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Better hybridsmall
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@pgleeson
pgleeson committed May 2, 2024
1 parent 9b2e50a commit 0c83616
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32 changes: 14 additions & 18 deletions NetPyNE/HybridSmall/HybridSmall.py
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Original file line number Diff line number Diff line change
Expand Up @@ -24,16 +24,11 @@
## PYR cell properties (HH)
cellRule = {'secs': {}}
cellRule['secs']['soma'] = {'geom': {}, 'topol': {}, 'mechs': {}} # soma properties
cellRule['secs']['soma']['geom'] = {'diam': 6.3, 'L': 5, 'Ra': 123.0, 'pt3d':[]}
cellRule['secs']['soma']['geom']['pt3d'].append((0, 0, 0, 20))
cellRule['secs']['soma']['geom']['pt3d'].append((0, 0, 20, 20))
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))
cellRule['secs']['soma']['geom']['pt3d'].append((0, 0, 18.8, 18.8))
cellRule['secs']['soma']['mechs']['hh'] = {'gnabar': 0.12, 'gkbar': 0.036, 'gl': 0.003, 'el': -70}

cellRule['secs']['dend'] = {'geom': {}, 'topol': {}, 'mechs': {}} # dend properties
cellRule['secs']['dend']['geom'] = {'diam': 5.0, 'L': 150.0, 'Ra': 150.0, 'cm': 1, 'pt3d': []}
cellRule['secs']['dend']['topol'] = {'parentSec': 'soma', 'parentX': 1.0, 'childX': 0}
cellRule['secs']['dend']['mechs']['pas'] = {'g': 0.0000357, 'e': -70}

netParams.cellParams['PYR_HH'] = cellRule # add dict to list of cell properties

## PYR cell properties (Izhi)
Expand All @@ -46,26 +41,27 @@


# Synaptic mechanism parameters
netParams.synMechParams['AMPA'] = {'mod': 'ExpSyn', 'tau': 0.1, 'e': 0}
netParams.synMechParams['syn1'] = {'mod': 'ExpSyn', 'tau': 30, 'e': 0}
netParams.synMechParams['syn2'] = {'mod': 'ExpSyn', 'tau': 4, 'e': 0}


# Stimulation parameters
netParams.stimSourceParams['bkg'] = {'type': 'NetStim', 'rate': 10, 'noise': 1}
netParams.stimTargetParams['bg->PYR_Izhi'] = {'source': 'bkg', 'conds': {'cellType': 'PYR_Izhi'},
'weight': 1, 'delay': 'uniform(1,5)', 'synMech': 'AMPA'}
netParams.stimTargetParams['bg->PYR_HH'] = {'source': 'bkg', 'conds': {'cellType': 'PYR_HH'},
'weight': 1, 'synMech': 'AMPA', 'sec': 'dend', 'loc': 1.0, 'delay': 'uniform(1,5)'}
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_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_HH', 'PYR_Izhi']},
'postConds': {'cellType': ['PYR_HH', 'PYR_Izhi']},
'weight': 0.2, # weight of each connection
'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
'convergence': 'uniform(0,5)', # convergence (num presyn targeting postsyn) is uniformly distributed between 1 and 10
'synMech': 'AMPA'}
'synMech': 'syn1'}



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90 changes: 39 additions & 51 deletions NeuroML2/HybridSmall.net.nml
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Original file line number Diff line number Diff line change
Expand Up @@ -21,52 +21,40 @@
<reverseRate type="HHExpRate" rate="0.125per_ms" midpoint="-65mV" scale="-80mV"/>
</gateHHrates>
</ionChannelHH>
<expOneSynapse id="AMPA" gbase="1uS" erev="0mV" tauDecay="0.1ms"/>
<expOneSynapse id="syn1" gbase="1uS" erev="0mV" tauDecay="30ms"/>
<expOneSynapse id="syn2" gbase="1uS" erev="0mV" tauDecay="4ms"/>
<cell id="CELL_PYR_HH">
<notes>Cell exported from NetPyNE:
{secs: {'soma': {'geom': {'diam': 6.3, 'L': 5, 'Ra': 123.0, 'pt3d': [(0, 0, 0, 20), (0, 0, 20, 20)]}, 'topol': {}, 'mechs': {'hh': {'gnabar': 0.12, 'gkbar': 0.036, 'gl': 0.003, 'el': -70}}}, 'dend': {'geom': {'diam': 5.0, 'L': 150.0, 'Ra': 150.0, 'cm': 1, 'pt3d': []}, 'topol': {'parentSec': 'soma', 'parentX': 1.0, 'childX': 0}, 'mechs': {'pas': {'g': 3.57e-05, 'e': -70}}}}}</notes>
{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="20.0"/>
<distal x="0.0" y="0.0" z="20.0" diameter="20.0"/>
</segment>
<segment id="1" name="dend">
<parent segment="0"/>
<distal x="0.0" y="150.0" z="0.0" diameter="5.0"/>
<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"/>
</segment>
<segmentGroup id="soma_SECTION" neuroLexId="sao864921383">
<member segment="0"/>
</segmentGroup>
<segmentGroup id="soma_group">
<include segmentGroup="soma_SECTION"/>
</segmentGroup>
<segmentGroup id="dend_SECTION" neuroLexId="sao864921383">
<member segment="1"/>
</segmentGroup>
<segmentGroup id="dend_group">
<include segmentGroup="dend_SECTION"/>
</segmentGroup>
</morphology>
<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"/>
<channelDensity id="na_soma_group" ionChannel="na_hh" condDensity="0.12 S_per_cm2" erev="50 mV" ion="na"/>
<channelDensity id="leak_dend_group" ionChannel="leak_hh" condDensity="3.57e-05 mS_per_cm2" erev="-70 mV" ion="non_specific"/>
<spikeThresh value="10 mV"/>
<specificCapacitance value="1 uF_per_cm2" segmentGroup="soma_group"/>
<specificCapacitance value="1 uF_per_cm2" segmentGroup="dend_group"/>
<initMembPotential value="-65 mV"/>
</membraneProperties>
<intracellularProperties>
<resistivity value="123.0 ohm_cm" segmentGroup="soma_group"/>
<resistivity value="150.0 ohm_cm" segmentGroup="dend_group"/>
</intracellularProperties>
</biophysicalProperties>
</cell>
<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"/>
<spikeGeneratorPoisson id="NetStim_bkg_PYR_HH_10_1_AMPA" averageRate="10 Hz"/>
<spikeGeneratorPoisson id="NetStim_bkg_PYR_Izhi_10_1_AMPA" averageRate="10 Hz"/>
<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_PYR_HH" size="3" type="populationList">
<property tag="color" value="0.41661987254534116 0.010169169457068361 0.8252065092537432"/>
Expand All @@ -93,43 +81,43 @@
<location x="81.868385993440555" y="93.398357254127419" z="51.077729265420288"/>
</instance>
</population>
<population id="Pop_NetStim_bkg_PYR_HH_10_1_AMPA" component="NetStim_bkg_PYR_HH_10_1_AMPA" size="3"/>
<population id="Pop_NetStim_bkg_PYR_Izhi_10_1_AMPA" component="NetStim_bkg_PYR_Izhi_10_1_AMPA" size="3"/>
<projection id="NetConn_PYR_Izhi_PYR_HH_AMPA" presynapticPopulation="PYR_Izhi" postsynapticPopulation="PYR_HH" synapse="AMPA">
<connectionWD id="0" preCellId="../PYR_Izhi/0/CELL_PYR_Izhi" postCellId="../PYR_HH/0/CELL_PYR_HH" weight="0.2" delay="12.369474744944261 ms"/>
<connectionWD id="1" preCellId="../PYR_Izhi/2/CELL_PYR_Izhi" postCellId="../PYR_HH/0/CELL_PYR_HH" weight="0.2" delay="12.97146338366091 ms"/>
<connectionWD id="2" preCellId="../PYR_Izhi/0/CELL_PYR_Izhi" postCellId="../PYR_HH/1/CELL_PYR_HH" weight="0.2" delay="14.241028963278428 ms"/>
<connectionWD id="3" preCellId="../PYR_Izhi/2/CELL_PYR_Izhi" postCellId="../PYR_HH/1/CELL_PYR_HH" weight="0.2" delay="11.661004595683124 ms"/>
<connectionWD id="4" preCellId="../PYR_Izhi/1/CELL_PYR_Izhi" postCellId="../PYR_HH/2/CELL_PYR_HH" weight="0.2" delay="13.099619872130592 ms"/>
<connectionWD id="5" preCellId="../PYR_Izhi/2/CELL_PYR_Izhi" postCellId="../PYR_HH/2/CELL_PYR_HH" weight="0.2" delay="14.315653269032612 ms"/>
<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_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_AMPA" presynapticPopulation="PYR_HH" postsynapticPopulation="PYR_HH" synapse="AMPA">
<connectionWD id="0" preCellId="../PYR_HH/0/CELL_PYR_HH" postCellId="../PYR_HH/1/CELL_PYR_HH" weight="0.2" delay="12.882266700443374 ms"/>
<connectionWD id="1" preCellId="../PYR_HH/2/CELL_PYR_HH" postCellId="../PYR_HH/1/CELL_PYR_HH" weight="0.2" delay="14.214732391680146 ms"/>
<connectionWD id="2" preCellId="../PYR_HH/0/CELL_PYR_HH" postCellId="../PYR_HH/2/CELL_PYR_HH" weight="0.2" delay="14.602870231822557 ms"/>
<connectionWD id="3" preCellId="../PYR_HH/1/CELL_PYR_HH" postCellId="../PYR_HH/2/CELL_PYR_HH" weight="0.2" delay="11.514025612022943 ms"/>
<projection id="NetConn_PYR_HH_PYR_HH_syn1" presynapticPopulation="PYR_HH" postsynapticPopulation="PYR_HH" synapse="syn1">
<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_AMPA" presynapticPopulation="PYR_HH" postsynapticPopulation="PYR_Izhi" synapse="AMPA">
<connectionWD id="0" preCellId="../PYR_HH/0/CELL_PYR_HH" postCellId="../PYR_Izhi/0/CELL_PYR_Izhi" weight="0.2" delay="12.913412871388646 ms"/>
<connectionWD id="1" preCellId="../PYR_HH/2/CELL_PYR_HH" postCellId="../PYR_Izhi/0/CELL_PYR_Izhi" weight="0.2" delay="11.564341090342863 ms"/>
<connectionWD id="2" preCellId="../PYR_HH/0/CELL_PYR_HH" postCellId="../PYR_Izhi/2/CELL_PYR_Izhi" weight="0.2" delay="13.45455050580457 ms"/>
<connectionWD id="3" preCellId="../PYR_HH/1/CELL_PYR_HH" postCellId="../PYR_Izhi/2/CELL_PYR_Izhi" weight="0.2" delay="12.817358977569082 ms"/>
<connectionWD id="4" preCellId="../PYR_HH/2/CELL_PYR_HH" postCellId="../PYR_Izhi/2/CELL_PYR_Izhi" weight="0.2" delay="15.581628749853062 ms"/>
<projection id="NetConn_PYR_HH_PYR_Izhi_syn1" presynapticPopulation="PYR_HH" postsynapticPopulation="PYR_Izhi" synapse="syn1">
<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_AMPA" presynapticPopulation="PYR_Izhi" postsynapticPopulation="PYR_Izhi" synapse="AMPA">
<connectionWD id="0" preCellId="../PYR_Izhi/2/CELL_PYR_Izhi" postCellId="../PYR_Izhi/0/CELL_PYR_Izhi" weight="0.2" delay="15.017115573506961 ms"/>
<connectionWD id="1" preCellId="../PYR_Izhi/0/CELL_PYR_Izhi" postCellId="../PYR_Izhi/2/CELL_PYR_Izhi" weight="0.2" delay="13.643281270729352 ms"/>
<connectionWD id="2" preCellId="../PYR_Izhi/1/CELL_PYR_Izhi" postCellId="../PYR_Izhi/2/CELL_PYR_Izhi" weight="0.2" delay="11.557444650642978 ms"/>
<projection id="NetConn_PYR_Izhi_PYR_Izhi_syn1" presynapticPopulation="PYR_Izhi" postsynapticPopulation="PYR_Izhi" synapse="syn1">
<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_bkg_PYR_HH_10_1_AMPA__PYR_HH" presynapticPopulation="Pop_NetStim_bkg_PYR_HH_10_1_AMPA" postsynapticPopulation="PYR_HH" synapse="AMPA">
<connectionWD id="0" preCellId="../Pop_NetStim_bkg_PYR_HH_10_1_AMPA[0]" postCellId="../PYR_HH/0/CELL_PYR_HH" weight="1.0" delay="4.364354378691791 ms"/>
<connectionWD id="1" preCellId="../Pop_NetStim_bkg_PYR_HH_10_1_AMPA[1]" postCellId="../PYR_HH/1/CELL_PYR_HH" weight="1.0" delay="2.9350596522132264 ms"/>
<connectionWD id="2" preCellId="../Pop_NetStim_bkg_PYR_HH_10_1_AMPA[2]" postCellId="../PYR_HH/2/CELL_PYR_HH" weight="1.0" delay="3.260543552632317 ms"/>
<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_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_bkg_PYR_Izhi_10_1_AMPA__PYR_Izhi" presynapticPopulation="Pop_NetStim_bkg_PYR_Izhi_10_1_AMPA" postsynapticPopulation="PYR_Izhi" synapse="AMPA">
<connectionWD id="0" preCellId="../Pop_NetStim_bkg_PYR_Izhi_10_1_AMPA[0]" postCellId="../PYR_Izhi/0/CELL_PYR_Izhi" weight="1.0" delay="2.859525935291423 ms"/>
<connectionWD id="1" preCellId="../Pop_NetStim_bkg_PYR_Izhi_10_1_AMPA[1]" postCellId="../PYR_Izhi/1/CELL_PYR_Izhi" weight="1.0" delay="3.166521908210935 ms"/>
<connectionWD id="2" preCellId="../Pop_NetStim_bkg_PYR_Izhi_10_1_AMPA[2]" postCellId="../PYR_Izhi/2/CELL_PYR_Izhi" weight="1.0" delay="3.9715051206360794 ms"/>
<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_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>

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