def _buildNeuroMesh(self):
comptlist = moose.wildcardFind(self.chemid.path + '/#[ISA=ChemCompt]')
sortedComptList = sorted(comptlist, key=lambda x: -x.volume)
# A little juggling here to put the chem pathways onto new meshes.
self.chemid.name = 'temp_chem'
newChemid = moose.Neutral(self.model.path + '/chem')
self.dendCompt = moose.NeuroMesh(newChemid.path + '/dend')
self.dendCompt.geometryPolicy = 'cylinder'
self.dendCompt.separateSpines = 0
if len(sortedComptList) == 3:
self.dendCompt.separateSpines = 1
self.spineCompt = moose.SpineMesh(newChemid.path + '/spine')
moose.connect(self.dendCompt, 'spineListOut', self.spineCompt,
'spineList')
self.psdCompt = moose.PsdMesh(newChemid.path + '/psd')
moose.connect(self.dendCompt, 'psdListOut', self.psdCompt,
'psdList', 'OneToOne')
#Move the old reac systems onto the new compartments.
self._moveCompt(sortedComptList[0], self.dendCompt)
if len(sortedComptList) == 3:
self._moveCompt(sortedComptList[1], self.spineCompt)
self._moveCompt(sortedComptList[2], self.psdCompt)
self.dendCompt.diffLength = self.diffusionLength
self.dendCompt.subTree = self.cellPortionElist
moose.delete(self.chemid)
self.chemid = newChemid
def makeModel():
model = moose.Neutral('/model')
# Make neuronal model. It has no channels, just for geometry
cell = moose.loadModel('./branching.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 = 0
compt0.geometryPolicy = 'cylinder'
#reacSystem = moose.loadModel( 'simpleOsc.g', '/model/chem', 'ee' )
makeChemModel(compt0) # Populate all compt with the chem system.
compt0.diffLength = 1e-6 # This will be over 100 compartments.
# This is the magic command that configures the diffusion compartments.
compt0.subTreePath = "/model/cell/#"
#compt0.cell = cell
# Build the solvers. No need for diffusion in this version.
ksolve0 = moose.Ksolve('/model/chem/compt0/ksolve')
dsolve0 = moose.Dsolve('/model/chem/compt0/dsolve')
stoich0 = moose.Stoich('/model/chem/compt0/stoich')
# Configure solvers
stoich0.compartment = compt0
stoich0.ksolve = ksolve0
stoich0.dsolve = dsolve0
stoich0.path = '/model/chem/compt0/#'
assert (stoich0.numVarPools == 2)
assert (stoich0.numProxyPools == 0)
assert (stoich0.numRates == 0)
moose.element('/model/chem/compt0/a[0]').concInit = aConcInit
twigs = findTwigs(compt0)
print(('twigs = ', twigs))
for i in twigs:
e = moose.element('/model/chem/compt0/b[' + str(i) + ']')
e.concInit = bConcInit
# Create the output tables
graphs = moose.Neutral('/model/graphs')
makeTab('a_soma', '/model/chem/compt0/a[0]')
makeTab('b_soma', '/model/chem/compt0/b[0]')
num = twigs[0]
makeTab('a_apical', '/model/chem/compt0/a[' + str(num) + ']')
makeTab('b_apical', '/model/chem/compt0/b[' + str(num) + ']')
def loadChem(diffLength):
chem = moose.Neutral('/model/chem')
neuroCompt = moose.NeuroMesh('/model/chem/kinetics')
neuroCompt.separateSpines = 1
neuroCompt.geometryPolicy = 'cylinder'
spineCompt = moose.SpineMesh('/model/chem/compartment_1')
moose.connect(neuroCompt, 'spineListOut', spineCompt, 'spineList',
'OneToOne')
psdCompt = moose.PsdMesh('/model/chem/compartment_2')
moose.connect(neuroCompt, 'psdListOut', psdCompt, 'psdList', 'OneToOne')
modelId = moose.loadModel('minimal.g', '/model/chem', 'ee')
neuroCompt.name = 'dend'
spineCompt.name = 'spine'
psdCompt.name = 'psd'
def loadChem(diffLength):
chem = moose.Neutral('/model/chem')
neuroCompt = moose.NeuroMesh('/model/chem/kinetics')
neuroCompt.separateSpines = 1
neuroCompt.geometryPolicy = 'cylinder'
spineCompt = moose.SpineMesh('/model/chem/compartment_1')
moose.connect(neuroCompt, 'spineListOut', spineCompt, 'spineList',
'OneToOne')
psdCompt = moose.PsdMesh('/model/chem/compartment_2')
#print 'Meshvolume[neuro, spine, psd] = ', neuroCompt.mesh[0].volume, spineCompt.mesh[0].volume, psdCompt.mesh[0].volume
moose.connect(neuroCompt, 'psdListOut', psdCompt, 'psdList', 'OneToOne')
modelId = moose.loadModel('psd_merged31d.g', '/model/chem', 'ee')
neuroCompt.name = 'dend'
spineCompt.name = 'spine'
psdCompt.name = 'psd'
def _buildNeuroMesh(self):
comptlist = moose.wildcardFind(self.chemid.path + '/#[ISA=ChemCompt]')
sortedComptList = sorted(comptlist, key=lambda x: -x.volume)
self.chemid.name = 'temp_chem'
newChemid = moose.Neutral(self.model.path + '/chem')
self.dendCompt = moose.NeuroMesh(newChemid.path + '/dend')
self.dendCompt.separateSpines = 1
self.dendCompt.geometryPolicy = 'cylinder'
self.spineCompt = moose.SpineMesh(newChemid.path + '/spine')
moose.connect(self.dendCompt, 'spineListOut', self.spineCompt,
'spineList')
self.psdCompt = moose.PsdMesh(newChemid.path + '/psd')
moose.connect(self.dendCompt, 'psdListOut', self.psdCompt, 'psdList',
'OneToOne')
#Move the old reac systems onto the new compartments.
self._moveCompt(sortedComptList[0], self.dendCompt)
self._moveCompt(sortedComptList[1], self.spineCompt)
self._moveCompt(sortedComptList[2], self.psdCompt)
self.dendCompt.diffLength = self.meshLambda
#print self.elecid
#print self.cellPortion
self.dendCompt.cellPortion(self.elecid, self.cellPortion)
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) # Populate all 3 compts with the chem system.
makeChemModel(compt1)
makeChemModel(compt2)
compt0.diffLength = 2e-6 # This will be over 100 compartments.
# This is the magic command that configures the diffusion compartments.
compt0.subTreePath = cell.path + "/##"
moose.showfields(compt0)
# Build the solvers. No need for diffusion in this version.
ksolve0 = moose.Ksolve('/model/chem/compt0/ksolve')
ksolve1 = moose.Gsolve('/model/chem/compt1/ksolve')
ksolve2 = moose.Gsolve('/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 == 3)
assert (stoich0.numProxyPools == 0)
assert (stoich0.numRates == 4)
assert (stoich1.numVarPools == 3)
assert (stoich1.numProxyPools == 0)
#assert( stoich1.numRates == 4 )
assert (stoich2.numVarPools == 3)
assert (stoich2.numProxyPools == 0)
#assert( stoich2.numRates == 4 )
#dsolve0.buildNeuroMeshJunctions( dsolve1, dsolve2 )
stoich0.buildXreacs(stoich1)
stoich1.buildXreacs(stoich2)
stoich0.filterXreacs()
stoich1.filterXreacs()
stoich2.filterXreacs()
moose.element('/model/chem/compt2/a[0]').concInit *= 1.5
# Create the output tables
num = compt0.numDiffCompts - 1
graphs = moose.Neutral('/model/graphs')
makeTab('a_soma', '/model/chem/compt0/a[0]')
makeTab('b_soma', '/model/chem/compt0/b[0]')
makeTab('a_apical', '/model/chem/compt0/a[' + str(num) + ']')
makeTab('b_apical', '/model/chem/compt0/b[' + str(num) + ']')
makeTab('a_spine', '/model/chem/compt1/a[5]')
makeTab('b_spine', '/model/chem/compt1/b[5]')
makeTab('a_psd', '/model/chem/compt2/a[5]')
makeTab('b_psd', '/model/chem/compt2/b[5]')
def makeNeuroMeshModel():
makeSpinyCompt()
diffLength = moose.element('/n/compt').length
diffLength = diffLength / 10.0
elec = moose.element('/n')
elec.name = 'elec'
model = moose.Neutral('/model')
moose.move(elec, model)
synInput = moose.element('/model/elec/compt/synInput')
synInput.refractT = 47e-3
chem = moose.Neutral('/model/chem')
neuroCompt = moose.NeuroMesh('/model/chem/neuroMesh')
neuroCompt.separateSpines = 1
neuroCompt.diffLength = diffLength
neuroCompt.geometryPolicy = 'cylinder'
spineCompt = moose.SpineMesh('/model/chem/spineMesh')
moose.connect(neuroCompt, 'spineListOut', spineCompt, 'spineList',
'OneToOne')
psdCompt = moose.PsdMesh('/model/chem/psdMesh')
moose.connect(neuroCompt, 'psdListOut', psdCompt, 'psdList', 'OneToOne')
createChemModel(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 'Assigning the cell model'
# Now to set up the model.
neuroCompt.cell = elec
ns = neuroCompt.numSegments
#assert( ns == 11 ) # dend, 5x (shaft+head)
ndc = neuroCompt.numDiffCompts
assert (ndc == 10)
ndc = neuroCompt.mesh.num
assert (ndc == 10)
sdc = spineCompt.mesh.num
assert (sdc == 5)
pdc = psdCompt.mesh.num
assert (pdc == 5)
#
# 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
# Have to pass a message between the various solvers.
foo = moose.vec('/model/chem/spineMesh/headGluR')
# oddly, numLocalFields does not work.
ca = moose.element('/model/chem/neuroMesh/Ca')
assert (ca.lastDimension == ndc)
moose.vec('/model/chem/spineMesh/headGluR').nInit = 100
moose.vec('/model/chem/psdMesh/psdGluR').nInit = 0
# set up adaptors
aCa = moose.Adaptor('/model/chem/spineMesh/adaptCa', 5)
adaptCa = moose.vec('/model/chem/spineMesh/adaptCa')
chemCa = moose.vec('/model/chem/spineMesh/Ca')
assert (len(adaptCa) == 5)
for i in range(5):
path = '/model/elec/head' + str(i) + '/ca'
elecCa = moose.element(path)
moose.connect(elecCa, 'concOut', adaptCa[i], 'input', 'Single')
moose.connect(adaptCa, 'outputSrc', chemCa, 'setConc', 'OneToOne')
adaptCa.outputOffset = 0.0001 # 100 nM offset in chem.
adaptCa.scale = 0.05 # 0.06 to 0.003 mM
aGluR = moose.Adaptor('/model/chem/psdMesh/adaptGluR', 5)
adaptGluR = moose.vec('/model/chem/psdMesh/adaptGluR')
chemR = moose.vec('/model/chem/psdMesh/psdGluR')
assert (len(adaptGluR) == 5)
for i in range(5):
path = '/model/elec/head' + str(i) + '/gluR'
elecR = moose.element(path)
moose.connect(adaptGluR[i], 'outputSrc', elecR, 'setGbar', 'Single')
#moose.connect( chemR, 'nOut', adaptGluR, 'input', 'OneToOne' )
# Ksolve isn't sending nOut. Not good. So have to use requestOut.
moose.connect(adaptGluR, 'requestOut', chemR, 'getN', 'OneToOne')
adaptGluR.outputOffset = 1e-7 # pS
adaptGluR.scale = 1e-6 / 100 # from n to pS
adaptK = moose.Adaptor('/model/chem/neuroMesh/adaptK')
chemK = moose.element('/model/chem/neuroMesh/kChan')
elecK = moose.element('/model/elec/compt/K')
moose.connect(adaptK, 'requestOut', chemK, 'getConc', 'OneToAll')
moose.connect(adaptK, 'outputSrc', elecK, 'setGbar', 'Single')
adaptK.scale = 0.3 # from mM to Siemens
"""
def makeModel():
numSeg = 5
diffConst = 0.0
# create container for model
model = moose.Neutral('model')
compt0 = moose.NeuroMesh('/model/compt0')
compt0.separateSpines = 1
compt0.geometryPolicy = 'cylinder'
compt1 = moose.SpineMesh('/model/compt1')
moose.connect(compt0, 'spineListOut', compt1, 'spineList', 'OneToOne')
compt2 = moose.PsdMesh('/model/compt2')
moose.connect(compt0, 'psdListOut', compt2, 'psdList', 'OneToOne')
# 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/compt0/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.diffConst = diffConst
b.diffConst = diffConst
c.diffConst = diffConst
a.concInit = 1
b.concInit = 12.1
c.concInit = 1
reac0.Kf = 1
reac0.Kb = 1
reac1.Kf = 1
reac1.Kb = 1
# Create a 'neuron' with a dozen spiny compartments.
elec = makeNeuron(numSeg)
# assign geometry to mesh
compt0.diffLength = 10e-6
#compt0.cell = elec
compt0.subTreePath = elec.path + "/##"
# Build the solvers. No need for diffusion in this version.
ksolve0 = moose.Ksolve('/model/compt0/ksolve')
ksolve1 = moose.Ksolve('/model/compt1/ksolve')
ksolve2 = moose.Ksolve('/model/compt2/ksolve')
stoich0 = moose.Stoich('/model/compt0/stoich')
stoich1 = moose.Stoich('/model/compt1/stoich')
stoich2 = moose.Stoich('/model/compt2/stoich')
# 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/#'
assert (stoich0.numVarPools == 1)
assert (stoich0.numProxyPools == 1)
assert (stoich0.numRates == 1)
assert (stoich1.numVarPools == 1)
assert (stoich1.numProxyPools == 1)
assert (stoich1.numRates == 1)
assert (stoich2.numVarPools == 1)
assert (stoich2.numProxyPools == 0)
assert (stoich2.numRates == 0)
stoich0.buildXreacs(stoich1)
stoich1.buildXreacs(stoich2)
stoich0.filterXreacs()
stoich1.filterXreacs()
stoich2.filterXreacs()
print((a.vec.volume, b.vec.volume, c.vec.volume))
a.vec.concInit = list(range(numSeg + 1, 0, -1))
b.vec.concInit = [5.0 * (1 + x) for x in range(numSeg)]
c.vec.concInit = list(range(1, numSeg + 1))
print((a.vec.concInit, b.vec.concInit, c.vec.concInit))
# 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
a1 = moose.element('/model/compt0/a[' + str(numSeg) + ']')
b1 = moose.element('/model/compt1/b[' + str(numSeg - 1) + ']')
c1 = moose.element('/model/compt2/c[' + str(numSeg - 1) + ']')
moose.connect(outputA, 'requestOut', a1, 'getConc')
moose.connect(outputB, 'requestOut', b1, 'getConc')
moose.connect(outputC, 'requestOut', c1, 'getConc')
def makeChemModel( cellId ):
# create container for model
r0 = 1e-6 # m
r1 = 1e-6 # m
num = 2800
diffLength = 1e-6 # m
diffConst = 5e-12 # m^2/sec
motorRate = 1e-6 # m/sec
concA = 1 # millimolar
model = moose.element( '/model' )
compartment = moose.NeuroMesh( '/model/compartment' )
# FIXME: No attribute cell
compartment.cell = cellId
compartment.diffLength = diffLength
print(("cell NeuroMesh parameters: numSeg and numDiffCompt: ", compartment.numSegments, compartment.numDiffCompts))
print(("compartment.numDiffCompts == num: ", compartment.numDiffCompts, num))
assert( compartment.numDiffCompts == num )
# create molecules and reactions
a = moose.Pool( '/model/compartment/a' )
b = moose.Pool( '/model/compartment/b' )
s = moose.Pool( '/model/compartment/s' )
e1 = moose.MMenz( '/model/compartment/e1' )
e2 = moose.MMenz( '/model/compartment/e2' )
e3 = moose.MMenz( '/model/compartment/e3' )
r1 = moose.Reac( '/model/compartment/r1' )
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
#b.motorConst = motorRate
# Make solvers
ksolve = moose.Ksolve( '/model/compartment/ksolve' )
dsolve = moose.Dsolve( '/model/compartment/dsolve' )
stoich = moose.Stoich( '/model/compartment/stoich' )
stoich.compartment = compartment
#ksolve.numAllVoxels = compartment.numDiffCompts
stoich.ksolve = ksolve
stoich.dsolve = dsolve
stoich.path = "/model/compartment/##"
assert( dsolve.numPools == 3 )
a.vec.concInit = [0.1]*num
a.vec[0].concInit += 0.5
a.vec[400].concInit += 0.5
a.vec[800].concInit += 0.5
a.vec[1200].concInit += 0.5
a.vec[1600].concInit += 0.5
a.vec[2000].concInit += 0.5
a.vec[2400].concInit += 0.5
#a.vec[num/2].concInit -= 0.1
b.vec.concInit = [0.1]*num
s.vec.concInit = [1]*num
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 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]')
