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Fig6_generate_data.py
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Fig6_generate_data.py
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import moose
import pylab
import numpy as np
import sys
import os
import matplotlib.pyplot as plt
from matplotlib import cm
import rdesigneur as rd
import xml.etree.ElementTree as ET
#import itertools
from scipy import stats
import time
baseFname = 'Fig6_data'
displayMoogli = False
displayScatter = False
displayRuns = False
dumpSpatialPlotsFlag = False
scatterParamToUseInStats = 0
realStartTime = time.time()
rdes = 0
spikeStartIndices = [1131, 2000, 500, 1490]
# The dataRange maps to the spikeStartIndices, but is a dendrite index.
dataRange = [[1810,1850],[770,820],[3620,3680],[2510,2550]]
aoc = np.zeros( len( dataRange ) )
# Stim amplitude is unitless, defined in units of A mol conc.
# Stim Width is unitless, defined as multiple of diffusion length.
# Stim Vel is unitless, defined in terms of diffusion length by time units of diff constt.
# diffConst is defined in terms of square of diffusion length by unit time.
# diffLength here is in SI units: m^2/s
#
params = {
'diffusionLength':1.0e-6, # Diffusion characteristic length, used as voxel length too.
'dendDiameter': 1e-6, # Diameter of section of dendrite in model
'dendLength': 100e-6, # Length of section of dendrite in model
'spineSizeScale': 1.0, # Length scaling for spines. Vol wil be x^3.
'diffConstCa':100.0e-12, # Diffusion constant of Ca
'diffConstMAPK': 5e-12, # Diffusion constant for MAPK
'diffConstPP': 2e-12, # Diff constant for MAPK-activated phosphatase
'CaActivateRafKf': 6e6, # 1/sec.mM: rate for activation of Raf by Ca
'blankVoxelsAtEnd':10, # of voxels to leave blank at end of cylinder
'preStimTime':1.0, # Time to run before turning on stimulus.
'stimBurstTime':2.0, # Time for a stimulus burst
'postStimTime':10.0, # Time to run after stimulus. ~3x decay time
'runtime':20.0, # Simulation run time
'checkPoint':1.0, # How often to do a checkpoint.
'chemPlotDt':0.05, # Plotting timestep for chemical signaling.
'elecPlotDt':0.1e-3, # Plotting timestep for electrical signaling.
'spineSpacing':1.0e-6, # Spacing between spines.
'stimSpacing':4, # Stimulus spacing, in terms of # of spines.
'meanSpikeRate':0.1, # Basal mean rate for all synapses.
'activeSpikeRate':20.0, # Active input rate on specified synapses.
'baseGabaSpikeRate':1.0, # 1 Hz.
'thetaGabaSpikeRate':0.5, # This is the peak, not the average theta.
'thetaFreq':8.0, #
'amparSynapseWeight': 30.0, #
'nmdarSynapseWeight': 30.0, #
'gabarSynapseWeight': 30.0, #
'LCaDensity': 0.0, # Channel density for LCa channels.
'adaptorScale':60.0e3, # Adaptor scale factor from conc to Na density in Seimens/m^2.
'CaPsdScale': 0.08, # Adaptor scale from psd elec Ca to chem conc.
'Em': -60.0e-3, # Resting potential of neuron
'refractoryPeriod':0.010, # 10 ms refractory time.
'cellModel': 'VHC-neuron.CNG.swc', # Cell morphology file
#'cellModel': 'h10.CNG.swc', # Cell morphology file
'chemModel': 'NN_mapk14.g', # Chemical model file.
'fnumber': 0, # Output file index
'seed': 1234, # Seeds random numbers
'sequence': 1234, # stimulus sequence.
'seqDx': 4.0e-6, # Sequence spatial interval
'seqDt': 3.0, # Sequence time interval
}
def attachStimulus( fname, rdes ):
compts = rdes.elecid.compartments
heads = []
lookupSpineIndexFromCompt = []
for i in compts:
sl = rdes.elecid.spinesOnCompartment[i]
lookupSpineIndexFromCompt.append( len( heads ) )
heads.extend( sl[1::2] )
ampar = moose.wildcardFind( '/model/elec/#/glu' )
assert( len(ampar) == len( heads ) )
moose.RandSpike( '/model/elec/spike', len( heads ) )
spikes = moose.vec( '/model/elec/spike' )
spikes.rate = params['meanSpikeRate']
spikes.refractT = params['refractoryPeriod']
amparSynWeight = params['amparSynapseWeight']
nmdarSynWeight = params['nmdarSynapseWeight']
for j in zip( heads, range( len( heads ) ) ):
sh = moose.element( j[0].path + '/glu/sh' )
sh.numSynapses = 1
sh.synapse[0].weight = amparSynWeight
moose.connect( spikes[j[1]], 'spikeOut', sh.synapse[0], 'addSpike' )
sh = moose.element( j[0].path + '/NMDA/sh' )
sh.numSynapses = 1
sh.synapse[0].weight = nmdarSynWeight
moose.connect( spikes[j[1]], 'spikeOut', sh.synapse[0], 'addSpike' )
thetaGaba = moose.Function( '/model/elec/thetaGabaRhythm' )
timeExpr = 'cos( 6.283 * t * ' + str(params['thetaFreq']/2.0) + ' )^2'
rateExpr = str( 2.0 * params['thetaGabaSpikeRate'])
thetaGaba.expr = str( params['baseGabaSpikeRate']) + ' + ' + rateExpr + ' * ' + timeExpr
print thetaGaba.expr,
gabar = moose.wildcardFind( '/model/elec/#/GABA' )
print " NUM-GABA = ", len(gabar)
rsGabar = moose.RandSpike( '/model/elec/gabaSpike', len( gabar ) )
moose.connect( thetaGaba, 'valueOut', rsGabar, 'setRate', 'OneToAll' )
gabaSpikes = moose.vec( '/model/elec/gabaSpike' )
#spikes.rate = params['meanSpikeRate']
gabaSpikes.refractT = params['refractoryPeriod']
gabarSynWeight = params['gabarSynapseWeight']
for i in range( len(gabar) ):
sh = moose.element( gabar[i].path + '/sh' )
sh.numSynapses = 1
sh.synapse[0].weight = gabarSynWeight
moose.connect( gabaSpikes[i], 'spikeOut', sh.synapse[0], 'addSpike' )
return lookupSpineIndexFromCompt
def attachStimulus2( fname ):
ampar = moose.wildcardFind( '/model/elec/#/glu' )
nmdar = moose.wildcardFind( '/model/elec/#/NMDA' )
numSyn = len( ampar )
assert( numSyn == len( nmdar ) );
moose.le( '/model' )
moose.RandSpike( '/model/elec/spike', len( ampar ) )
spikes = moose.vec( '/model/elec/spike' )
spikes.rate = params['meanSpikeRate']
spikes.refractT = params['refractoryPeriod']
amparSynWeight = params['amparSynapseWeight']
nmdarSynWeight = params['nmdarSynapseWeight']
for i in range( numSyn ):
sh = moose.element( ampar[i].path + '/sh' )
sh.numSynapses = 1
sh.synapse[0].weight = amparSynWeight
moose.connect( spikes[i], 'spikeOut', sh.synapse[0], 'addSpike' )
sh = moose.element( nmdar[i].path + '/sh' )
sh.numSynapses = 1
sh.synapse[0].weight = nmdarSynWeight
moose.connect( spikes[i], 'spikeOut', sh.synapse[0], 'addSpike' )
def dumpPlots( fname ):
currt = moose.element( '/clock' ).currentTime
#print "os.rename( " + fname + ".xplot", fname + ".old )"
os.rename( fname + ".xplot", fname + ".old" )
print 'Current sim time = ', currt, ", user time = ", time.time() - realStartTime
sys.stdout.flush()
fd = open( fname + ".xplot", "w" )
for ii in params:
fd.write('% ' + ii + ' ' + str( params[ii] ) + '\n' )
fd.flush()
fd.close()
for i in rdes.plotNames:
# Args are tabname, plot title, index, scale, units
for j in moose.vec( i[0] ):
plotLabel = i[1].replace( " ", "_" ) + "." + str(j.index)
j.xplot( fname + ".xplot", plotLabel )
def dumpSpatialPlots( fname ):
global aoc
fd2 = open( fname + "_spatial.xplot", "a" )
currt = moose.element( '/clock' ).currentTime
elist = {}
elist['spineCa'] = moose.vec( '/model/chem/spine/Ca' )
elist['Ca4_CaM'] = moose.vec( '/model/chem/dend/DEND/CaM/CaM_dash_Ca4' )
elist['dendCa'] = moose.vec( '/model/chem/dend/DEND/Ca' )
#elist['dendKA_p'] = moose.vec( '/model/chem/dend/DEND/K_A_p' )
elist['dendMAPK_p'] = moose.vec( '/model/chem/dend/DEND/P_MAPK' )
#elist['dendPP'] = moose.vec( '/model/chem/dend/DEND/phosphatase' )
#elist['dend_regPP'] = moose.vec( '/model/chem/dend/DEND/reg_phosphatase' )
if dumpSpatialPlotsFlag:
for key, elm in elist.items():
fd2.write( "\n/newplot" )
fd2.write( "\n/plotname " + key + "_" + str(currt) + "\n" )
for v in elm.conc:
fd2.write( str( v ) + "\n" )
fd2.flush()
fd2.close()
### Here we dump the running total for Area of Curve.
conc = elist['dendMAPK_p'].conc
fd3 = open( fname + ".aoc", "a" )
fd3.write( str(currt) )
for i in range( len( dataRange ) ):
aoc[i] += sum( conc[ dataRange[i][0]: dataRange[i][1] ] )
fd3.write( '\t' + str(aoc[i] ) )
fd3.write( '\n' )
fd3.flush()
fd3.close()
def convertSeq( arg ):
x = int( arg )
ret = [0] * 5
for i in range( 5 ):
ret[-i-1] = x % 10
x /= 10
return ret
def printStuff( sequence, firstSpineOnCompt, rdes ):
for i in sequence:
for j in spikeStartIndices:
spikeIdx = firstSpineOnCompt[j] + i * params['stimSpacing']
headPath = '/model/elec/head' + str( spikeIdx )
head = moose.element( headPath )
#headCa = moose.element( headPath + '/Ca_conc' )
#headGlu = moose.element( headPath + '/glu' )
#headNmda = moose.element( headPath + '/NMDA' )
print i, j, spikeIdx, head.name, rdes.elecid.parentCompartmentOfSpine[head].name
def main():
global rdes
global params
sequence = [0,1,2,3,4]
#print params['sequence'], sequence
for ii in range( len( sys.argv ) ):
if sys.argv[ii][:2] == '--':
argName = sys.argv[ii][2:]
if argName in params:
if type( params[argName] ) is str:
params[argName] = sys.argv[ii+1]
elif type( params[argName] ) is int:
params[argName] = int( sys.argv[ii+1] )
else:
params[argName] = float(sys.argv[ii+1])
params[ 'stimSpacing' ] = int( round(params['seqDx']/params['spineSpacing']) )
if params['stimBurstTime'] >= params['seqDt']:
params['stimBurstTime'] = params['seqDt']
# Type correction hack
#params['stimSpacing'] = int( params['stimSpacing'] )
#params['fnumber'] = int( params['fnumber'] )
#params['sequence'] = int( params['sequence'] )
sequence = convertSeq( params['sequence'] )
fname = baseFname + '.' + str( int( params['fnumber'] ) ) + '.' + str( int( params['sequence'] ) )
print params['sequence'], sequence, fname
diffusionLength = params['diffusionLength']
dendLength = params['dendLength']
diffusionLength = params['diffusionLength']
library = moose.Neutral( '/library' )
if displayMoogli:
ml = [
['#', '1', '.', 'Vm', 'Memb potential'],
['#', '1', 'Ca_conc', 'Ca', '[Ca]', 0, 10, 0.001],
]
else:
ml = []
chanpath = os.path.dirname( os.path.realpath(__file__)) + '/proto21.'
moose.seed( params['seed'] )
rdes = rd.rdesigneur(
useGssa = False,
turnOffElec = False,
chemPlotDt = params['chemPlotDt'],
diffusionLength = diffusionLength,
spineProto = [['makeExcSpine()', 'spine']],
chanProto = [
[ chanpath + 'make_K_AHP()', 'K_AHP' ],
[ chanpath + 'make_K_A()', 'K_A' ],
[ chanpath + 'make_K_C()', 'K_C' ],
[ chanpath + 'make_K_DR()', 'K_DR' ],
[ chanpath + 'make_Na()', 'Na' ],
[ chanpath + 'make_Ca_conc()', 'Ca_conc' ],
[ chanpath + 'make_Ca()', 'Ca' ],
[ chanpath + 'make_NMDA()', 'NMDA' ],
[ chanpath + 'make_glu()', 'glu' ],
[ chanpath + 'make_GABA()', 'GABA' ],
],
chemProto = [[params['chemModel'], 'chem']],
cellProto = [[params['cellModel'], 'elec']],
chanDistrib = [
["Ca_conc", "#", "tau", "0.0133" ],
["Ca", "#dend#,#basal#,#apical#", "Gbar", str( params["LCaDensity"] ) ],
["Ca", "#soma#", "Gbar", "40" ],
["Na", "#dend#,#basal#", "Gbar", "60" ],
["Na", "#soma#", "Gbar", "600" ],
["Na", "#apical#", "Gbar", "40+40*exp(-p/200e-6)" ],
["K_DR", "#dend#,#basal#", "Gbar", "(p < 400e-6)*200" ],
["K_DR", "#soma#", "Gbar", "250" ],
["K_DR", "#apical#", "Gbar", "60+40*(p < 125e-6)" ],
["K_AHP", "#", "Gbar", "8" ],
["K_C", "#basal#,#dend#,#apical#", "Gbar", "50+150*exp(-p/200e-6)" ],
["K_C", "#soma#", "Gbar", "100" ],
["K_A", "#soma#", "Gbar", "50" ],
["K_A", "#dend#,#apical#", "Gbar", "50*(1 + 2.0e-6/(dia + 0.1e-6))" ],
["GABA", "#apical#,#dend#,#basal#", "Gbar", "10 + 30*(p < 125e-6)" ],
],
spineDistrib = [['spine','#dend#,#apical#', str(params['spineSpacing']),'1e-7', str( params['spineSizeScale'] ), '0.0' ]],
chemDistrib = [['chem', '#', 'install', '1' ]],
adaptorList = [
[ 'Ca_conc', 'Ca', 'psd/Ca_input', 'concInit', 2e-6, params['CaPsdScale'] ],
[ 'Ca_conc', 'Ca','dend/DEND/Ca_input','concInit',2.0e-6,0.0001],
[ 'dend/DEND/channel_p', 'conc', 'Na', 'modulation', 1.0, params['adaptorScale']],
],
plotList = [
['soma', '1', '.', 'Vm', 'Soma Vm'],
['head1732', '1', 'Ca_conc', 'Ca', 'head1732 eCa'],
['apical_36_2', '1', 'dend/DEND/P_MAPK', 'conc', 'dend36_2_P_MAPK'],
['apical_36_2', '1', 'dend/DEND/Ca', 'conc', 'dend36_2 Ca'],
['head1732', '1', 'spine/Ca', 'conc', 'spine1732_Ca'],
['head1732', '1', 'psd/Ca', 'conc', 'psd1732_Ca'],
['apical_36_3', '1', 'dend/DEND/P_MAPK', 'conc', 'dend36_3_P_MAPK'],
['apical_36_3', '1', 'dend/DEND/Ca', 'conc', 'dend36_3_Ca'],
['head1735', '1', 'spine/Ca', 'conc', 'spine1735_Ca'],
['head1735', '1', 'psd/Ca', 'conc', 'psd1735_Ca'],
['apical_36_5', '1', 'dend/DEND/P_MAPK', 'conc', 'dend36_5_P_MAPK'],
['apical_36_5', '1', 'dend/DEND/Ca', 'conc', 'dend36_5_Ca'],
['head1738', '1', 'spine/Ca', 'conc', 'spine1738_Ca'],
['head1738', '1', 'psd/Ca', 'conc', 'psd1738_Ca'],
['apical_36_6', '1', 'dend/DEND/P_MAPK', 'conc', 'dend36_6_P_MAPK'],
['apical_36_6', '1', 'dend/DEND/Ca', 'conc', 'dend36_6_Ca'],
['head1741', '1', 'spine/Ca', 'conc', 'spine1741_Ca'],
['head1741', '1', 'psd/Ca', 'conc', 'psd1741_Ca'],
['apical_36_7', '1', 'dend/DEND/P_MAPK', 'conc', 'dend36_7_P_MAPK'],
['apical_36_7', '1', 'dend/DEND/Ca', 'conc', 'dend36_7_Ca'],
['head1744', '1', 'spine/Ca', 'conc', 'spine1744_Ca'],
['head1744', '1', 'psd/Ca', 'conc', 'psd1744_Ca'],
['apical_70_4', '1', 'dend/DEND/P_MAPK', 'conc', 'dend70_4_P_MAPK'],
['apical_70_4', '1', 'dend/DEND/Ca', 'conc', 'dend70_4_Ca'],
['head3573', '1', 'spine/Ca', 'conc', 'spine3573_Ca'],
['head3573', '1', 'psd/Ca', 'conc', 'psd3573_Ca'],
['apical_70_5', '1', 'dend/DEND/P_MAPK', 'conc', 'dend70_5_P_MAPK'],
['apical_70_5', '1', 'dend/DEND/Ca', 'conc', 'dend70_5_Ca'],
['head3577', '1', 'spine/Ca', 'conc', 'spine3577_Ca'],
['head3577', '1', 'psd/Ca', 'conc', 'psd3577_Ca'],
['apical_70_6', '1', 'dend/DEND/P_MAPK', 'conc', 'dend70_6_P_MAPK'],
['apical_70_6', '1', 'dend/DEND/Ca', 'conc', 'dend70_6_Ca'],
['head3581', '1', 'spine/Ca', 'conc', 'spine3581_Ca'],
['head3581', '1', 'psd/Ca', 'conc', 'psd3581_Ca'],
['apical_70_8', '1', 'dend/DEND/P_MAPK', 'conc', 'dend70_8_P_MAPK'],
['apical_70_8', '1', 'dend/DEND/Ca', 'conc', 'dend70_8_Ca'],
['head3585', '1', 'spine/Ca', 'conc', 'spine3585_Ca'],
['head3585', '1', 'psd/Ca', 'conc', 'psd3585_Ca'],
['apical_70_9', '1', 'dend/DEND/P_MAPK', 'conc', 'dend70_9_P_MAPK'],
['apical_70_9', '1', 'dend/DEND/Ca', 'conc', 'dend70_9_Ca'],
['head3589', '1', 'spine/Ca', 'conc', 'spine3589_Ca'],
['head3589', '1', 'psd/Ca', 'conc', 'psd3589_Ca'],
['apical_16_15', '1', 'dend/DEND/P_MAPK', 'conc', 'dend16_15_P_MAPK'],
['apical_16_15', '1', 'dend/DEND/Ca', 'conc', 'dend16_15_Ca'],
['head733', '1', 'spine/Ca', 'conc', 'spine733_Ca'],
['head733', '1', 'psd/Ca', 'conc', 'psd733_Ca'],
['apical_52_12', '1', 'dend/DEND/P_MAPK', 'conc', 'dend52_12_P_MAPK'],
['apical_52_12', '1', 'dend/DEND/Ca', 'conc', 'dend52_12_Ca'],
['head2425', '1', 'spine/Ca', 'conc', 'spine2425_Ca'],
['head2425', '1', 'psd/Ca', 'conc', 'psd2425_Ca'],
],
moogList = ml
)
############## Set spine dimensions ##########################
# This is now done in the rdesigneur spineDistrib
#moose.element( '/library/spine/shaft' ).diameter *= params['shaftDiaScale']
#moose.element( '/library/spine/head' ).diameter *= params['headDiaScale']
############## Set Ca diffusion const ##########################
for ca in moose.wildcardFind( '/library/##/Ca[ISA=PoolBase]' ):
ca.diffConst = params['diffConstCa']
############## Set MAPK diffusion const ##########################
temp = params['diffConstMAPK']
moose.element( '/library/chem/dend/DEND/P_MAPK' ).diffConst = temp
moose.element( '/library/chem/dend/DEND/MAPK' ).diffConst = temp
############## Set PP diffusion const ##########################
temp = params['diffConstPP']
moose.element( '/library/chem/dend/DEND/reg_phosphatase' ).diffConst = temp
moose.element( '/library/chem/dend/DEND/inact_phosphatase' ).diffConst = temp
############## Set resting potential ##########################
for i in moose.wildcardFind( "/library/##[][ISA=CompartmentBase]" ):
i.Em = params[ 'Em' ]
i.initVm = params[ 'Em' ]
############## Set sensitivity to Ca ##########################
moose.element( '/library/chem/dend/DEND/Ca_activate_Raf' ).Kf = params['CaActivateRafKf']
#################### Build the model ##########################
rdes.buildModel()
#moose.showfields( '/model/chem/dend/DEND/PKA/KA' )
#moose.le( '/model/elec' )
#print "NUM PLOTS = ", len( rdes.plotNames)
firstSpineOnCompt = attachStimulus( fname, rdes )
fd = open( fname + ".xplot", "w" )
fd.flush()
fd2 = open( fname + "_spatial.xplot", "w" )
fd.close()
checkPoint = params['checkPoint']
moose.setClock( 19, checkPoint )
periodicOutput = moose.PyRun( '/model/graphs/periodicOutput' )
periodicOutput.tick = 19
periodicOutput.runString = 'dumpPlots( "' + fname + '" )'
periodicOutput.initString = 'print "Starting PeriodicOutput"'
spatOutput = moose.PyRun( '/model/graphs/spatOutput' )
spatOutput.tick = 18
spatOutput.runString = 'dumpSpatialPlots( "' + fname + '" )'
spatOutput.initString = 'print "Starting Spatial Output"'
moose.reinit()
moose.seed( 1 )
printStuff( sequence, firstSpineOnCompt, rdes )
spikes = moose.vec( '/model/elec/spike' )
runtime = params['runtime']
if displayMoogli:
rdes.displayMoogli( 0.05, runtime, 0.0 )
moose.start( params['preStimTime'] )
'''
ni = len( spikes ) / 8.0
spikeStartIndices = [ int( (i + 0.5) * ni ) for i in range( 8 ) ]
print "########## len(spikes) = ", len(spikes)
print "########## spikeStartIndices = ", spikeStartIndices
'''
stimIntervalTime = params['seqDt'] - params['stimBurstTime']
assert( stimIntervalTime >= 0 )
for i in sequence:
for j in spikeStartIndices:
spikeIdx = firstSpineOnCompt[j] + i * params['stimSpacing']
spikes[spikeIdx].rate = params['activeSpikeRate']
moose.start( params['stimBurstTime'] )
for j in spikeStartIndices:
spikeIdx = firstSpineOnCompt[j] + i * params['stimSpacing']
spikes[spikeIdx].rate = params['meanSpikeRate']
if ( stimIntervalTime > 0.0 ):
moose.start( stimIntervalTime )
moose.start( params['postStimTime'] )
quit()
if __name__ == '__main__':
main()