diff --git a/NetPyNE/HybridSmall/HybridSmall.py b/NetPyNE/HybridSmall/HybridSmall.py index f86cf3c..25de36c 100644 --- a/NetPyNE/HybridSmall/HybridSmall.py +++ b/NetPyNE/HybridSmall/HybridSmall.py @@ -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) @@ -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'} diff --git a/NeuroML2/HybridSmall.net.nml b/NeuroML2/HybridSmall.net.nml index 4be6bb7..189e2d0 100644 --- a/NeuroML2/HybridSmall.net.nml +++ b/NeuroML2/HybridSmall.net.nml @@ -21,18 +21,15 @@ - + + 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}}}}} +{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}}}}} - - - - - - + + @@ -40,33 +37,24 @@ - - - - - - - - - - - + + @@ -93,43 +81,43 @@ - - - - - - - - - + + + + + + + + + - - - - - + + + + + - - - - - - + + + + + + - - - - + + + + - - - - + + + + - - - - + + + +