../PYR_Izhi/0/CELL_PYR_Izhi" weight="0.0" delay="15.017115573506961 ms"/>
<connectionWD id="1" preCellId="../PYR_Izhi/0/CELL_PYR_Izhi" postCellId="../PYR_Izhi/2/CELL_PYR_Izhi" weight="0.0" delay="13.643281270729352 ms"/>
<connectionWD id="2" preCellId="../PYR_Izhi/1/CELL_PYR_Izhi" postCellId="../PYR_Izhi/2/CELL_PYR_Izhi" weight="0.0" delay="11.557444650642978 ms"/>
</projection>
<projection id="NetConn_NetStim_bkg2_PYR_HH_20_1_syn1__PYR_HH" presynapticPopulation="Pop_NetStim_bkg2_PYR_HH_20_1_syn1" postsynapticPopulation="PYR_HH" synapse="syn1">
<connectionWD id="0" preCellId="../Pop_NetStim_bkg2_PYR_HH_20_1_syn1[0]" postCellId="../PYR_HH/0/CELL_HH_PYR" weight="0.005" delay="0 ms"/>
<connectionWD id="1" preCellId="../Pop_NetStim_bkg2_PYR_HH_20_1_syn1[1]" postCellId="../PYR_HH/1/CELL_HH_PYR" weight="0.005" delay="0 ms"/>
<connectionWD id="2" preCellId="../Pop_NetStim_bkg2_PYR_HH_20_1_syn1[2]" postCellId="../PYR_HH/2/CELL_HH_PYR" weight="0.005" delay="0 ms"/>
<connectionWD id="0" preCellId="../Pop_NetStim_bkg2_PYR_HH_20_1_syn1[0]" postCellId="../PYR_HH/0/CELL_PYR_HH" weight="0.005" delay="0 ms"/>
<connectionWD id="1" preCellId="../Pop_NetStim_bkg2_PYR_HH_20_1_syn1[1]" postCellId="../PYR_HH/1/CELL_PYR_HH" weight="0.005" delay="0 ms"/>
<connectionWD id="2" preCellId="../Pop_NetStim_bkg2_PYR_HH_20_1_syn1[2]" postCellId="../PYR_HH/2/CELL_PYR_HH" weight="0.005" delay="0 ms"/>
</projection>
<projection id="NetConn_NetStim_bkg1_PYR_Izhi_20_0_syn2__PYR_Izhi" presynapticPopulation="Pop_NetStim_bkg1_PYR_Izhi_20_0_syn2" postsynapticPopulation="PYR_Izhi" synapse="syn2">
<connectionWD id="0" preCellId="../Pop_NetStim_bkg1_PYR_Izhi_20_0_syn2[0]" postCellId="../PYR_Izhi/0/CELL_Izhi_PYR" weight="0.01" delay="0 ms"/>
<connectionWD id="1" preCellId="../Pop_NetStim_bkg1_PYR_Izhi_20_0_syn2[1]" postCellId="../PYR_Izhi/1/CELL_Izhi_PYR" weight="0.01" delay="0 ms"/>
<connectionWD id="2" preCellId="../Pop_NetStim_bkg1_PYR_Izhi_20_0_syn2[2]" postCellId="../PYR_Izhi/2/CELL_Izhi_PYR" weight="0.01" delay="0 ms"/>
<connectionWD id="0" preCellId="../Pop_NetStim_bkg1_PYR_Izhi_20_0_syn2[0]" postCellId="../PYR_Izhi/0/CELL_PYR_Izhi" weight="0.01" delay="0 ms"/>
<connectionWD id="1" preCellId="../Pop_NetStim_bkg1_PYR_Izhi_20_0_syn2[1]" postCellId="../PYR_Izhi/1/CELL_PYR_Izhi" weight="0.01" delay="0 ms"/>
<connectionWD id="2" preCellId="../Pop_NetStim_bkg1_PYR_Izhi_20_0_syn2[2]" postCellId="../PYR_Izhi/2/CELL_PYR_Izhi" weight="0.01" delay="0 ms"/>
</projection>
</network>
</neuroml>
24 changes: 12 additions & 12 deletions NeuroML2/LEMS_HybridSmall.xml
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Expand Up @@ -18,27 +18,27 @@

<Simulation id="Sim_HybridSmall" length="1000.0ms" step="0.005ms" target="HybridSmall" seed="12345"> <!-- Note seed: ensures same random numbers used every run -->
<Display id="DispPop__PYR_HH" title="Membrane potentials of cells in PYR_HH" timeScale="1ms" xmin="-100.0" xmax="1100.0" ymin="-90" ymax="50">
<Line id="PYR_HH[0]: v" quantity="PYR_HH/0/CELL_HH_PYR/v" scale="1mV" color="#d54f33" timeScale="1ms"/>
<Line id="PYR_HH[1]: v" quantity="PYR_HH/1/CELL_HH_PYR/v" scale="1mV" color="#0534e4" timeScale="1ms"/>
<Line id="PYR_HH[2]: v" quantity="PYR_HH/2/CELL_HH_PYR/v" scale="1mV" color="#98e752" timeScale="1ms"/>
<Line id="PYR_HH[0]: v" quantity="PYR_HH/0/CELL_PYR_HH/v" scale="1mV" color="#d54f33" timeScale="1ms"/>
<Line id="PYR_HH[1]: v" quantity="PYR_HH/1/CELL_PYR_HH/v" scale="1mV" color="#0534e4" timeScale="1ms"/>
<Line id="PYR_HH[2]: v" quantity="PYR_HH/2/CELL_PYR_HH/v" scale="1mV" color="#98e752" timeScale="1ms"/>
</Display>

<Display id="DispPop__PYR_Izhi" title="Membrane potentials of cells in PYR_Izhi" timeScale="1ms" xmin="-100.0" xmax="1100.0" ymin="-90" ymax="50">
<Line id="PYR_Izhi[0]: v" quantity="PYR_Izhi/0/CELL_Izhi_PYR/v" scale="1mV" color="#bca074" timeScale="1ms"/>
<Line id="PYR_Izhi[1]: v" quantity="PYR_Izhi/1/CELL_Izhi_PYR/v" scale="1mV" color="#632794" timeScale="1ms"/>
<Line id="PYR_Izhi[2]: v" quantity="PYR_Izhi/2/CELL_Izhi_PYR/v" scale="1mV" color="#8a5d88" timeScale="1ms"/>
<Line id="PYR_Izhi[0]: v" quantity="PYR_Izhi/0/CELL_PYR_Izhi/v" scale="1mV" color="#bca074" timeScale="1ms"/>
<Line id="PYR_Izhi[1]: v" quantity="PYR_Izhi/1/CELL_PYR_Izhi/v" scale="1mV" color="#632794" timeScale="1ms"/>
<Line id="PYR_Izhi[2]: v" quantity="PYR_Izhi/2/CELL_PYR_Izhi/v" scale="1mV" color="#8a5d88" timeScale="1ms"/>
</Display>

<OutputFile id="Volts_file__PYR_HH" fileName="Sim_HybridSmall.PYR_HH.v.dat">
<OutputColumn id="v_PYR_HH_0_CELL_HH_PYR_v" quantity="PYR_HH/0/CELL_HH_PYR/v"/>
<OutputColumn id="v_PYR_HH_1_CELL_HH_PYR_v" quantity="PYR_HH/1/CELL_HH_PYR/v"/>
<OutputColumn id="v_PYR_HH_2_CELL_HH_PYR_v" quantity="PYR_HH/2/CELL_HH_PYR/v"/>
<OutputColumn id="v_PYR_HH_0_CELL_PYR_HH_v" quantity="PYR_HH/0/CELL_PYR_HH/v"/>
<OutputColumn id="v_PYR_HH_1_CELL_PYR_HH_v" quantity="PYR_HH/1/CELL_PYR_HH/v"/>
<OutputColumn id="v_PYR_HH_2_CELL_PYR_HH_v" quantity="PYR_HH/2/CELL_PYR_HH/v"/>
</OutputFile>

<OutputFile id="Volts_file__PYR_Izhi" fileName="Sim_HybridSmall.PYR_Izhi.v.dat">
<OutputColumn id="v_PYR_Izhi_0_CELL_Izhi_PYR_v" quantity="PYR_Izhi/0/CELL_Izhi_PYR/v"/>
<OutputColumn id="v_PYR_Izhi_1_CELL_Izhi_PYR_v" quantity="PYR_Izhi/1/CELL_Izhi_PYR/v"/>
<OutputColumn id="v_PYR_Izhi_2_CELL_Izhi_PYR_v" quantity="PYR_Izhi/2/CELL_Izhi_PYR/v"/>
<OutputColumn id="v_PYR_Izhi_0_CELL_PYR_Izhi_v" quantity="PYR_Izhi/0/CELL_PYR_Izhi/v"/>
<OutputColumn id="v_PYR_Izhi_1_CELL_PYR_Izhi_v" quantity="PYR_Izhi/1/CELL_PYR_Izhi/v"/>
<OutputColumn id="v_PYR_Izhi_2_CELL_PYR_Izhi_v" quantity="PYR_Izhi/2/CELL_PYR_Izhi/v"/>
</OutputFile>

</Simulation>
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