def setupTable(name, obj, qtyname, tablePath=None, threshold=None):
'''This is replacement function for moose.utils.setupTable
It stores qtyname from obj.
'''
assert qtyname[0].isupper(), "First character must be uppercase character"
debug.printDebug("DEBUG"
, "Setting up table for: {} -> get{}".format(obj.path, qtyname)
)
if tablePath is None:
tablePath = '{}/{}'.format(obj.path, 'data')
debug.printDebug("WARN"
, "Using default table path: {}".format(tablePath)
, frame = inspect.currentframe()
)
if not moose.exists(obj.path):
raise RuntimeError("Unknown path {}".format(obj.path))
moose.Neutral(tablePath)
table = moose.Table('{}/{}'.format(tablePath, name))
if threshold is None:
moose.connect(table, "requestOut", obj, "get{}".format(qtyname))
else:
raise UserWarning("TODO: Table with threshold is not implemented yet")
return table
def make_NMDA( name ):
if moose.exists( '/library/' + name ):
return
NMDA = moose.NMDAChan( '/library/' + name )
NMDA.Ek = 0.0
NMDA.tau1 = 20.0e-3
NMDA.tau2 = 20.0e-3
NMDA.Gbar = 5 * SOMA_A
NMDA.CMg = 1.2 # [Mg]ext in mM
NMDA.KMg_A = 1.0/0.28
NMDA.KMg_B = 1.0/62
NMDA.temperature = 300 # Temperature in Kelvin.
NMDA.extCa = 1.5 # [Ca]ext in mM
NMDA.intCa = 0.00008 # [Ca]int in mM
NMDA.intCaScale = 1 # Scale factor from elec Ca units to mM
NMDA.intCaOffset = 0.00008 # Basal [Ca]int in mM
NMDA.condFraction = 0.02 # Fraction of conductance due to Ca
addmsg1 = moose.Mstring( NMDA.path + '/addmsg1' )
addmsg1.value = '. ICaOut ../Ca_conc current'
addmsg2 = moose.Mstring( NMDA.path + '/addmsg2' )
addmsg2.value = '../Ca_conc concOut . assignIntCa'
sh = moose.SimpleSynHandler( NMDA.path + '/sh' )
moose.connect( sh, 'activationOut', NMDA, 'activation' )
sh.numSynapses = 1
sh.synapse[0].weight = 1
return NMDA
def example():
"""
The RandSpike class generates spike events from a Poisson process
and sends out a trigger via its `spikeOut` message. It is very
common to approximate the spiking in many neurons as a Poisson
process, i.e., the probability of `k` spikes in any interval `t`
is given by the Poisson distribution:
exp(-ut)(ut)^k/k!
for k = 0, 1, 2, ... u is the rate of spiking (the mean of the
Poisson distribution). See `wikipedia
<http://en.wikipedia.org/wiki/Poisson_process>`__ for details.
Many cortical neuron types spontaneously fire action
potentials. These are called ectopic spikes. In this example we
simulate this with a RandSpike object with rate 10 spikes/s and
send this to a single compartmental neuron via a synapse.
In this model the synaptic conductance is set so high that each
incoming spike evokes an action potential.
"""
ectopic = moose.RandSpike('ectopic_input')
ectopic.rate = 10.0
cellmodel = create_cell()
moose.connect(ectopic, 'spikeOut',
cellmodel['synhandler'].synapse[0], 'addSpike')
tab_vm = moose.Table('/Vm')
moose.connect(tab_vm, 'requestOut', cellmodel['neuron'], 'getVm')
moose.reinit()
moose.start(SIMTIME)
return tab_vm
def createFunction(fb,setpool,objB,objA):
fapath1 = fb.path.replace(objB,objA)
fapath = fapath1.replace('[0]','')
if not moose.exists(fapath):
# if fb.parent.className in ['CubeMesh','CyclMesh']:
# des = moose.Function('/'+objA+'/'+fb.parent.name+'/'+fb.name)
# elif fb.parent.className in ['Pool','ZombiePool','BufPool','ZombieBufPool']:
# for akey in list(poolListina[findCompartment(fb).name]):
# if fb.parent.name == akey.name:
# des = moose.Function(akey.path+'/'+fb.name)
des = moose.Function(fapath)
else:
des = moose.element(fapath)
inputB = moose.element(fb.path+'/x').neighbors["input"]
moose.connect(des, 'valueOut', moose.element(setpool),'setN' )
inputA = []
inputA = moose.element(fapath+'/x').neighbors["input"]
if not inputA:
for src in inputB:
pool = ((src.path).replace(objB,objA)).replace('[0]','')
numVariables = des.numVars
expr = ""
expr = (des.expr+'+'+'x'+str(numVariables))
expr = expr.lstrip("0 +")
expr = expr.replace(" ","")
des.expr = expr
moose.connect( pool, 'nOut', des.x[numVariables], 'input' )
def run(nogui):
reader = NML2Reader(verbose=True)
filename = 'test_files/NML2_SingleCompHHCell.nml'
print('Loading: %s'%filename)
reader.read(filename, symmetric=True)
msoma = reader.getComp(reader.doc.networks[0].populations[0].id,0,0)
print(msoma)
data = moose.Neutral('/data')
pg = reader.getInput('pulseGen1')
inj = moose.Table('%s/pulse' % (data.path))
moose.connect(inj, 'requestOut', pg, 'getOutputValue')
vm = moose.Table('%s/Vm' % (data.path))
moose.connect(vm, 'requestOut', msoma, 'getVm')
simdt = 1e-6
plotdt = 1e-4
simtime = 300e-3
#moose.showmsg( '/clock' )
for i in range(8):
moose.setClock( i, simdt )
moose.setClock( 8, plotdt )
moose.reinit()
moose.start(simtime)
print("Finished simulation!")
t = np.linspace(0, simtime, len(vm.vector))
if not nogui:
import matplotlib.pyplot as plt
vfile = open('moose_v_hh.dat','w')
for i in range(len(t)):
vfile.write('%s\t%s\n'%(t[i],vm.vector[i]))
vfile.close()
plt.subplot(211)
plt.plot(t, vm.vector * 1e3, label='Vm (mV)')
plt.legend()
plt.title('Vm')
plt.subplot(212)
plt.title('Input')
plt.plot(t, inj.vector * 1e9, label='injected (nA)')
#plt.plot(t, gK.vector * 1e6, label='K')
#plt.plot(t, gNa.vector * 1e6, label='Na')
plt.legend()
plt.figure()
test_channel_gates()
plt.show()
plt.close()
def makeCellProto( name ):
elec = moose.Neuron( '/library/' + name )
ecompt = []
soma = rd.buildCompt( elec, 'soma', somaDia, somaDia, -somaDia, RM, RA, CM )
dend = rd.buildCompt( elec, 'dend', dendLen, dendDia, 0, RM, RA, CM )
moose.connect( soma, 'axial', dend, 'raxial' )
elec.buildSegmentTree()
def create_cell():
"""Create a single-compartment Hodgking-Huxley neuron with a
synaptic channel.
This uses the :func:`ionchannel.create_1comp_neuron` function for
model creation.
Returns a dict containing the neuron, the synchan and the
synhandler for accessing the synapse,
"""
neuron = create_1comp_neuron('/neuron')
#: SynChan for post synaptic neuron
synchan = moose.SynChan('/neuron/synchan')
synchan.Gbar = 1e-8
synchan.tau1 = 2e-3
synchan.tau2 = 2e-3
msg = moose.connect(neuron, 'channel', synchan, 'channel')
#: Create SynHandler to handle spike event input and set the
#: activation input of synchan
synhandler = moose.SimpleSynHandler('/neuron/synhandler')
synhandler.synapse.num = 1
synhandler.synapse[0].delay = 5e-3
moose.connect(synhandler, 'activationOut', synchan, 'activation')
return {'neuron': neuron,
'synchan': synchan,
'synhandler': synhandler}
def create_hhcomp(parent='/library', name='hhcomp', diameter=-30e-6, length=0.0):
"""Create a compartment with Hodgkin-Huxley type ion channels (Na and
K).
Returns a 3-tuple: (compartment, nachannel, kchannel)
"""
comp, sarea = create_passive_comp(parent, name, diameter, length)
if moose.exists('/library/na'):
moose.copy('/library/na', comp.path, 'na')
else:
create_na_chan(parent=comp.path)
na = moose.element('%s/na' % (comp.path))
# Na-conductance 120 mS/cm^2
na.Gbar = 120e-3 * sarea * 1e4
na.Ek = 115e-3 + EREST_ACT
moose.connect(comp, 'channel', na, 'channel')
if moose.exists('/library/k'):
moose.copy('/library/k', comp.path, 'k')
else:
create_k_chan(parent=comp.path)
k = moose.element('%s/k' % (comp.path))
# K-conductance 36 mS/cm^2
k.Gbar = 36e-3 * sarea * 1e4
k.Ek = -12e-3 + EREST_ACT
moose.connect(comp, 'channel', k, 'channel')
return comp, na, k
def main( runTime ):
try:
moose.delete('/acc92')
print("Deleted old model")
except Exception as e:
print("Could not clean. model not loaded yet")
moose.loadModel('acc92_caBuff.g',loadpath,'gsl')
ca = moose.element(loadpath+'/kinetics/Ca')
pr = moose.element(loadpath+'/kinetics/protein')
clockdt = moose.Clock('/clock').dts
moose.setClock(8, 0.1)#simdt
moose.setClock(18, 0.1)#plotdt
print clockdt
print " \t \t simdt ", moose.Clock('/clock').dts[8],"plotdt ",moose.Clock('/clock').dts[18]
ori = ca.concInit
tablepath = loadpath+'/kinetics/Ca'
tableele = moose.element(tablepath)
table = moose.Table2(tablepath+'.con')
x = moose.connect(table, 'requestOut', tablepath, 'getConc')
tablepath1 = loadpath+'/kinetics/protein'
tableele1 = moose.element(tablepath1)
table1 = moose.Table2(tablepath1+'.con')
x1 = moose.connect(table1, 'requestOut', tablepath1, 'getConc')
ca.concInit = ori
print("[INFO] Running for 4000 with Ca.conc %s " % ca.conc)
moose.start(4000)
ca.concInit = 5e-03
print("[INFO] Running for 20 with Ca.conc %s " % ca.conc)
moose.start(20)
ca.concInit = ori
moose.start( runTime ) #here give the interval time
ca.concInit = 5e-03
print("[INFO] Running for 20 with Ca.conc %s " % ca.conc)
moose.start(20)
ca.concInit = ori
print("[INFO] Running for 2000 with Ca.conc %s " % ca.conc)
moose.start(2000)
pylab.figure()
pylab.subplot(2, 1, 1)
t = numpy.linspace(0.0, moose.element("/clock").runTime, len(table.vector)) # sec
pylab.plot( t, table.vector, label="Ca Conc (interval- 8000s)" )
pylab.legend()
pylab.subplot(2, 1, 2)
t1 = numpy.linspace(0.0, moose.element("/clock").runTime, len(table1.vector)) # sec
pylab.plot( t1, table1.vector, label="Protein Conc (interval- 8000s)" )
pylab.legend()
pylab.savefig( os.path.join( dataDir, '%s_%s.png' % (table1.name, runTime) ) )
print('[INFO] Saving data to csv files in %s' % dataDir)
tabPath1 = os.path.join( dataDir, '%s_%s.csv' % (table.name, runTime))
numpy.savetxt(tabPath1, numpy.matrix([t, table.vector]).T, newline='\n')
tabPath2 = os.path.join( dataDir, '%s_%s.csv' % (table1.name, runTime) )
numpy.savetxt(tabPath2, numpy.matrix([t1, table1.vector]).T, newline='\n')
def make_NMDA(): if moose.exists( 'NMDA' ): return NMDA = moose.SynChan( 'NMDA' ) NMDA.Ek = 0.0 NMDA.tau1 = 20.0e-3 NMDA.tau2 = 20.0e-3 NMDA.Gbar = 5 * SOMA_A block = moose.MgBlock( '/library/NMDA/block' ) block.CMg = 1.2 # [Mg] in mM block.Zk = 2 block.KMg_A = 1.0/0.28 block.KMg_B = 1.0/62 moose.connect( NMDA, 'channelOut', block, 'origChannel', 'OneToOne' ) addmsg1 = moose.Mstring( '/library/NMDA/addmsg1' ) addmsg1.value = '.. channel ./block channel' #Here we want to also tell the cell reader to _remove_ the original #Gk, Ek term going from the channel to the compartment, as this is # now handled by the MgBlock. #addmsg2 = moose.Mstring( 'NMDA/addmsg2' #addmsg2.value = 'DropMsg .. channel' addmsg3 = moose.Mstring( '/library/NMDA/addmsg3' ) addmsg3.value = '.. VmOut . Vm'
def singleCompt( name, params ):
mod = moose.copy( '/library/' + name + '/' + name, '/model' )
A = moose.element( mod.path + '/A' )
Z = moose.element( mod.path + '/Z' )
Z.nInit = 1
Ca = moose.element( mod.path + '/Ca' )
CaStim = moose.element( Ca.path + '/CaStim' )
runtime = params['preStimTime'] + params['stimWidth'] + params['postStimTime']
steptime = 100
CaStim.expr += ' + x2 * (t > ' + str( runtime ) + ' ) * ( t < ' + str( runtime + steptime ) + ' )'
print(CaStim.expr)
tab = moose.Table2( '/model/' + name + '/Atab' )
#for i in range( 10, 19 ):
#moose.setClock( i, 0.01 )
ampl = moose.element( mod.path + '/ampl' )
phase = moose.element( mod.path + '/phase' )
moose.connect( tab, 'requestOut', A, 'getN' )
ampl.nInit = params['stimAmplitude'] * 1
phase.nInit = params['preStimTime']
ksolve = moose.Ksolve( mod.path + '/ksolve' )
stoich = moose.Stoich( mod.path + '/stoich' )
stoich.compartment = mod
stoich.ksolve = ksolve
stoich.path = mod.path + '/##'
runtime += 2 * steptime
moose.reinit()
moose.start( runtime )
t = np.arange( 0, runtime + 1e-9, tab.dt )
return name, t, tab.vector
def loadModel(filename, chanProto, chanDistrib, passiveDistrib):
"""Load the model and insert channels """
global modelName
global nchans, ncompts
# Load in the swc file.
modelName = "elec"
cellProto = [ ( filename, modelName ) ]
rdes = rd.rdesigneur( cellProto = cellProto
, combineSegments = True
, passiveDistrib = passiveDistrib
, chanProto = chanProto
, chanDistrib = chanDistrib
)
rdes.buildModel('/model')
compts = moose.wildcardFind( "/model/%s/#[ISA=CompartmentBase]"%modelName )
setupStimuls( compts[0] )
for compt in compts:
vtab = moose.Table( '%s/vm' % compt.path )
moose.connect( vtab, 'requestOut', compt, 'getVm' )
_records[compt.path] = vtab
nchans = len(set([x.path for x in
moose.wildcardFind('/model/elec/##[TYPE=ZombieHHChannel]')])
)
_logger.info("Total channels: %s" % nchans)
return _records
def setup_model(model_path, synapse_locations, passive=False, solver='hsolve'):
"""Set up a single cell model under `model_path` with synapses
created in the compartments listed in `synapse_locations`.
`model_path` - location where the model should be created.
`synapse_locations`: compartment names for the synapses.
"""
cell = moose.copy(make_prototype(passive), model_path)
if solver.lower() == 'hsolve':
hsolve = moose.HSolve( '%s/solve' % (cell.path))
hsolve.dt = simdt
hsolve.target = cell.path
syninfo_list = []
for compname in synapse_locations:
comppath = '%s/%s' % (cell.path, compname)
print('1111 Creating synapse in', comppath)
compartment = moose.element(comppath)
syninfo = make_synapse(compartment)
syninfo_list.append(syninfo)
# connect pulse stimulus
stim_path = '%s/%s/stim' % (cell.path, compname)
print('2222 Creating stimuls in', stim_path)
stim = moose.PulseGen(stim_path)
moose.connect(stim, 'output', syninfo['spike'], 'Vm')
syninfo['stimulus'] = stim
return {'neuron': cell,
'syninfo': syninfo_list}
def create_squid(parent):
"""Create a single compartment squid model."""
soma = moose.SymCompartment(parent.path + '/soma')
Em = EREST_ACT + 10.613e-3
soma.Em = Em
soma.initVm = EREST_ACT
soma.Cm = 7.85e-9 * 0.5
soma.Rm = 4.2e5 * 5.0
soma.Ra = 7639.44e3
nachan = moose.HHChannel(parent.path + '/soma/Na')
nachan.Xpower = 3
xGate = moose.HHGate(nachan.path + '/gateX')
xGate.setupAlpha(Na_m_params + [VDIVS, VMIN, VMAX])
# This is important: one can run without it but the output will diverge.
xGate.useInterpolation = 1
nachan.Ypower = 1
yGate = moose.HHGate(nachan.path + '/gateY')
yGate.setupAlpha(Na_h_params + [VDIVS, VMIN, VMAX])
yGate.useInterpolation = 1
nachan.Gbar = 0.942e-3
nachan.Ek = 115e-3 + EREST_ACT
moose.connect(nachan, 'channel', soma, 'channel', 'OneToOne')
kchan = moose.HHChannel(parent.path + '/soma/K')
kchan.Xpower = 4.0
xGate = moose.HHGate(kchan.path + '/gateX')
xGate.setupAlpha(K_n_params + [VDIVS, VMIN, VMAX])
xGate.useInterpolation = 1
kchan.Gbar = 0.2836e-3
kchan.Ek = -12e-3 + EREST_ACT
moose.connect(kchan, 'channel', soma, 'channel', 'OneToOne')
return soma
def main():
""" This example illustrates loading, running of an SBML model defined in XML format.\n
The model 00001-sbml-l3v1.xml is taken from l3v1 SBML testcase.\n
Plots are setup.\n
Model is run for 20sec.\n
As a general rule we created model under '/path/model' and plots under '/path/graphs'.\n
"""
mfile = os.path.join( script_dir, 'chem_models/00001-sbml-l3v1.xml')
runtime = 20.0
# Loading the sbml file into MOOSE, models are loaded in path/model
sbmlId = moose.readSBML(mfile,'sbml')
s1 = moose.element('/sbml/model/compartment/S1')
s2= moose.element('/sbml/model/compartment/S2')
# Creating MOOSE Table, Table2 is for the chemical model
graphs = moose.Neutral( '/sbml/graphs' )
outputs1 = moose.Table2 ( '/sbml/graphs/concS1')
outputs2 = moose.Table2 ( '/sbml/graphs/concS2')
# connect up the tables
moose.connect( outputs1,'requestOut', s1, 'getConc' );
moose.connect( outputs2,'requestOut', s2, 'getConc' );
# Reset and Run
moose.reinit()
moose.start(runtime)
def main():
makeModel()
solver = moose.GslStoich("/model/compartment/solver")
solver.path = "/model/compartment/##"
solver.method = "rk5"
mesh = moose.element("/model/compartment/mesh")
moose.connect(mesh, "remesh", solver, "remesh")
moose.setClock(5, 1.0) # clock for the solver
moose.useClock(5, "/model/compartment/solver", "process")
moose.reinit()
moose.start(100.0) # Run the model for 100 seconds.
a = moose.element("/model/compartment/a")
b = moose.element("/model/compartment/b")
# move most molecules over to b
b.conc = b.conc + a.conc * 0.9
a.conc = a.conc * 0.1
moose.start(100.0) # Run the model for 100 seconds.
# move most molecules back to a
a.conc = a.conc + b.conc * 0.99
b.conc = b.conc * 0.01
moose.start(100.0) # Run the model for 100 seconds.
# Iterate through all plots, dump their contents to data.plot.
for x in moose.wildcardFind("/model/graphs/conc#"):
moose.element(x[0]).xplot("scriptKineticSolver.plot", x[0].name)
quit()
def make_spiny_compt():
comptLength = 100e-6
comptDia = 4e-6
numSpines = 5
compt = create_squid()
compt.inject = 1e-7
compt.x0 = 0
compt.y0 = 0
compt.z0 = 0
compt.x = comptLength
compt.y = 0
compt.z = 0
compt.length = comptLength
compt.diameter = comptDia
synInput = moose.SpikeGen( '/n/compt/synInput' )
synInput.refractT = 47e-3
synInput.threshold = -1.0
synInput.edgeTriggered = 0
synInput.Vm( 0 )
cell = moose.element( '/n' )
for i in range( numSpines ):
r = create_spine_with_receptor( compt, cell, i, i/float(numSpines) )
r.synapse.num = 1
syn = moose.element( r.path + '/synapse' )
moose.connect( synInput, 'spikeOut', syn, 'addSpike', 'Single' )
syn.weight = 0.2
syn.delay = i * 1.0e-4
"""
def make_NMDA(): if moose.exists( 'NMDA' ): return NMDA = moose.SynChan( 'NMDA' ) NMDA.Ek = 0.0 NMDA.tau1 = 20.0e-3 NMDA.tau2 = 20.0e-3 NMDA.Gbar = 5 * SOMA_A block = moose.MgBlock( '/library/NMDA/block' ) block.CMg = 1.2 # [Mg] in mM block.Zk = 2 block.KMg_A = 1.0/0.28 block.KMg_B = 1.0/62 moose.connect( NMDA, 'channelOut', block, 'origChannel', 'OneToOne' ) addmsg1 = moose.Mstring( '/library/NMDA/addmsg1' ) addmsg1.value = '.. channel ./block channel' #Here we want to also tell the cell reader to _remove_ the original #Gk, Ek term going from the channel to the compartment, as this is # now handled by the MgBlock. #addmsg2 = moose.Mstring( 'NMDA/addmsg2' #addmsg2.value = 'DropMsg .. channel' addmsg1 = moose.Mstring( '/library/NMDA/addmsg1' ) addmsg1.value = '.. VmOut ./block Vm' addmsg2 = moose.Mstring( '/library/NMDA/addmsg2' ) addmsg2.value = './block IkOut ../Ca_conc current' addmsg3 = moose.Mstring( '/library/NMDA/addmsg3' ) addmsg3.value = '.. VmOut . Vm' sh = moose.SimpleSynHandler( 'NMDA/sh' ) moose.connect( sh, 'activationOut', NMDA, 'activation' ) sh.numSynapses = 1 sh.synapse[0].weight = 1
def connectSynapse(self, spikegen, synapse):
''' Add synapse. '''
assert isinstance(synapse, moose.SynChan), type(synapse)
#utils.dump("INFO"
# , "Connecting ({})\n\t`{}`\n\t`{}`".format(
# "Sparse"
# , spikegen.path
# , synapse.vec.path
# )
# , frame = inspect.currentframe()
# )
# Following 6 lines are from snippet Izhikevich_with_synapse.py file. I
# am not sure whether this is the right way to make a synpase. However,
# let's try this till we get a non-zero result after simulation.
spikeStim = moose.PulseGen('%s/spike_stim' % (synapse.parent.path))
spikeStim.delay[0] = 50.0
spikeStim.level[0] = 1.0
spikeStim.width[0] = 100.0
moose.connect(spikeStim, 'output', spikegen, 'Vm')
m = moose.connect(spikegen, "spikeOut"
, synapse.synapse.vec, "addSpike"
, "Sparse"
)
m.setRandomConnectivity(1.0, 1)
return m
def make_synapses(spikegen, synchan, delay=5e-3):
"""
Create synapses from spikegens to synchans in a manner similar to
OneToAll connection.
spikegen: list of spikegen objects
These are sources of synaptic event messages.
synchan: list of synchan objects
These are the targets of the synaptic event messages.
delay: mean delay of synaptic transmission.
Individual delays are normally distributed with sd=0.1*mean.
"""
scount = len(spikegen)
for ii, sid in enumerate(synchan):
s = moose.SynChan(sid)
sh = moose.SimpleSynHandler( sid.path + "/synh" )
moose.connect( sh, "activationOut", s, "activation" )
sh.synapse.num = scount
delay_list = np.random.normal(delay, delay*0.1, scount)
# print delay_list
for jj in range(scount):
sh.synapse[jj].delay = delay_list[jj]
# Connect all spikegens to this synchan except that from
# same compartment - we assume if parents are same the two belong to the same compartment
if s.parent.path != spikegen[jj].parent.path:
m = moose.connect(spikegen[jj], 'spikeOut', moose.element(sh.path + '/synapse'), 'addSpike')
def two_populations(size=2):
"""An example with two population connected via synapses."""
net = moose.Neutral('network2')
pop_a = create_population(moose.Neutral('/network2/pop_A'), size)
pop_b = create_population(moose.Neutral('/network2/pop_B'), size)
make_synapses(pop_a['spikegen'], pop_b['synchan'])
make_synapses(pop_b['spikegen'], pop_a['synchan'])
pulse = moose.PulseGen('/network2/net2_pulse')
pulse.firstLevel = 1e-9
pulse.firstDelay = 0.05 # disable the pulsegen
pulse.firstWidth = 0.02
moose.connect(pulse, 'output', pop_a['compartment'][0], 'injectMsg')
data = moose.Neutral('/data')
vm_a = [moose.Table('/data/net2_Vm_A_%d' % (ii)) for ii in range(size)]
for tab, comp in zip(vm_a, pop_a['compartment']):
moose.connect(tab, 'requestOut', comp, 'getVm')
vm_b = [moose.Table('/data/net2_Vm_B_%d' % (ii)) for ii in range(size)]
for tab, comp in zip(vm_b, pop_b['compartment']):
moose.connect(tab, 'requestOut', comp, 'getVm')
gksyn_a = [moose.Table('/data/net2_Gk_syn_a_%d' % (ii)) for ii in range(size)]
for tab, synchan in zip(gksyn_a, pop_a['synchan']):
moose.connect(tab, 'requestOut', synchan, 'getGk')
gksyn_b = [moose.Table('/data/net2_Gk_syn_b_%d' % (ii)) for ii in range(size)]
for tab, synchan in zip(gksyn_b, pop_b['synchan']):
moose.connect(tab, 'requestOut', synchan, 'getGk')
pulsetable = moose.Table('/data/net2_pulse')
pulsetable.connect('requestOut', pulse, 'getOutputValue')
return {'vm_a': vm_a,
'vm_b': vm_b,
'gksyn_a': gksyn_a,
'gksyn_b': gksyn_b,
'pulse': pulsetable,}
def creaetHHComp(parent='/library', name='hhcomp', diameter=1e-6, length=1e-6):
"""Create a compartment with Hodgkin-Huxley type ion channels (Na and
K).
Returns a 3-tuple: (compartment, nachannel, kchannel)
"""
compPath = '{}/{}'.format(parent, name)
mc = MooseCompartment( compPath, length, diameter, {})
c = mc.mc_
sarea = mc.surfaceArea
if moose.exists('/library/na'):
moose.copy('/library/na', c.path, 'na')
else:
create_na_chan(parent = c.path)
na = moose.element('%s/na' % (c.path))
# Na-conductance 120 mS/cm^2
na.Gbar = 120e-3 * sarea * 1e4
na.Ek = 115e-3 + EREST_ACT
moose.connect(c, 'channel', na, 'channel')
if moose.exists('/library/k'):
moose.copy('/library/k', c.path, 'k')
else:
create_k_chan(parent = c.path)
k = moose.element('%s/k' % (c.path))
# K-conductance 36 mS/cm^2
k.Gbar = 36e-3 * sarea * 1e4
k.Ek = -12e-3 + EREST_ACT
moose.connect(c, 'channel', k, 'channel')
return (c, na, k)
def make_synapse(path):
"""Create a synapse with two time constants."""
syn = moose.SynChan(path)
syn.tau1 = 5.0 # ms
syn.tau2 = 1.0 # ms
syn.Gbar = 1.0 # mS
syn.Ek = 0.0
synsh = moose.SimpleSynHandler( path + '/sh' )
synsh.synapse.num = 1
# syn.bufferTime = 1.0 # ms
synsh.synapse.delay = 1.0
synsh.synapse.weight = 1.0
print(('Synapses:', len(synsh.synapse), 'w=', synsh.synapse[0].weight))
spikegen = moose.SpikeGen('%s/spike' % (syn.parent.path))
spikegen.edgeTriggered = False # Make it fire continuously when input is high
spikegen.refractT = 10.0 # With this setting it will fire at 1 s / 10 ms = 100 Hz
spikegen.threshold = 0.5
# This will send alternatind -1 and +1 to SpikeGen to make it fire
spike_stim = moose.PulseGen('%s/spike_stim' % (syn.parent.path))
spike_stim.delay[0] = 50.0
spike_stim.level[0] = 1.0
spike_stim.width[0] = 100.0
moose.connect(spike_stim, 'output', spikegen, 'Vm')
m = moose.connect(spikegen, 'spikeOut', synsh.synapse[0], 'addSpike')
return syn, spikegen
def _addSpine( self, parent, spineProto, pos, angle, x, y, z, size, k ):
spine = moose.copy( spineProto, parent.parent, 'spine' + str(k) )
kids = spine[0].children
coords = []
ppos = np.array( [parent.x0, parent.y0, parent.z0] )
for i in kids:
#print i.name, k
j = i[0]
j.name += str(k)
#print 'j = ', j
coords.append( [j.x0, j.y0, j.z0] )
coords.append( [j.x, j.y, j.z] )
self._scaleSpineCompt( j, size )
moose.move( i, self.elecid )
origin = coords[0]
#print 'coords = ', coords
# Offset it so shaft starts from surface of parent cylinder
origin[0] -= parent.diameter / 2.0
coords = np.array( coords )
coords -= origin # place spine shaft base at origin.
rot = np.array( [x, [0,0,0], [0,0,0]] )
coords = np.dot( coords, rot )
moose.delete( spine )
moose.connect( parent, "raxial", kids[0], "axial" )
self._reorientSpine( kids, coords, ppos, pos, size, angle, x, y, z )
def create_squid():
"""Create a single compartment squid model."""
parent = moose.Neutral ('/n' )
compt = moose.Compartment( '/n/compt' )
Em = EREST_ACT + 10.613e-3
compt.Em = Em
compt.initVm = EREST_ACT
compt.Cm = 7.85e-9
compt.Rm = 4.2e5
compt.Ra = 7639.44e3
nachan = moose.HHChannel( '/n/compt/Na' )
nachan.Xpower = 3
xGate = moose.HHGate(nachan.path + '/gateX')
xGate.setupAlpha(Na_m_params +
[VDIVS, VMIN, VMAX])
nachan.Ypower = 1
yGate = moose.HHGate(nachan.path + '/gateY')
yGate.setupAlpha(Na_h_params +
[VDIVS, VMIN, VMAX])
nachan.Gbar = 0.942e-3
nachan.Ek = 115e-3+EREST_ACT
moose.connect(nachan, 'channel', compt, 'channel', 'OneToOne')
kchan = moose.HHChannel( '/n/compt/K' )
kchan.Xpower = 4.0
xGate = moose.HHGate(kchan.path + '/gateX')
xGate.setupAlpha(K_n_params +
[VDIVS, VMIN, VMAX])
kchan.Gbar = 0.2836e-3
kchan.Ek = -12e-3+EREST_ACT
moose.connect(kchan, 'channel', compt, 'channel', 'OneToOne')
return compt
def test_crossing_single():
"""This function creates an ematrix of two PulseGen elements and
another ematrix of two Table elements.
The two pulsegen elements have same amplitude but opposite phase.
Table[0] is connected to PulseGen[1] and Table[1] to Pulsegen[0].
In the plot you should see two square pulses of opposite phase.
"""
size = 2
pg = moose.PulseGen('pulsegen', size)
for ix, ii in enumerate(pg.vec):
pulse = moose.element(ii)
pulse.delay[0] = 1.0
pulse.width[0] = 2.0
pulse.level[0] = (-1)**ix
tab = moose.Table('table', size)
moose.connect(tab.vec[0], 'requestOut', pg.vec[1], 'getOutputValue', 'Single')
moose.connect(tab.vec[1], 'requestOut', pg.vec[0], 'getOutputValue', 'Single')
print 'Neighbors:'
for t in tab.vec:
print t.path
for n in moose.element(t).neighbors['requestOut']:
print 'requestOut <-', n.path
moose.setClock(0, 0.1)
moose.useClock(0, '/##', 'process')
moose.start(5)
for ii in tab.vec:
t = moose.Table(ii).vector
print len(t)
pylab.plot(t)
pylab.show()
def make_spiny_compt(root_path, number,synInput):
comptLength = 100e-6
comptDia = 4e-6
numSpines = Number_Of_Spines
cell = moose.Neutral (root_path+"/cell"+str(number))
compt = create_squid(cell)
compt.inject = INJECT_CURRENT
compt.x0 = 0
compt.y0 = 0
compt.z0 = 0
compt.x = comptLength
compt.y = 0
compt.z = 0
compt.length = comptLength
compt.diameter = comptDia
for i in range( numSpines ):
r = create_spine_with_receptor( compt, cell, i, i/float(numSpines) )
r.synapse.num = 1
syn = moose.element( r.path + '/synapse' )
moose.connect( synInput, 'spikeOut', syn, 'addSpike', 'Single' )
syn.weight = 0.2
syn.delay = i * 1.0e-4
"""
def main():
######## Put your favourite cell model here ######
##This one is from PMID 22730554: Suo et al J. Mol Cell Biol 2012
filename = 'cells/ko20x-07.CNG.swc'
moose.Neutral( '/library' )
rdes = rd.rdesigneur( \
cellProto = [[ filename, 'elec' ] ],\
passiveDistrib = passiveDistrib_,
chanProto = chanProto_,
chanDistrib = chanDistrib_
)
rdes.buildModel( '/model' )
moose.reinit()
################## Now we store plots ########################
somaVm = moose.Table( '/somaVm' )
moose.connect( somaVm, 'requestOut', rdes.soma, 'getVm' )
################## Now we set up the display ########################
compts = moose.wildcardFind( "/model/elec/#[ISA=CompartmentBase]" )
compts[0].inject = inject
print("Setting Up 3D Display")
app = QtGui.QApplication(sys.argv)
vm_viewer = create_vm_viewer(rdes, somaVm)
vm_viewer.show()
vm_viewer.start()
return app.exec_()
def create_population(container, size):
"""Create a population of `size` single compartmental neurons with Na+
and K+ channels. Also create SpikeGen objects and SynChan objects
connected to these which can act as plug points for setting up
synapses later.
This uses ..ref::`ionchannel.create_1comp_neuron`.
"""
path = container.path
print path, size, type(path)
comps = create_1comp_neuron("{}/neuron".format(path), number=size)
synpath = path + "/synchan"
print synpath, size, type(size)
synchan = moose.vec(synpath, n=size, dtype="SynChan")
synchan.Gbar = 1e-8
synchan.tau1 = 2e-3
synchan.tau2 = 2e-3
m = moose.connect(comps, "channel", synchan, "channel", "OneToOne")
synhandler = moose.vec("{}/synhandler".format(path), n=size, dtype="SimpleSynHandler")
moose.connect(synhandler, "activationOut", synchan, "activation", "OneToOne")
spikegen = moose.vec("{}/spikegen".format(path), n=size, dtype="SpikeGen")
spikegen.threshold = 0.0
m = moose.connect(comps, "VmOut", spikegen, "Vm", "OneToOne")
return {"compartment": comps, "spikegen": spikegen, "synchan": synchan, "synhandler": synhandler}
def createSquid():
"""Create a single compartment squid model."""
parent = moose.Neutral ('/n' )
elec = moose.Neutral ('/n/elec' )
compt = moose.SymCompartment( '/n/elec/compt' )
Em = EREST_ACT + 10.613e-3
compt.Em = Em
compt.initVm = EREST_ACT
compt.Cm = 7.85e-9 * 0.5
compt.Rm = 4.2e5 * 5.0
compt.Ra = 7639.44e3
compt.length = 100e-6
compt.diameter = 4e-6
nachan = moose.HHChannel( '/n/elec/compt/Na' )
nachan.Xpower = 3
xGate = moose.HHGate(nachan.path + '/gateX')
xGate.setupAlpha(Na_m_params + [VDIVS, VMIN, VMAX])
xGate.useInterpolation = 1
nachan.Ypower = 1
yGate = moose.HHGate(nachan.path + '/gateY')
yGate.setupAlpha(Na_h_params + [VDIVS, VMIN, VMAX])
yGate.useInterpolation = 1
nachan.Gbar = 0.942e-3
nachan.Ek = 115e-3+EREST_ACT
moose.connect(nachan, 'channel', compt, 'channel', 'OneToOne')
kchan = moose.HHChannel( '/n/elec/compt/K' )
kchan.Xpower = 4.0
xGate = moose.HHGate(kchan.path + '/gateX')
xGate.setupAlpha(K_n_params + [VDIVS, VMIN, VMAX])
xGate.useInterpolation = 1
kchan.Gbar = 0.2836e-3
kchan.Ek = -12e-3+EREST_ACT
moose.connect(kchan, 'channel', compt, 'channel', 'OneToOne')
return compt
gktab = moose.Table('/data/CaT_Gk')
iktab = moose.Table('/data/CaT_Ik')
dend.Cm = Cm
dend.Rm = Rm
dend.Em = Em
dend.initVm = Vm_0
dend.diameter = dend_diameter
dend.length = dend_length
pulse.delay[0] = 8.
pulse.width[0] = 500e-3
pulse.level[0] = inject
pulse.delay[1] = 1e9
m = moose.connect(pulse, 'output', dend, 'injectMsg')
moose.connect(vmtab, 'requestOut', dend, 'getVm')
chan_proto.chanlib()
chan = addOneChan('CaT', gbar, dend)
moose.connect(gktab, 'requestOut', chan, 'getGk')
moose.connect(iktab, 'requestOut', chan, 'getIk')
diftab = []
buftab = []
difs, difb = add_difshells_and_buffers(dend)
if pumps:
pump = moose.MMPump('/model/dend/pump')
pump.Vmax = kcat
pump.Kd = km
def addPlot(objpath, field, plot):
assert moose.exists(objpath)
tab = moose.Table('/graphs/' + plot)
obj = moose.element(objpath)
moose.connect(tab, 'requestOut', obj, field)
return tab
def makeTab(plotname, molpath):
tab = moose.Table2('/model/graphs/' + plotname) # Make output table
# connect up the tables
moose.connect(tab, 'requestOut', moose.element(molpath), 'getConc')
def makeChemModel(compt):
"""
This function sets up a simple oscillatory chemical system within
the script. The reaction system is::
s ---a---> a // s goes to a, catalyzed by a.
s ---a---> b // s goes to b, catalyzed by a.
a ---b---> s // a goes to s, catalyzed by b.
b -------> s // b is degraded irreversibly to s.
in sum, **a** has a positive feedback onto itself and also forms **b**.
**b** has a negative feedback onto **a**.
Finally, the diffusion constant for **a** is 1/10 that of **b**.
"""
# create container for model
diffConst = 10e-12 # m^2/sec
motorRate = 1e-6 # m/sec
concA = 1 # millimolar
# create molecules and reactions
a = moose.Pool(compt.path + '/a')
b = moose.Pool(compt.path + '/b')
s = moose.Pool(compt.path + '/s')
e1 = moose.MMenz(compt.path + '/e1')
e2 = moose.MMenz(compt.path + '/e2')
e3 = moose.MMenz(compt.path + '/e3')
r1 = moose.Reac(compt.path + '/r1')
a.concInit = 0.1
b.concInit = 0.1
s.concInit = 1
moose.connect(e1, 'sub', s, 'reac')
moose.connect(e1, 'prd', a, 'reac')
moose.connect(a, 'nOut', e1, 'enzDest')
e1.Km = 1
e1.kcat = 1
moose.connect(e2, 'sub', s, 'reac')
moose.connect(e2, 'prd', b, 'reac')
moose.connect(a, 'nOut', e2, 'enzDest')
e2.Km = 1
e2.kcat = 0.5
moose.connect(e3, 'sub', a, 'reac')
moose.connect(e3, 'prd', s, 'reac')
moose.connect(b, 'nOut', e3, 'enzDest')
e3.Km = 0.1
e3.kcat = 1
moose.connect(r1, 'sub', b, 'reac')
moose.connect(r1, 'prd', s, 'reac')
r1.Kf = 0.3 # 1/sec
r1.Kb = 0 # 1/sec
# Assign parameters
a.diffConst = diffConst / 10
b.diffConst = diffConst
s.diffConst = 0
def create_table(tablename, tablecomp, compproperty):
tab = moose.Table(tablename)
moose.connect(tab, "requestOut", tablecomp, compproperty)
return tab
def makeModel():
model = moose.Neutral('/model')
# Make neuronal model. It has no channels, just for geometry
cell = moose.loadModel('./spinyNeuron.p', '/model/cell', 'Neutral')
# We don't want the cell to do any calculations. Disable everything.
for i in moose.wildcardFind('/model/cell/##'):
i.tick = -1
# create container for model
model = moose.element('/model')
chem = moose.Neutral('/model/chem')
# The naming of the compartments is dicated by the places that the
# chem model expects to be loaded.
compt0 = moose.NeuroMesh('/model/chem/compt0')
compt0.separateSpines = 1
compt0.geometryPolicy = 'cylinder'
compt1 = moose.SpineMesh('/model/chem/compt1')
moose.connect(compt0, 'spineListOut', compt1, 'spineList', 'OneToOne')
compt2 = moose.PsdMesh('/model/chem/compt2')
moose.connect(compt0, 'psdListOut', compt2, 'psdList', 'OneToOne')
#reacSystem = moose.loadModel( 'simpleOsc.g', '/model/chem', 'ee' )
makeChemModel(compt0, True) # Populate all 3 compts with the chem system.
makeChemModel(compt1, False)
makeChemModel(compt2, True)
compt0.diffLength = 2e-6 # This will be over 100 compartments.
# This is the magic command that configures the diffusion compartments.
compt0.cell = cell
moose.showfields(compt0)
# Build the solvers. No need for diffusion in this version.
ksolve0 = moose.Ksolve('/model/chem/compt0/ksolve')
if useGssa:
ksolve1 = moose.Gsolve('/model/chem/compt1/ksolve')
ksolve2 = moose.Gsolve('/model/chem/compt2/ksolve')
else:
ksolve1 = moose.Ksolve('/model/chem/compt1/ksolve')
ksolve2 = moose.Ksolve('/model/chem/compt2/ksolve')
dsolve0 = moose.Dsolve('/model/chem/compt0/dsolve')
dsolve1 = moose.Dsolve('/model/chem/compt1/dsolve')
dsolve2 = moose.Dsolve('/model/chem/compt2/dsolve')
stoich0 = moose.Stoich('/model/chem/compt0/stoich')
stoich1 = moose.Stoich('/model/chem/compt1/stoich')
stoich2 = moose.Stoich('/model/chem/compt2/stoich')
# Configure solvers
stoich0.compartment = compt0
stoich1.compartment = compt1
stoich2.compartment = compt2
stoich0.ksolve = ksolve0
stoich1.ksolve = ksolve1
stoich2.ksolve = ksolve2
stoich0.dsolve = dsolve0
stoich1.dsolve = dsolve1
stoich2.dsolve = dsolve2
stoich0.path = '/model/chem/compt0/#'
stoich1.path = '/model/chem/compt1/#'
stoich2.path = '/model/chem/compt2/#'
assert (stoich0.numVarPools == 1)
assert (stoich0.numProxyPools == 0)
assert (stoich0.numRates == 1)
assert (stoich1.numVarPools == 1)
assert (stoich1.numProxyPools == 0)
if useGssa:
assert (stoich1.numRates == 2)
assert (stoich2.numRates == 2)
else:
assert (stoich1.numRates == 1)
assert (stoich2.numRates == 1)
assert (stoich2.numVarPools == 1)
assert (stoich2.numProxyPools == 0)
dsolve0.buildNeuroMeshJunctions(dsolve1, dsolve2)
stoich0.buildXreacs(stoich1)
stoich1.buildXreacs(stoich2)
stoich0.filterXreacs()
stoich1.filterXreacs()
stoich2.filterXreacs()
Ca_input_dend = moose.vec('/model/chem/compt0/Ca_input')
print len(Ca_input_dend)
for i in range(60):
Ca_input_dend[3 + i * 3].conc = 2.0
Ca_input_PSD = moose.vec('/model/chem/compt2/Ca_input')
print len(Ca_input_PSD)
for i in range(5):
Ca_input_PSD[2 + i * 2].conc = 1.0
# Create the output tables
num = compt0.numDiffCompts - 1
graphs = moose.Neutral('/model/graphs')
makeTab('Ca_soma', '/model/chem/compt0/Ca[0]')
makeTab('Ca_d1', '/model/chem/compt0/Ca[1]')
makeTab('Ca_d2', '/model/chem/compt0/Ca[2]')
makeTab('Ca_d3', '/model/chem/compt0/Ca[3]')
makeTab('Ca_s3', '/model/chem/compt1/Ca[3]')
makeTab('Ca_s4', '/model/chem/compt1/Ca[4]')
makeTab('Ca_s5', '/model/chem/compt1/Ca[5]')
makeTab('Ca_p3', '/model/chem/compt2/Ca[3]')
makeTab('Ca_p4', '/model/chem/compt2/Ca[4]')
makeTab('Ca_p5', '/model/chem/compt2/Ca[5]')
def add_difshells_and_buffers(comp):
if difshell_no < 1:
return [], []
difshell = []
shell_thickness = dend.diameter / difshell_no / 2.
difbuffer = []
for i in range(difshell_no):
shell_radius = comp.diameter / 2 - i * shell_thickness
dif = add_difshell(comp, i, shell_thickness, shell_radius)
difshell.append(dif)
if i > 0:
moose.connect(difshell[i - 1], "outerDifSourceOut", difshell[i],
"fluxFromOut")
moose.connect(difshell[i], "innerDifSourceOut", difshell[i - 1],
"fluxFromIn")
if difbuff_no > 0:
difbuffer.append([])
for j in range(difbuff_no):
buf = add_difbuffer_to_dishell(comp, i, j, shell_thickness,
shell_radius)
difbuffer[i].append(buf)
moose.connect(difshell[i], "concentrationOut", buf,
"concentration")
moose.connect(buf, "reactionOut", difshell[i], "reaction")
if i > 0:
moose.connect(difbuffer[i - 1][j], "outerDifSourceOut",
difbuffer[i][j], "fluxFromOut")
moose.connect(difbuffer[i][j], "innerDifSourceOut",
difbuffer[i - 1][j], "fluxFromIn")
return difshell, difbuffer
def main(simtime):
# Simulation information.
simtime = simtime
simdt = 0.25e-5
plotdt = 0.25e-3
# Cell Compartment infromation
diameter = 30e-6
length = 50e-6
Em = EREST_ACT + 10.613e-3
CM = 1e-6 * 1e4
RM = 1 / (0.3E-3 * 1e4)
# Channel information.
sa, x_sa = compute_comp_area(diameter, length)
na_g = 120E-3 * sa * 1E4
na_ek = 115E-3 + EREST_ACT
k_g = 36e-3 * sa * 1E4
k_ek = -12E-3 + EREST_ACT
# Stimulus information
inj_delay = 20E-3
inj_amp = 0.3E-9
inj_width = 40E-3
# Create cell
soma = create_compartment('soma',
length,
diameter,
RM,
CM,
initVM=EREST_ACT,
ELEAK=Em)
# Create channels
K_chan = create_channel(chan_name='K',
vdivs=VDIVS,
vmin=VMIN,
vmax=VMAX,
x_params=K_n_params,
xpow=4)
Na_chan = create_channel(chan_name='Na',
vdivs=VDIVS,
vmin=VMIN,
vmax=VMAX,
x_params=Na_m_params,
xpow=3,
y_params=Na_h_params,
ypow=1)
# Set conductances
nachan = moose.copy(Na_chan, soma.path, 'Na', 1)
kchan = moose.copy(K_chan, soma.path, 'K', 1)
nachan = set_channel_conductance(nachan, na_g, na_ek)
kchan = set_channel_conductance(kchan, k_g, k_ek)
# Add channels to soma
moose.connect(nachan, 'channel', soma, 'channel', 'OneToOne')
moose.connect(kchan, 'channel', soma, 'channel', 'OneToOne')
# connect pulse gen
pulse_inject = create_pulse_generator(soma,
inj_width,
inj_amp,
delay=inj_delay)
# Output table
soma_v_table = create_output_table(table_element='/output',
table_name='somaVm')
soma_i_table = create_output_table(table_element='/output',
table_name='somaIm')
# Connect output tables
moose.connect(soma_v_table, 'requestOut', soma, 'getVm')
moose.connect(soma_i_table, 'requestOut', pulse_inject, 'getOutputValue')
# Set moose simulation clocks
for lable in range(7):
moose.setClock(lable, simdt)
moose.setClock(8, plotdt)
# Run simulation
moose.reinit()
moose.start(simtime)
# Plot output tables.
v_plot = plot_vm_table(simtime,
soma_v_table,
soma_i_table,
title="soma voltage")
plt.grid(True)
plt.legend(['v', 'i'])
plt.show()
def main():
'''
On the command-line, in moose-examples/snippets directory, run ``python IntegrateFireZoo.py``.
The script will ask you which neuron you want to simulate and you can choose and run what you want.
Play with the parameters of the IF neurons in the source code.
'''
neuronChoices = {'LIF':moose.LIF, 'QIF':moose.QIF, 'ExIF':moose.ExIF, 'AdExIF':moose.AdExIF,
'AdThreshIF':moose.AdThreshIF, 'IzhIF':moose.IzhIF}
#### CHOOSE ONE OF THE NEURON KEYS AS choiceKey FROM BELOW DICTIONARY ####
#choiceKey = 'LIF'
#### No need, am inputting it from the user on the terminal
choiceKeys = list(neuronChoices.keys()) # keys() does not retain the order in dict defn above!
choiceIndex = eval(str(input('Choose a number corresponding to your desired neuron: '+str([(i,key) for (i,key) in enumerate(choiceKeys)])+' -- ')))
choiceKey = choiceKeys[choiceIndex]
neuronChoice = neuronChoices[choiceKey]
# ###########################################
# Initialize neuron group
# ###########################################
# neuron instantiation
network = neuronChoice( 'network' ); # choose neuron type above
moose.le( '/network' )
network.vec.Em = Vrest
network.vec.thresh = Vt_base
network.vec.refractoryPeriod = refrT
network.vec.Rm = R
network.vec.vReset = Vreset
network.vec.Cm = tau/R
network.vec.initVm = Vrest
# neuron specific parameters and current injected I
if choiceKey == 'LIF':
network.vec.inject = 5e-10 # Amp # injected current I
if choiceKey == 'QIF':
network.vec.a0 = a0
network.vec.vCritical = vCritical
network.vec.inject = 5e-10 # Amp # injected current I
elif choiceKey == 'ExIF':
network.vec.deltaThresh = deltaThresh
network.vec.vPeak = vPeak # reset at vPeak, not at thresh
network.vec.inject = 5e-9 # Amp # injected current I
elif choiceKey == 'AdExIF':
network.vec.deltaThresh = deltaThresh
network.vec.vPeak = vPeak # reset at vPeak, not at thresh
network.vec.a0 = a0AdEx
network.vec.b0 = b0
network.vec.tauW = tauW
network.vec.inject = 5e-9 # Amp # injected current I
elif choiceKey == 'AdThreshIF':
network.vec.a0 = a0AdTh
network.vec.threshJump = threshJump
network.vec.tauThresh = tauThresh
network.vec.inject = 1e-9 # Amp # injected current I
elif choiceKey == 'IzhIF':
network.vec.a = a
network.vec.b = b
network.vec.d = d
network.vec.uInit = uRest # Just sets the initial value of u
network.vec.vPeak = vPeak # reset at vPeak, not at thresh
network.vec.inject = 5e-9 # Amp # injected current I
print(("Injecting current =",network.vec[0].inject,"in",choiceKey,"neuron."))
# ###########################################
# Setting up table
# ###########################################
Vm = moose.Table( '/plotVm' )
moose.connect( network, 'VmOut', Vm, 'input', 'OneToOne')
spikes = moose.Table( '/plotSpikes' )
moose.connect( network, 'spikeOut', spikes, 'input', 'OneToOne')
# ###########################################
# Simulate the current injection
# ###########################################
dt = 5e-6 # s
runtime = 0.02 # s
# moose simulation
moose.useClock( 1, '/network', 'process' )
moose.useClock( 2, '/plotSpikes', 'process' )
moose.useClock( 3, '/plotVm', 'process' )
moose.setClock( 0, dt )
moose.setClock( 1, dt )
moose.setClock( 2, dt )
moose.setClock( 3, dt )
moose.setClock( 9, dt )
moose.reinit()
moose.start(runtime)
# ###########################################
# Plot the simulated Vm-s and STDP curve
# ###########################################
# Voltage plots
Vmseries = Vm.vector
numsteps = len(Vmseries)
if choiceKey not in ['ExIF','AdExIF','IzhIF']:
# insert spikes so that Vm reset at thresh doesn't look weird
# for ExIF, etc. reset is at vPeak, so not weird.
for t in spikes.vector:
Vmseries[int(t/dt)-1] = 30e-3 # V
timeseries = np.arange(0.,1000*numsteps*dt-1e-10,dt*1000)
plt.figure(facecolor='w')
plt.plot(timeseries,Vmseries*1000,color='r') # neuron's Vm
plt.xlabel('time (ms)')
plt.ylabel('Vm (mV)')
plt.title(choiceKey+"neuron, current="+str(network.vec[0].inject)+"A")
plt.show()
def connect_CaConc(compartment_list, temperature=None):
""" Connect the Ca pools and channels within each of the compartments in compartment_list
Ca channels should have a child Mstring named 'ion' with value set in MOOSE.
Ca dependent channels like KCa should have a child Mstring called 'ionDependency' with value set in MOOSE.
Call this only after instantiating cell so that all channels and pools have been created. """
for compartment in compartment_list:
caconc = None
for child in compartment.children:
if child.className == "CaConc":
caconc = moose.element(child)
break
if caconc is not None:
child = get_child_Mstring(caconc, "phi")
if child is not None:
caconc.B = float(
child.value
) # B = phi by definition -- see neuroml 1.8.1 defn
else:
## B has to be set for caconc based on thickness of Ca shell and compartment l and dia,
## OR based on the Mstring phi under CaConc path.
## I am using a translation from Neuron for mitral cell, hence this method.
## In Genesis, gmax / (surfacearea*thick) is set as value of B!
caconc.B = (1 / (2 * FARADAY) /
(math.pi * compartment.diameter *
compartment.length * caconc.thick))
for neutralwrap in compartment.children:
if neutralwrap.className == "HHChannel":
channel = moose.HHChannel(child)
## If child Mstring 'ion' is present and is Ca, connect channel current to caconc
for childid in channel.children:
# in async13, gates which have not been created still 'exist'
# i.e. show up as a child, but cannot be wrapped.
try:
child = moose.element(childid)
if child.className == "Mstring":
child = moose.Mstring(child)
assert child
if child.name == "ion":
if child.value in ["Ca", "ca"]:
moose.connect(channel, "IkOut", caconc,
"current")
# print 'Connected IkOut of',channel.path,'to current of',caconc.path
## temperature is used only by Nernst part here...
if child.name == "nernst_str":
nernst = moose.Nernst(channel.path +
"/nernst")
nernst_params = child.value.split(",")
nernst.Cout = float(nernst_params[0])
nernst.valence = int(nernst_params[1])
nernst.Temperature = temperature
moose.connect(nernst, "Eout", channel,
"setEk")
moose.connect(caconc, "concOut", nernst,
"ci")
# print 'Connected Nernst',nernst.path
except TypeError:
pass
if neutralwrap.className == "HHChannel2D":
channel = moose.HHChannel2D(child)
## If child Mstring 'ionDependency' is present, connect caconc Ca conc to channel
for childid in channel.children:
# in async13, gates which have not been created still 'exist'
# i.e. show up as a child, but cannot be wrapped.
try:
child = moose.element(childid)
if (child.className == "Mstring"
and child.name == "ionDependency"):
child = moose.Mstring(child)
if child.value in ["Ca", "ca"]:
moose.connect(caconc, "concOut", channel,
"concen")
# print 'Connected concOut of',caconc.path,'to concen of',channel.path
except TypeError as e:
logger_.warning(e)
def creat_moose_tables():
soma_v_table = create_output_table(table_element='/output',
table_name='somaVm')
soma_i_table = create_output_table(table_element='/output',
table_name='somIm')
soma_i_table1 = create_output_table(table_element='/output',
table_name='somIm1')
soma_i_table2 = create_output_table(table_element='/output',
table_name='somIm2')
soma_i_table3 = create_output_table(table_element='/output',
table_name='somIm3')
soma_i_table4 = create_output_table(table_element='/output',
table_name='somIm4')
moose.connect(soma_v_table, 'requestOut', moose.element('/soma'), 'getVm')
moose.connect(soma_i_table, 'requestOut', moose.element('/soma/Ca_V2'),
'getIk')
moose.connect(soma_i_table1, 'requestOut', moose.element('/soma/Ca_V1'),
'getIk')
moose.connect(soma_i_table2, 'requestOut', moose.element('/soma/K'),
'getIk')
moose.connect(soma_i_table3, 'requestOut', moose.element('/soma/ca_cc'),
'getIk')
moose.connect(soma_i_table4, 'requestOut', moose.element('/soma/CaPool'),
'getCa')
return {
'vm': [soma_v_table],
'internal_currents': [
soma_i_table, soma_i_table1, soma_i_table2, soma_i_table3,
soma_i_table4
]
}
def buildOnePlot( path, field = 'getConc' ):
elist = moose.vec( '/model/chem/' + path )
tabname = path.replace( '/', '_' )
tab = moose.Table2( '/graphs/' + tabname, len( elist ) ).vec
moose.connect( tab, 'requestOut', elist, field, 'OneToOne' )
def makePlot(name, src, field, tick):
tab = moose.Table('/graphs/' + name)
moose.connect(tab, 'requestOut', src, 'get' + field)
tab.tick = tick
return tab
def makeChemProto(name, Aexpr, Bexpr, params):
sw = params['stimWidth']
diffLength = params['diffusionLength']
dca = params['diffConstA'] * diffLength * diffLength
dcb = params['diffConstB'] * diffLength * diffLength
# Objects
chem = moose.Neutral('/library/' + name)
compt = moose.CubeMesh('/library/' + name + '/' + name)
A = moose.Pool(compt.path + '/A')
B = moose.Pool(compt.path + '/B')
Z = moose.BufPool(compt.path + '/Z')
Ca = moose.BufPool(compt.path + '/Ca')
phase = moose.BufPool(compt.path + '/phase')
vel = moose.BufPool(compt.path + '/vel')
ampl = moose.BufPool(compt.path + '/ampl')
Adot = moose.Function(A.path + '/Adot')
Bdot = moose.Function(B.path + '/Bdot')
CaStim = moose.Function(Ca.path + '/CaStim')
A.diffConst = dca
B.diffConst = dcb
# Equations
Adot.expr = parseExpr(Aexpr, params, True)
Bdot.expr = parseExpr(Bexpr, params, False)
CaStim.expr = 'x2 * exp( -((x0 - t)^2)/(2* ' + str(sw * sw) + ') )'
print(Adot.expr)
print(Bdot.expr)
print(CaStim.expr)
# Connections
Adot.x.num = 4
moose.connect(Ca, 'nOut', Adot.x[0], 'input')
moose.connect(A, 'nOut', Adot.x[1], 'input')
moose.connect(B, 'nOut', Adot.x[2], 'input')
moose.connect(Z, 'nOut', Adot.x[3], 'input')
moose.connect(Adot, 'valueOut', A, 'increment')
Bdot.x.num = 3
if name == 'negFF':
moose.connect(Ca, 'nOut', Bdot.x[0], 'input')
else:
moose.connect(A, 'nOut', Bdot.x[0], 'input')
moose.connect(B, 'nOut', Bdot.x[1], 'input')
moose.connect(Z, 'nOut', Bdot.x[2], 'input')
moose.connect(Bdot, 'valueOut', B, 'increment')
CaStim.x.num = 3
moose.connect(phase, 'nOut', CaStim.x[0], 'input')
moose.connect(vel, 'nOut', CaStim.x[1], 'input')
moose.connect(ampl, 'nOut', CaStim.x[2], 'input')
moose.connect(CaStim, 'valueOut', Ca, 'setN')
return compt
def enzymeMerge(comptD, comptS, key, poolListind):
war_msg = ""
RE_Duplicated, RE_Notcopiedyet, RE_Dangling = [], [], []
comptDpath = moose.element(comptD[key]).path
comptSpath = moose.element(comptS[key]).path
objD = moose.element(comptDpath).parent.name
objS = moose.element(comptSpath).parent.name
#nzyListina => enzyListind
enzyListind = moose.wildcardFind(comptDpath + '/##[ISA=EnzBase]')
enzyListins = moose.wildcardFind(comptSpath + '/##[ISA=EnzBase]')
for es in enzyListins:
eSsubname, eSprdname = [], []
eSsubname = subprdList(es, "sub")
eSprdname = subprdList(es, "prd")
allexists, allexistp = False, False
allclean = False
poolinDlist = poolListind[findCompartment(es).name]
for pD in poolinDlist:
if es.parent.name == pD.name:
edpath = es.parent.path.replace(objS, objD)
if not moose.exists(edpath + '/' + es.name):
#This will take care
# -- If same enzparent name but different enzyme name
# -- or different parent/enzyme name
if eSsubname and eSprdname:
allexists = checkexist(eSsubname, objS, objD)
allexistp = checkexist(eSprdname, objS, objD)
if allexists and allexistp:
enzPool = moose.element(pD.path)
edpath = es.parent.path.replace(objS, objD)
enz = moose.element(
moose.copy(es, moose.element(edpath)))
enzPool = enz.parent
if es.className in ["ZombieEnz", "Enz"]:
moose.connect(moose.element(enz), "enz",
enzPool, "reac")
if es.className in ["ZombieMMenz", "MMenz"]:
moose.connect(enzPool, "nOut", enz, "enzDest")
connectObj(enz, eSsubname, "sub", comptD, war_msg)
connectObj(enz, eSprdname, "prd", comptD, war_msg)
allclean = True
else:
# didn't find sub or prd for this Enzyme
RE_Notcopiedyet.append(es)
else:
# -- it is dagging reaction
RE_Dangling.append(es)
else:
#Same Enzyme name
# -- Same substrate and product including same volume then don't copy
# -- different substrate/product or if sub/prd's volume is different then DUPLICATE the Enzyme
allclean = False
ed = moose.element(es.path.replace(objS, objD))
eDsubname = subprdList(ed, "sub")
eSsubname = subprdList(es, "sub")
hasSamenoofsublen, hasSameS, hasSamevols = same_len_name_vol(
eDsubname, eSsubname)
eDprdname = subprdList(ed, "prd")
eSprdname = subprdList(es, "prd")
hasSamenoofprdlen, hasSameP, hasSamevolp = same_len_name_vol(
eDprdname, eSprdname)
if not all((hasSamenoofsublen, hasSameS, hasSamevols,
hasSamenoofprdlen, hasSameP, hasSamevolp)):
# May be different substrate or product or volume of Sub/prd may be different,
# Duplicating the enzyme
if eSsubname and eSprdname:
allexists, allexistp = False, False
allexists = checkexist(eSsubname, objS, objD)
allexistp = checkexist(eSprdname, objS, objD)
if allexists and allexistp:
es.name = es.name + "_duplicated"
if es.className in ["ZombieEnz", "Enz"]:
edpath = es.parent.path.replace(objS, objD)
enz = moose.copy(es, moose.element(edpath))
moose.connect(enz, 'enz', edpath, 'reac')
if es.className in ["ZombieMMenz", "MMenz"]:
edpath = es.parent.path.replace(objS, objD)
enz = moose.copy(es, moose.element(edpath))
enzinfo = moose.Annotator(enz.path +
'/info')
moose.connect(
moose.element(enz).parent, "nOut",
moose.element(enz), "enzDest")
#moose.connect(moose.element(enz),"enz",moose.element(enz).parent,"reac")
connectObj(enz, eSsubname, "sub", comptD,
war_msg)
connectObj(enz, eSprdname, "prd", comptD,
war_msg)
RE_Duplicated.append(enz)
allclean = True
else:
allclean = False
else:
allclean = True
if not allclean:
# didn't find sub or prd for this enzyme
# -- it may be connected Enzyme cplx
if eSsubname and eSprdname:
RE_Notcopiedyet.append(es)
else:
RE_Dangling.append(es)
return RE_Duplicated, RE_Notcopiedyet, RE_Dangling
def Vclam(delay, width, delay_2, r, c, gain, sat, gain_p, tau_1, tau_2, psat):
pulseg = moose.PulseGen('pulse')
pulseg.firstDelay = delay
pulseg.firstWidth = width
pulseg.secondDelay = delay_2
lp = moose.RC('lowpass')
lp.R = r
lp.C = c
DA = moose.DiffAmp('diffamp')
DA.gain = gain
DA.saturation = sat
pid = moose.PIDController('PID')
pid.gain = gain_p
pid.tauI = tau_1
pid.tauD = tau_2
pid.saturation = psat
comp = moose.element("/proto")
moose.connect(pulseg, "output", lp, "injectIn")
moose.connect(lp, "output", DA, "plusIn")
moose.connect(DA, "output", pid, "commandIn")
moose.connect(comp, "VmOut", pid, "sensedIn")
moose.connect(pid, "output", comp, "injectMsg")
tab = moose.Table("/data/Im")
moose.connect(tab, "requestOut", comp, "getIm")
return tab
def main():
# Simulation information.
simtime = 0.1
simdt = 0.25e-5
plotdt = 0.25e-3
# Cell Compartment infromation
diameter = 30e-6
length = 50e-6
Em = EREST_ACT + 10.613e-3
CM = 1e-6 * 1e4
RM = 1 / (0.3E-3 * 1e4)
RA = 4
# Stimulus information
inj_delay = 20E-3
inj_amp = 1E-9
inj_width = 40E-3
# Create cell
chicken_model = create_swc_model(
root_name='E19',
file_name='E19-cell_filling-caudal.CNG.swc',
RM=RM,
CM=CM,
RA=RA,
ELEAK=Em,
initVM=Em)
soma = moose.element('/E19[0]/soma')
# Create channels
channels_set = create_set_of_channels(channel_settings, VDIVS, VMIN, VMAX)
# Fetch all compartment paths.
moose_paths = []
for comp in moose.wildcardFind(chicken_model.path +
'/#[TYPE=Compartment]'):
moose_paths.append(comp.path)
# Copy all channels to compartments.
for channel_name, channel_obj in channels_set.items():
copy_connect_channel_moose_paths(channel_obj, channel_name,
moose_paths)
# connect pulse gen
pulse_inject = create_pulse_generator(soma,
inj_width,
inj_amp,
delay=inj_delay)
# Output table
soma_v_table = create_output_table(table_element='/output',
table_name='somaVm')
soma_i_table = create_output_table(table_element='/output',
table_name='somaIm')
chicken_dend_table = create_output_table(table_element='/output',
table_name='chkdend')
# Connect output tables
moose.connect(soma_v_table, 'requestOut', soma, 'getVm')
moose.connect(soma_i_table, 'requestOut', pulse_inject, 'getOutputValue')
moose.connect(chicken_dend_table, 'requestOut',
moose.element('/E19[0]/dend_36_0'), 'getVm')
# Set moose simulation clocks
for lable in range(7):
moose.setClock(lable, simdt)
moose.setClock(8, plotdt)
# Run simulation
moose.reinit()
moose.start(simtime)
# Plot output tables.
v_plot = plot_vm_table(simtime,
soma_v_table,
soma_i_table,
chicken_dend_table,
title="soma vs dend with K and Na gbars")
v_plot.legend(['soma_V', 'i', 'dend_V'])
plt.grid(True)
plt.show()
def makeReacs():
# Parameters
volume = 1e-15
CaInitConc = 60e-6
NA = 6.022e23
tauI = 1
tauG = 0.1
model = moose.Neutral('/cells')
compartment = moose.CubeMesh('/cells/compartment')
compartment.volume = volume
# Make pools
Ca = moose.BufPool('/cells/compartment/Ca')
tgtCa = moose.BufPool('/cells/compartment/tgtCa')
m = moose.Pool('/cells/compartment/m')
chan = moose.Pool('/cells/compartment/chan')
# Make Funcs
f1 = moose.Func('/cells/compartment/f1')
f2 = moose.Func('/cells/compartment/f2')
# connect up
moose.connect(f1, 'valueOut', m, 'increment')
moose.connect(f2, 'valueOut', chan, 'increment')
moose.connect(Ca, 'nOut', f1, 'xIn')
moose.connect(tgtCa, 'nOut', f1, 'yIn')
moose.connect(m, 'nOut', f2, 'xIn')
moose.connect(chan, 'nOut', f2, 'yIn')
# Set params
Ca.concInit = CaInitConc
tgtCa.concInit = tgtCaInitConc
m.concInit = 0.0
chan.concInit = 0.0
volscale = 1.0
f1.expr = str(volscale / tauI) + " * (x-y)"
f2.expr = str(volscale / tauG) + " * (x-y)"
#Plotting
channelPlot = makePlot('channelConc', chan, 'Conc', 18)
mPlot = makePlot('mConc', m, 'Conc', 18)
caPlot = makePlot('Ca', Ca, 'Conc', 18)
targetPlot = makePlot('tgtCa', tgtCa, 'Conc', 18)
return (channelPlot, mPlot, caPlot)
def _setup_network(self):
## Set up the neurons without connections
ExcInhNetBase._setup_network(self)
## Now, add in the connections...
## Each pre-synaptic spike cause Vm of post-neuron to rise by
## synaptic weight in one time step i.e. delta-fn synapse.
## Since LIF neuron is derived from Compartment class,
## conductance-based synapses (SynChan class) can also be used.
## E to E synapses can be plastic
## Two ways to do this:
## 1) Each LIF neuron has one incoming postsynaptic SynHandler,
## which collects the activation from all presynaptic neurons,
## but then a common Ca pool is used.
## 2) Each LIF neuron has multiple postsyanptic SynHandlers,
## one for each pre-synaptic neuron, i.e. one per synapse,
## then each synapse has a different Ca pool.
## Here we go with option 2) as per Higgins et al 2014 (Brunel private email)
## separate SynHandler per EE synapse, thus NmaxExc*excC
if CaPlasticity:
self.synsEE = moose.GraupnerBrunel2012CaPlasticitySynHandler( \
'/network/synsEE', self.NmaxExc*self.excC )
else:
self.synsEE = moose.SimpleSynHandler( \
'/network/synsEE', self.NmaxExc*self.excC )
moose.useClock(0, '/network/synsEE', 'process')
## I to E synapses are not plastic
self.synsIE = moose.SimpleSynHandler('/network/synsIE', self.NmaxExc)
## all synapses to I neurons are not plastic
self.synsI = moose.SimpleSynHandler('/network/synsI',
self.N - self.NmaxExc)
## connect all SynHandlers to their respective neurons
for i in range(self.NmaxExc):
moose.connect( self.synsIE.vec[i], 'activationOut', \
self.network.vec[i], 'activation' )
for i in range(self.NmaxExc, self.N):
moose.connect( self.synsI.vec[i-self.NmaxExc], 'activationOut', \
self.network.vec[i], 'activation' )
## Connections from some Exc/Inh neurons to each Exc neuron
for i in range(0, self.NmaxExc):
self.synsIE.vec[i].numSynapses = self.incC - self.excC
## Connections from some Exc neurons to each Exc neuron
## draw excC number of neuron indices out of NmaxExc neurons
preIdxs = random.sample(range(self.NmaxExc), self.excC)
## connect these presynaptically to i-th post-synaptic neuron
for synnum, preIdx in enumerate(preIdxs):
synidx = i * self.excC + synnum
synHand = self.synsEE.vec[synidx]
## connect each synhandler to the post-synaptic neuron
moose.connect( synHand, 'activationOut', \
self.network.vec[i], 'activation' )
## important to set numSynapses = 1 for each synHandler,
## doesn't create synapses if you set the full array of SynHandlers
synHand.numSynapses = 1
synij = synHand.synapse[0]
connectExcId = moose.connect( self.network.vec[preIdx], \
'spikeOut', synij, 'addSpike')
synij.delay = syndelay
if CaPlasticity:
## set parameters for the Ca Plasticity SynHandler
## have to be set for each SynHandler
## doesn't set for full array at a time
synHand.CaInit = 0.0
synHand.tauCa = tauCa
synHand.tauSyn = tauSyn
synHand.CaPre = CaPre
synHand.CaPost = CaPost
synHand.delayD = delayD
synHand.thetaD = thetaD
synHand.thetaP = thetaP
synHand.gammaD = gammaD
synHand.gammaP = gammaP
synHand.weightMax = 1.0 # bounds on the weight
synHand.weightMin = 0.0
synHand.weightScale = \
self.J*2.0 # 0.2 mV, weight*weightScale is activation
# typically weight <~ 0.5, so activation <~ J
synHand.noisy = noisy
synHand.noiseSD = noiseSD
synHand.bistable = bistable
moose.connect( self.network.vec[i], \
'spikeOut', synHand, 'addPostSpike')
synij.weight = eqWeight # activation = weight*weightScale
# weightScale = 2*J
# weight <~ 0.5
## Randomly set 5% of them to be 1.0
if np.random.uniform() < 0.05:
synij.weight = 1.0
else:
synij.weight = self.J # no weightScale here, activation = weight
## Connections from some Inh neurons to each Exc neuron
## draw inhC=incC-excC number of neuron indices out of inhibitory neurons
preIdxs = random.sample(range(self.NmaxExc, self.N),
self.incC - self.excC)
## connect these presynaptically to i-th post-synaptic neuron
for synnum, preIdx in enumerate(preIdxs):
synij = self.synsIE.vec[i].synapse[synnum]
connectInhId = moose.connect( self.network.vec[preIdx], \
'spikeOut', synij, 'addSpike')
synij.delay = syndelay
synij.weight = -self.scaleI * self.J # activation = weight
## Connections from some Exc/Inh neurons to each Inh neuron
for i in range(self.N - self.NmaxExc):
## each neuron has incC number of synapses
self.synsI.vec[i].numSynapses = self.incC
## draw excC number of neuron indices out of NmaxExc neurons
preIdxs = random.sample(range(self.NmaxExc), self.excC)
## connect these presynaptically to i-th post-synaptic neuron
for synnum, preIdx in enumerate(preIdxs):
synij = self.synsI.vec[i].synapse[synnum]
connectExcId = moose.connect( self.network.vec[preIdx], \
'spikeOut', synij, 'addSpike')
synij.delay = syndelay
synij.weight = self.J # activation = weight
## draw inhC=incC-excC number of neuron indices out of inhibitory neurons
preIdxs = random.sample(range(self.NmaxExc, self.N),
self.incC - self.excC)
## connect these presynaptically to i-th post-synaptic neuron
for synnum, preIdx in enumerate(preIdxs):
synij = self.synsI.vec[i].synapse[self.excC + synnum]
connectInhId = moose.connect( self.network.vec[preIdx], \
'spikeOut', synij, 'addSpike')
synij.delay = syndelay
synij.weight = -self.scaleI * self.J # activation = weight
moose.useClock(0, '/network/synsIE', 'process')
moose.useClock(0, '/network/synsI', 'process')
def makeModel():
# create container for model
model = moose.Neutral('model')
compt0 = moose.CubeMesh('/model/compt0')
compt0.volume = 1e-18
compt1 = moose.CubeMesh('/model/compt1')
compt1.volume = 1e-19
compt2 = moose.CubeMesh('/model/compt2')
compt2.volume = 1e-20
# Position containers so that they abut each other, with
# compt1 in the middle.
side = compt1.dy
compt0.y1 += side
compt0.y0 += side
compt2.x1 += side
compt2.x0 += side
print(('Volumes = ', compt0.volume, compt1.volume, compt2.volume))
# create molecules and reactions
a = moose.Pool('/model/compt0/a')
b = moose.Pool('/model/compt1/b')
c = moose.Pool('/model/compt2/c')
reac0 = moose.Reac('/model/compt1/reac0')
reac1 = moose.Reac('/model/compt1/reac1')
# connect them up for reactions
moose.connect(reac0, 'sub', a, 'reac')
moose.connect(reac0, 'prd', b, 'reac')
moose.connect(reac1, 'sub', b, 'reac')
moose.connect(reac1, 'prd', c, 'reac')
# Assign parameters
a.concInit = 1
b.concInit = 12.1
c.concInit = 1
reac0.Kf = 0.1
reac0.Kb = 0.1
reac1.Kf = 0.1
reac1.Kb = 0.1
# Create the output tables
graphs = moose.Neutral('/model/graphs')
outputA = moose.Table2('/model/graphs/concA')
outputB = moose.Table2('/model/graphs/concB')
outputC = moose.Table2('/model/graphs/concC')
# connect up the tables
moose.connect(outputA, 'requestOut', a, 'getConc')
moose.connect(outputB, 'requestOut', b, 'getConc')
moose.connect(outputC, 'requestOut', c, 'getConc')
# Build the solvers. No need for diffusion in this version.
ksolve0 = moose.Gsolve('/model/compt0/ksolve0')
ksolve1 = moose.Gsolve('/model/compt1/ksolve1')
ksolve2 = moose.Gsolve('/model/compt2/ksolve2')
stoich0 = moose.Stoich('/model/compt0/stoich0')
stoich1 = moose.Stoich('/model/compt1/stoich1')
stoich2 = moose.Stoich('/model/compt2/stoich2')
# Configure solvers
stoich0.compartment = compt0
stoich1.compartment = compt1
stoich2.compartment = compt2
stoich0.ksolve = ksolve0
stoich1.ksolve = ksolve1
stoich2.ksolve = ksolve2
stoich0.path = '/model/compt0/#'
stoich1.path = '/model/compt1/#'
stoich2.path = '/model/compt2/#'
stoich1.buildXreacs(stoich0)
stoich1.buildXreacs(stoich2)
stoich0.filterXreacs()
stoich1.filterXreacs()
stoich2.filterXreacs()
def test_ksolver_parallel(nthreads=4):
"""
This example implements a reaction-diffusion like system which is
bistable and propagates losslessly. It is based on the NEURON example
rxdrun.py, but incorporates more compartments and runs for a longer time.
The system is implemented as a hybrid of a reaction and a function which
sets its rates. Please see rxdFuncDiffusion.py for a variant that uses
just a function object to set up the system.
"""
dt = 0.1
# define the geometry
compt = moose.CylMesh('/cylinder')
compt.r0 = compt.r1 = 1
# compt.diffLength = 1e-6
compt.x1 = 1e-2
assert compt.numDiffCompts == int(
compt.x1 / compt.diffLength), (compt.numDiffCompts,
compt.x1 / compt.diffLength)
print('No of compartment %d' % compt.numDiffCompts)
#define the molecule. Its geometry is defined by its parent volume, cylinder
c = moose.Pool('/cylinder/pool')
c.diffConst = 1 # define diffusion constant
# There is an implicit reaction substrate/product. MOOSE makes it explicit.
buf = moose.BufPool('/cylinder/buf')
buf.nInit = 1
# The reaction is something entirely peculiar, not a chemical thing.
reaction = moose.Reac('/cylinder/reac')
reaction.Kb = 0
# so here we set up a function calculation to do the same thing.
func = moose.Function('/cylinder/reac/func')
func.expr = "(1 - x0) * (0.3 - x0)"
func.x.num = 1 #specify number of input variables.
#Connect the reaction to the pools
moose.connect(reaction, 'sub', c, 'reac')
moose.connect(reaction, 'prd', buf, 'reac')
#Connect the function to the reaction
moose.connect(func, 'valueOut', reaction, 'setNumKf')
#Connect the molecules to the func
moose.connect(c, 'nOut', func.x[0], 'input')
#Set up solvers
ksolve = moose.Ksolve('/cylinder/ksolve')
ksolve.numThreads = nthreads
dsolve = moose.Dsolve('/cylinder/dsolve')
stoich = moose.Stoich('/cylinder/stoich')
stoich.compartment = compt
stoich.ksolve = ksolve
stoich.dsolve = dsolve
stoich.path = '/cylinder/##'
for i in range(10, 18):
moose.setClock(i, dt)
#initialize
x = np.arange(0, compt.x1, compt.diffLength)
c.vec.nInit = [(q < 0.2 * compt.x1) for q in x]
expected = [(0.2, 0.40000000000000013),
(2.6704795776286974e-07, 1.2678976830753021e-17),
(8.167639617309419e-14, 3.8777269301457245e-24),
(2.498062905267963e-20, 1.1860363878961374e-30),
(7.64029581501609e-27, 3.6273808003690943e-37)]
# Run and plot it.
moose.reinit()
updateDt = 50
runtime = updateDt * 4
yvec = c.vec.n
u1, m1 = np.mean(yvec), np.std(yvec)
print(u1, m1)
assert np.isclose((u1, m1), expected[0], atol=1e-5).all(), expected[0]
t1 = time.time()
for i, t in enumerate(range(0, runtime - 1, updateDt)):
moose.start(updateDt)
yvec = c.vec.n
u1, m1 = np.mean(yvec), np.std(yvec)
print(u1, m1)
np.isclose((u1, m1), expected[i + 1], atol=1e-5).all(), expected[i + 1]
return time.time() - t1
def main():
"""
This example implements a reaction-diffusion like system which is
bistable and propagates losslessly. It is based on the NEURON example
rxdrun.py, but incorporates more compartments and runs for a longer time.
The system is implemented in a function rather than as a proper system
of chemical reactions. Please see rxdReacDiffusion.py for a variant that
uses a reaction plus a function object to control its rates.
"""
print(('[DEBUG] Using moose from %s' % moose.__file__))
dt = 0.1
# define the geometry
compt = moose.CylMesh('/cylinder')
compt.r0 = compt.r1 = 1
compt.x1 = 100
compt.diffLength = 0.2
assert (compt.numDiffCompts == compt.x1 / compt.diffLength)
#define the molecule. Its geometry is defined by its parent volume, cylinder
c = moose.Pool('/cylinder/pool')
c.diffConst = 1 # define diffusion constant
# Here we set up a function calculation
func = moose.Function('/cylinder/pool/func')
func.expr = "-x0 * (0.3 - x0) * (1 - x0)"
func.x.num = 1 #specify number of input variables.
#Connect the molecules to the func
moose.connect(c, 'nOut', func.x[0], 'input')
#Connect the function to the pool
moose.connect(func, 'valueOut', c, 'increment')
#Set up solvers
ksolve = moose.Ksolve('/cylinder/ksolve')
dsolve = moose.Dsolve('/cylinder/dsolve')
stoich = moose.Stoich('/cylinder/stoich')
stoich.ksolve = ksolve
stoich.dsolve = dsolve
stoich.compartment = compt
stoich.path = '/cylinder/##'
#initialize
x = numpy.arange(0, compt.x1, compt.diffLength)
c.vec.nInit = [(q < 0.2 * compt.x1) for q in x]
# Run and plot it.
moose.reinit()
updateDt = 50
runtime = updateDt * 4
plt = pylab.plot(x, c.vec.n, label='t = 0 ')
t1 = time.time()
for t in range(0, runtime - 1, updateDt):
moose.start(updateDt)
plt = pylab.plot(x, c.vec.n, label='t = ' + str(t + updateDt))
print(("Time = %f " % (time.time() - t1)))
print(("Time = %s " % (time.time() - t1)))
pylab.ylim(0, 1.05)
pylab.legend()
pylab.show()
def buildPlots( rdes ):
numPlots = 10
caPsd = moose.vec( '/model/chem/psd/Ca' )
caHead = moose.vec( '/model/chem/spine/Ca' )
psdR = moose.vec( '/model/chem/psd/tot_PSD_R' )
numSpines = rdes.spineCompt.mesh.num
assert( 2 * numSpines == len( rdes.spineComptElist ) )
if not moose.exists( '/graphs' ):
moose.Neutral( '/graphs' )
assert( len( caPsd ) == numSpines )
assert( len( caHead ) == numSpines )
if numSpines < numPlots:
caPsdTab = moose.Table2( '/graphs/caPsdTab', numSpines ).vec
caHeadTab = moose.Table2( '/graphs/caHeadTab', numSpines ).vec
psdRtab = moose.Table2( '/graphs/psdRtab', numSpines ).vec
for i in range( numSpines ):
moose.connect( caPsdTab[i], 'requestOut', caPsd[i], 'getConc' )
moose.connect( caHeadTab[i], 'requestOut', caHead[i], 'getConc')
moose.connect( psdRtab[i], 'requestOut', psdR[i], 'getN' )
else:
caPsdTab = moose.Table2( '/graphs/caPsdTab', numPlots ).vec
caHeadTab = moose.Table2( '/graphs/caHeadTab', numPlots ).vec
psdRtab = moose.Table2( '/graphs/psdRtab', numPlots ).vec
dx = numSpines / numPlots
for i in range( numPlots ):
moose.connect( caPsdTab[i], 'requestOut', caPsd[i*dx], 'getConc' )
moose.connect( caHeadTab[i], 'requestOut', caHead[i*dx], 'getConc' )
moose.connect( psdRtab[i], 'requestOut', psdR[i*dx], 'getN' )
vtab = moose.Table( '/graphs/vtab' )
moose.connect( vtab, 'requestOut', rdes.soma, 'getVm' )
eSpineCaTab = moose.Table( '/graphs/eSpineCaTab' )
path = rdes.spineComptElist[1].path + "/Ca_conc"
moose.connect( eSpineCaTab, 'requestOut', path, 'getCa' )
eSpineVmTab = moose.Table( '/graphs/eSpineVmTab' )
moose.connect( eSpineVmTab, 'requestOut', rdes.spineComptElist[1], 'getVm' )
eSpineGkTab = moose.Table( '/graphs/eSpineGkTab' )
path = rdes.spineComptElist[1].path + "/NMDA"
moose.connect( eSpineGkTab, 'requestOut', path, 'getGk' )
def vclamp_demo(simtime=50.0, dt=1e-2):
## It is good practice to modularize test elements inside a
## container
container = moose.Neutral('/vClampDemo')
## Create a compartment with properties of a squid giant axon
comp = SquidAxon('/vClampDemo/axon')
# Create and setup the voltage clamp object
clamp = moose.VClamp('/vClampDemo/vclamp')
## The defaults should work fine
# clamp.mode = 2
# clamp.tau = 10*dt
# clamp.ti = dt
# clamp.td = 0
# clamp.gain = comp.Cm / dt
## Setup command voltage time course
command = moose.PulseGen('/vClampDemo/command')
command.delay[0] = 10.0
command.width[0] = 20.0
command.level[0] = 50.0
command.delay[1] = 1e9
moose.connect(command, 'output', clamp, 'commandIn')
## Connect the Voltage Clamp to the compartemnt
moose.connect(clamp, 'currentOut', comp, 'injectMsg')
moose.connect(comp, 'VmOut', clamp, 'sensedIn')
## setup stimulus recroding - this is the command pulse
stimtab = moose.Table('/vClampDemo/vclamp_command')
moose.connect(stimtab, 'requestOut', command, 'getOutputValue')
## Set up Vm recording
vmtab = moose.Table('/vClampDemo/vclamp_Vm')
moose.connect(vmtab, 'requestOut', comp, 'getVm')
## setup command potential recording - this is the filtered input
## to PID controller
commandtab = moose.Table('/vClampDemo/vclamp_filteredcommand')
moose.connect(commandtab, 'requestOut', clamp, 'getCommand')
## setup current recording
Imtab = moose.Table('/vClampDemo/vclamp_inject')
moose.connect(Imtab, 'requestOut', clamp, 'getCurrent')
# Scheduling
moose.setClock(0, dt)
moose.setClock(1, dt)
moose.setClock(2, dt)
moose.setClock(3, dt)
moose.useClock(0, '%s/##[TYPE=Compartment]' % (container.path), 'init')
moose.useClock(0, '%s/##[TYPE=PulseGen]' % (container.path), 'process')
moose.useClock(1, '%s/##[TYPE=Compartment]' % (container.path), 'process')
moose.useClock(2, '%s/##[TYPE=HHChannel]' % (container.path), 'process')
moose.useClock(2, '%s/##[TYPE=VClamp]' % (container.path), 'process')
moose.useClock(3, '%s/##[TYPE=Table]' % (container.path), 'process')
moose.reinit()
print 'RC filter in VClamp:: tau:', clamp.tau
print 'PID controller in VClamp:: ti:', clamp.ti, 'td:', clamp.td, 'gain:', clamp.gain
moose.start(simtime)
print 'Finished simulation for %g seconds' % (simtime)
tseries = linspace(0, simtime, len(vmtab.vector))
subplot(211)
title('Membrane potential and clamp voltage')
plot(tseries, vmtab.vector, 'g-', label='Vm (mV)')
plot(tseries, commandtab.vector, 'b-', label='Filtered command (mV)')
plot(tseries, stimtab.vector, 'r-', label='Command (mV)')
xlabel('Time (ms)')
ylabel('Voltage (mV)')
legend()
# print len(commandtab.vector)
subplot(212)
title('Current through clamp circuit')
# plot(tseries, stimtab.vector, label='stimulus (uA)')
plot(tseries, Imtab.vector, label='injected current (uA)')
xlabel('Time (ms)')
ylabel('Current (uA)')
legend()
show()
def makeNeuroMeshModel():
diffLength = 20e-6 # But we only want diffusion over part of the model.
numSyn = 13
elec = loadElec()
synInput = moose.SpikeGen('/model/elec/synInput')
synInput.refractT = 47e-3
synInput.threshold = -1.0
synInput.edgeTriggered = 0
synInput.Vm(0)
synInput.refractT = 47e-3
for i in range(numSyn):
name = '/model/elec/spine_head_14_' + str(i + 1)
r = moose.element(name + '/glu')
r.synapse.num = 1
syn = moose.element(r.path + '/synapse')
moose.connect(synInput, 'spikeOut', syn, 'addSpike', 'Single')
syn.weight = 0.2 * i * (numSyn - 1 - i)
syn.delay = i * 1.0e-3
neuroCompt = moose.NeuroMesh('/model/neuroMesh')
#print 'neuroMeshvolume = ', neuroCompt.mesh[0].volume
neuroCompt.separateSpines = 1
neuroCompt.diffLength = diffLength
neuroCompt.geometryPolicy = 'cylinder'
spineCompt = moose.SpineMesh('/model/spineMesh')
#print 'spineMeshvolume = ', spineCompt.mesh[0].volume
moose.connect(neuroCompt, 'spineListOut', spineCompt, 'spineList',
'OneToOne')
psdCompt = moose.PsdMesh('/model/psdMesh')
#print 'psdMeshvolume = ', psdCompt.mesh[0].volume
moose.connect(neuroCompt, 'psdListOut', psdCompt, 'psdList', 'OneToOne')
loadChem(neuroCompt, spineCompt, psdCompt)
# Put in the solvers, see how they fare.
nmksolve = moose.GslStoich('/model/chem/neuroMesh/ksolve')
nmksolve.path = '/model/chem/neuroMesh/##'
nmksolve.compartment = moose.element('/model/chem/neuroMesh')
nmksolve.method = 'rk5'
nm = moose.element('/model/chem/neuroMesh/mesh')
moose.connect(nm, 'remesh', nmksolve, 'remesh')
#print "neuron: nv=", nmksolve.numLocalVoxels, ", nav=", nmksolve.numAllVoxels, nmksolve.numVarPools, nmksolve.numAllPools
#print 'setting up smksolve'
smksolve = moose.GslStoich('/model/chem/spineMesh/ksolve')
smksolve.path = '/model/chem/spineMesh/##'
smksolve.compartment = moose.element('/model/chem/spineMesh')
smksolve.method = 'rk5'
sm = moose.element('/model/chem/spineMesh/mesh')
moose.connect(sm, 'remesh', smksolve, 'remesh')
#print "spine: nv=", smksolve.numLocalVoxels, ", nav=", smksolve.numAllVoxels, smksolve.numVarPools, smksolve.numAllPools
#
#print 'setting up pmksolve'
pmksolve = moose.GslStoich('/model/chem/psdMesh/ksolve')
pmksolve.path = '/model/chem/psdMesh/##'
pmksolve.compartment = moose.element('/model/chem/psdMesh')
pmksolve.method = 'rk5'
pm = moose.element('/model/chem/psdMesh/mesh')
moose.connect(pm, 'remesh', pmksolve, 'remesh')
#print "psd: nv=", pmksolve.numLocalVoxels, ", nav=", pmksolve.numAllVoxels, pmksolve.numVarPools, pmksolve.numAllPools
#
print 'neuroMeshvolume = ', neuroCompt.mesh[0].volume
#print 'Assigning the cell model'
# Now to set up the model.
#neuroCompt.cell = elec
neuroCompt.cellPortion(
elec,
'/model/elec/lat_14_#,/model/elec/spine_neck#,/model/elec/spine_head#')
"""
ns = neuroCompt.numSegments
#assert( ns == 11 ) # dend, 5x (shaft+head)
ndc = neuroCompt.numDiffCompts
#print 'numDiffCompts = ', ndc
assert( ndc == 145 )
ndc = neuroCompt.mesh.num
#print 'NeuroMeshNum = ', ndc
assert( ndc == 145 )
sdc = spineCompt.mesh.num
#print 'SpineMeshNum = ', sdc
assert( sdc == 13 )
pdc = psdCompt.mesh.num
#print 'PsdMeshNum = ', pdc
assert( pdc == 13 )
"""
mesh = moose.vec('/model/chem/neuroMesh/mesh')
#for i in range( ndc ):
# print 's[', i, '] = ', mesh[i].volume
mesh2 = moose.vec('/model/chem/spineMesh/mesh')
# for i in range( sdc ):
# print 's[', i, '] = ', mesh2[i].volume
#print 'numPSD = ', moose.element( '/model/chem/psdMesh/mesh' ).localNumField
mesh = moose.vec('/model/chem/psdMesh/mesh')
#print 'psd mesh.volume = ', mesh.volume
#for i in range( pdc ):
# print 's[', i, '] = ', mesh[i].volume
#
# We need to use the spine solver as the master for the purposes of
# these calculations. This will handle the diffusion calculations
# between head and dendrite, and between head and PSD.
smksolve.addJunction(nmksolve)
#print "spine: nv=", smksolve.numLocalVoxels, ", nav=", smksolve.numAllVoxels, smksolve.numVarPools, smksolve.numAllPools
smksolve.addJunction(pmksolve)
#print "psd: nv=", pmksolve.numLocalVoxels, ", nav=", pmksolve.numAllVoxels, pmksolve.numVarPools, pmksolve.numAllPools
ndc = neuroCompt.numDiffCompts
#print 'numDiffCompts = ', ndc
assert (ndc == 13)
ndc = neuroCompt.mesh.num
#print 'NeuroMeshNum = ', ndc
assert (ndc == 13)
sdc = spineCompt.mesh.num
#print 'SpineMeshNum = ', sdc
assert (sdc == 13)
pdc = psdCompt.mesh.num
#print 'PsdMeshNum = ', pdc
assert (pdc == 13)
"""
print 'neuroCompt'
for i in range( ndc ):
print i, neuroCompt.stencilIndex[i]
print i, neuroCompt.stencilRate[i]
print 'spineCompt'
for i in range( sdc * 3 ):
print i, spineCompt.stencilIndex[i]
print i, spineCompt.stencilRate[i]
print 'psdCompt'
for i in range( pdc ):
print i, psdCompt.stencilIndex[i]
print i, psdCompt.stencilRate[i]
print 'Spine parents:'
pavoxel = spineCompt.parentVoxel
for i in range( sdc ):
print i, pavoxel[i]
"""
# oddly, numLocalFields does not work.
#moose.le( '/model/chem/neuroMesh' )
ca = moose.element('/model/chem/neuroMesh/DEND/Ca')
assert (ca.lastDimension == ndc)
"""
CaNpsd = moose.vec( '/model/chem/psdMesh/PSD/PP1_PSD/CaN' )
print 'numCaN in PSD = ', CaNpsd.nInit, ', vol = ', CaNpsd.volume
CaNspine = moose.vec( '/model/chem/spineMesh/SPINE/CaN_BULK/CaN' )
print 'numCaN in spine = ', CaNspine.nInit, ', vol = ', CaNspine.volume
"""
# set up adaptors
aCa = moose.Adaptor('/model/chem/psdMesh/adaptCa', pdc)
adaptCa = moose.vec('/model/chem/psdMesh/adaptCa')
chemCa = moose.vec('/model/chem/psdMesh/PSD/Ca')
assert (len(adaptCa) == pdc)
assert (len(chemCa) == pdc)
for i in range(pdc):
path = '/model/elec/spine_head_14_' + str(i + 1) + '/NMDA_Ca_conc'
elecCa = moose.element(path)
moose.connect(elecCa, 'concOut', adaptCa[i], 'input', 'Single')
moose.connect(adaptCa, 'outputSrc', chemCa, 'setConc', 'OneToOne')
adaptCa.inputOffset = 0.0 #
adaptCa.outputOffset = 80e-6 # 80 nM offset in chem.
adaptCa.scale = 1e-5 # 520 to 0.0052 mM
def writeEnz(modelpath, f, sceneitems):
error = ""
enzList = moose.wildcardFind(modelpath + '/##[0][ISA=EnzBase]')
for enz in enzList:
if findCompartment(enz) == moose.element('/'):
error = error + " \n " + enz.path + " doesn't have compartment ignored to write to genesis"
else:
x = random.randrange(0, 10)
y = random.randrange(0, 10)
textcolor = ""
color = ""
k1 = 0
k2 = 0
k3 = 0
nInit = 0
concInit = 0
n = 0
conc = 0
if len(moose.element(enz).neighbors['enzDest']) == 1:
enzParent = moose.element(
moose.element(enz).neighbors['enzDest'][0])
if not enzParent.isA['PoolBase']:
print(" raise exception enz doesn't have pool as parent %s",
moose.element(enz).path)
return False
else:
vol = enzParent.volume * NA * 1e-3
isMichaelisMenten = 0
enzClass = enz.className
if (enzClass == "ZombieMMenz" or enzClass == "MMenz"):
k1 = enz.numKm
k3 = enz.kcat
k2 = 4.0 * k3
k1 = (k2 + k3) / k1
isMichaelisMenten = 1
elif (enzClass == "ZombieEnz" or enzClass == "Enz"):
k1 = enz.k1
k2 = enz.k2
k3 = enz.k3
if enz.neighbors['cplx']:
cplx = enz.neighbors['cplx'][0]
nInit = cplx.nInit
else:
cplx = moose.Pool(enz.path + "/cplx")
moose.Annotator(cplx.path + '/info')
moose.connect(enz, 'cplx', cplx, 'reac')
nInit = cplx.nInit
einfo = enz.path + '/info'
if moose.exists(einfo):
x = sceneitems[enz]['x']
y = sceneitems[enz]['y']
color = moose.Annotator(einfo).getField('color')
color = getColorCheck(color, GENESIS_COLOR_SEQUENCE)
textcolor = moose.Annotator(einfo).getField('textColor')
textcolor = getColorCheck(textcolor,
GENESIS_COLOR_SEQUENCE)
else:
error = error + "\n x and y co-ordinates are not specified for `" + enz.name + "` zero will be assigned \n "
if color == "" or color == " ":
color = getRandomColor()
if textcolor == "" or textcolor == " ":
textcolor = getRandomColor()
f.write("simundump kenz /kinetics/" + trimPath(enz) + " " +
str(int(0)) + " " + str(concInit) + " " + str(conc) +
" " + str(nInit) + " " + str(n) + " " + str(vol) +
" " + str(k1) + " " + str(k2) + " " + str(k3) + " " +
str(0) + " " + str(isMichaelisMenten) + " " + "\"\"" +
" " + str(textcolor) + " " + str(color) + " \"\"" +
" " + str(int(x)) + " " + str(int(y)) + " " +
str(int(0)) + "\n")
return enzList, error
def makeModel():
# create container for model
num = 1 # number of compartments
model = moose.Neutral( '/model' )
compartment = moose.CylMesh( '/model/compartment' )
compartment.x1 = 1.0e-6 # Set it to a 1 micron single-voxel cylinder
# create molecules and reactions
u = moose.Pool( '/model/compartment/u' )
#####################################################################
# Put in endo compartment. Add molecule s
endo = moose.EndoMesh( '/model/endo' )
endo.isMembraneBound = True
endo.surround = compartment
rXfer = moose.Reac( '/model/endo/rXfer' )
et = moose.Pool( '/model/endo/t' )
es = moose.Pool( '/model/endo/s' )
#####################################################################
moose.connect( rXfer, 'sub', u, 'reac' )
moose.connect( rXfer, 'sub', et, 'reac' )
moose.connect( rXfer, 'prd', es, 'reac' )
u.concInit = 1.0
et.concInit = 1.0
#####################################################################
# [u0] = 1 in compt, [t0] = 1 in endo, [s0] = 0
# [u] + [s]/8 = [u0] ; [t] + [s] = [t0]; nu + ns = nu0, nt + ns = nt0
# At equil, numKf*nu*nt = numKb*ns
# Express all # in terms of ns.
# nu = nu0-ns; nt = nt0-ns Also, nu0 = 8*nt0
# So numKf*(nu0-ns)*(nt0-ns) = numKb*ns
# Target level is nt = ns = nt0/2
# So numKf*( 8nt0 - nt0/2)*nt0/2 = numKb*nt0/2
# So 7.5*nt0 = numKb/numKf
rXfer.numKb = 0.1
rXfer.numKf = 0.1/(7.5 * et.nInit)
#print( "Rates = {}, {}".format( rXfer.Kf, rXfer.Kb ))
#####################################################################
fixXreacs.fixXreacs( '/model' )
#fixXreacs.restoreXreacs( '/model' )
#fixXreacs.fixXreacs( '/model' )
#####################################################################
# Make solvers
ksolve = moose.Ksolve( '/model/compartment/ksolve' )
dsolve = moose.Dsolve( '/model/compartment/dsolve' )
eksolve = moose.Ksolve( '/model/endo/ksolve' )
edsolve = moose.Dsolve( '/model/endo/dsolve' )
stoich = moose.Stoich( '/model/compartment/stoich' )
stoich.compartment = compartment
stoich.ksolve = ksolve
stoich.dsolve = dsolve
stoich.path = "/model/compartment/##"
assert( dsolve.numPools == 1 )
estoich = moose.Stoich( '/model/endo/stoich' )
estoich.compartment = endo
estoich.ksolve = eksolve
estoich.dsolve = edsolve
estoich.path = "/model/endo/##"
assert( edsolve.numPools == 3 )
edsolve.buildMeshJunctions( dsolve )
plot1 = moose.Table2( '/model/plot1' )
plot2 = moose.Table2( '/model/plot2' )
plot3 = moose.Table2( '/model/plot3' )
moose.connect( '/model/plot1', 'requestOut', u, 'getN' )
moose.connect( '/model/plot2', 'requestOut', et, 'getN' )
moose.connect( '/model/plot3', 'requestOut', es, 'getN' )
plot4 = moose.Table2( '/model/plot4' )
plot5 = moose.Table2( '/model/plot5' )
plot6 = moose.Table2( '/model/plot6' )
moose.connect( '/model/plot4', 'requestOut', u, 'getConc' )
moose.connect( '/model/plot5', 'requestOut', et, 'getConc' )
moose.connect( '/model/plot6', 'requestOut', es, 'getConc' )
def main():
"""
In this example we walk through creation of a vector of IntFire
elements and setting up synaptic connection between them. Synapse on
IntFire elements is an example of ElementField - elements that do not
exist on their own, but only as part of another element. This example
also illustrates various operations on `vec` objects and
ElementFields.
"""
size = 1024 # number of IntFire objects in a vec
delayMin = 0
delayMax = 4
Vmax = 1.0
thresh = 0.8
refractoryPeriod = 0.4
connectionProbability = 0.1
weightMax = 0.5
# The above sets the constants we shall use in this example. Now we create a vector of IntFire elements of size `size`.
net = moose.IntFire('/network', size)
# This creates a `vec` of `IntFire` elements of size 1024 and returns the first `element`, i.e. "/network[0]".
net = moose.element('/network[0]')
# You need now to provide synaptic input to the network
synh = moose.SimpleSynHandler('/network/synh', size)
# These need to be connected to the nodes in the network
moose.connect(synh, 'activationOut', net, 'activation', 'OneToOne')
# You can access the underlying vector of elements using the `vec` field on any element. This is very useful for vectorized field access:
net.vec.Vm = [thresh / 2.0] * size
# The right part of the assigment creates a Python list of length `size` with each element set to `thresh/2.0`, which is 0.4. You can index into the `vec` to access individual elements' field:
print((net.vec[1].Vm))
# `SimpleSynHandler` class has an `ElementField` called `synapse`. It is just like a `vec` above in terms of field access, but by default its size is 0.
print((len(synh.synapse)))
# To actually create synapses, you can explicitly assign the `num` field of this, or set the `numSynapses` field of the `IntFire` element. There are some functions which can implicitly set the size of the `ElementField`.
synh.numSynapses = 3
print((len(synh.synapse)))
synh.synapse.num = 4
print((len(synh.synapse)))
# Now you can index into `net.synapse` as if it was an array.
print(('Before:', synh.synapse[0].delay))
synh.synapse[0].delay = 1.0
print(('After:', synh.synapse[0].delay))
# You could do the same vectorized assignment as with `vec` directly:
synh.synapse.weight = [0.2] * len(synh.synapse)
print((synh.synapse.weight))
# You can create the synapses and assign the weights and delays using loops:
for syn in synh.vec:
syn.synapse.num = random.randint(1, 10)
# create synapse fields with random size between 1 and 10, end points included
# Below is one (inefficient) way of setting the individual weights of the elements in 'synapse'
for ii in range(len(syn.synapse)):
syn.synapse[ii].weight = random.random() * weightMax
# This is a more efficient way - rhs of `=` is list comprehension in Python and rather fast
syn.synapse.delay = [
delayMin + random.random() * delayMax for ii in range(len(syn.synapse))
]
# An even faster way will be to use numpy.random.rand(size) which produces array of random numbers uniformly distributed between 0 and 1
syn.synapse.delay = delayMin + nprand.rand(len(syn.synapse)) * delayMax
# Now display the results, we use slice notation on `vec` to show the values of delay and weight for the first 5 elements in `/network`
for syn in synh.vec[:5]:
print(('Delays for synapses on ', syn.path, ':', syn.synapse.delay))
print(('Weights for synapses on ', syn.path, ':', syn.synapse.weight))
def make_model():
sinePeriod = 50
maxFiringRate = 10
refractT = 0.05
for i in range(20):
moose.setClock(i, dt)
############### Create objects ###############
stim = moose.StimulusTable('stim')
spike = moose.RandSpike('spike')
syn = moose.SimpleSynHandler('syn')
fire = moose.IntFire('fire')
stats1 = moose.SpikeStats('stats1')
stats2 = moose.Stats('stats2')
plots = moose.Table('plots')
plot1 = moose.Table('plot1')
plot2 = moose.Table('plot2')
plotf = moose.Table('plotf')
############### Set up parameters ###############
stim.vector = [
maxFiringRate * numpy.sin(x * 2 * numpy.pi / sinePeriod)
for x in range(sinePeriod)
]
stim.startTime = 0
stim.stopTime = sinePeriod
stim.loopTime = sinePeriod
stim.stepSize = 0
stim.stepPosition = 0
stim.doLoop = 1
spike.refractT = refractT
syn.synapse.num = 1
syn.synapse[0].weight = 1
syn.synapse[0].delay = 0
fire.thresh = 100 # Don't want it to spike, just to integrate
fire.tau = 1.0 / maxFiringRate
stats1.windowLength = int(1 / dt)
stats2.windowLength = int(1 / dt)
############### Connect up circuit ###############
moose.connect(stim, 'output', spike, 'setRate')
moose.connect(spike, 'spikeOut', syn.synapse[0], 'addSpike')
moose.connect(spike, 'spikeOut', stats1, 'addSpike')
moose.connect(syn, 'activationOut', fire, 'activation')
moose.connect(stats2, 'requestOut', fire, 'getVm')
moose.connect(plots, 'requestOut', stim, 'getOutputValue')
moose.connect(plot1, 'requestOut', stats1, 'getWmean')
moose.connect(plot2, 'requestOut', stats2, 'getWmean')
moose.connect(plotf, 'requestOut', fire, 'getVm')
def makeModel():
# create container for model
num = 1 # number of compartments
model = moose.Neutral('/model')
compartment = moose.CylMesh('/model/compartment')
compartment.x1 = 1.0e-6 # Set it to a 1 micron single-voxel cylinder
# create molecules and reactions
s = moose.Pool('/model/compartment/s')
rXfer = moose.Reac('/model/compartment/rXfer')
#####################################################################
# Put in endo compartment. Add molecule s
endo = moose.EndoMesh('/model/endo')
endo.isMembraneBound = True
endo.surround = compartment
es = moose.Pool('/model/endo/s')
erXfer = moose.Reac('/model/compartment/erXfer')
#####################################################################
moose.connect(erXfer, 'sub', es, 'reac')
moose.connect(erXfer, 'prd', s, 'reac')
moose.connect(rXfer, 'sub', s, 'reac')
moose.connect(rXfer, 'prd', es, 'reac')
rXfer.Kf = 0.04 # 0.04/sec
rXfer.Kb = 0.0 # 0.02/sec
erXfer.Kf = 0.02 # 0.04/sec
erXfer.Kb = 0.0 # 0.02/sec
#####################################################################
fixXreacs.fixXreacs('/model')
fixXreacs.restoreXreacs('/model')
fixXreacs.fixXreacs('/model')
#####################################################################
rx = moose.element('/model/compartment/rXfer')
erx = moose.element('/model/compartment/erXfer')
# Make solvers
ksolve = moose.Ksolve('/model/compartment/ksolve')
dsolve = moose.Dsolve('/model/dsolve')
eksolve = moose.Ksolve('/model/endo/ksolve')
edsolve = moose.Dsolve('/model/endo/dsolve')
stoich = moose.Stoich('/model/compartment/stoich')
stoich.compartment = compartment
stoich.ksolve = ksolve
stoich.dsolve = dsolve
stoich.path = "/model/compartment/##"
assert (dsolve.numPools == 2)
s.vec.concInit = [1] * num
estoich = moose.Stoich('/model/endo/stoich')
estoich.compartment = endo
estoich.ksolve = eksolve
estoich.dsolve = edsolve
estoich.path = "/model/endo/##"
assert (edsolve.numPools == 1)
edsolve.buildMeshJunctions(dsolve)
plot1 = moose.Table2('/model/plot1')
plot2 = moose.Table2('/model/plot2')
moose.connect('/model/plot1', 'requestOut', s, 'getN')
moose.connect('/model/plot2', 'requestOut', es, 'getN')
plot3 = moose.Table2('/model/plot3')
plot4 = moose.Table2('/model/plot4')
moose.connect('/model/plot3', 'requestOut', s, 'getConc')
moose.connect('/model/plot4', 'requestOut', es, 'getConc')