def create_ca_rxd(self):
cainf = 100e-6
taur = self.p_all['L5Pyr_dend_taur_cad'] # temporary
# drive_channel = -(10000) * self.ica_soma / (.2)
# [sec for sec in h.allsec() if 'soma' in sec.name()]
ca_reg = rxd.Region(h.allsec(),
nrn_region='i',
name='ca_reg',
geometry=rxd.Shell(0.9848, 1))
ca = rxd.Species(ca_reg, d=0.3, name='ca', charge=2, initial=cainf)
ca_pump = rxd.Rate(ca, (cainf - ca) / taur)
self.ca = ca
self.ca_reg = ca_reg
self.ca_pump = ca_pump
#Create cell
cell = Neuron()
'''
stim = h.IClamp(cell.soma(0.5))
stim.delay = 50
stim.dur = 50
stim.amp = 1
'''
time = h.Vector().record(h._ref_t)
print(5)
ecs = rxd.Extracellular(-Lx/2.0, -Ly/2.0,
-Lz/2.0, Lx/2.0, Ly/2.0, Lz/2.0, dx=1,
volume_fraction=alpha, tortuosity=tort)
print(6)
k = rxd.Species(ecs, name='k', d=2.62, charge=1, initial=lambda nd: 50
if nd.x3d**2 + nd.y3d**2 + nd.z3d**2 < r0**2 else 3,
ecs_boundary_conditions=3)
na = rxd.Species(ecs, name='na', d=1.78, charge=1, initial=148,
ecs_boundary_conditions=148)
pc.set_maxstep(100)
h.finitialize()
sys.stdout.write('\ninit')
sys.stdout.flush()
def progress_bar(tstop, size=40):
prog = h.t / float(tstop)
fill = int(size * prog)
empt = size - fill
# extracellular
ecs = rxd.Extracellular(xl, yl, zl, xh, yh, zh, dx=50)
# Who?
def init(ics, ecs):
return lambda nd: ecs if isinstance(nd, rxd.node.NodeExtracellular
) else ics
# ions
k = rxd.Species([cyt, mem, ecs],
name='k',
d=1,
charge=1,
initial=init(54.4, 2.5))
na = rxd.Species([cyt, mem, ecs],
name='na',
d=1,
charge=1,
initial=init(10.0, 140.0))
x = rxd.Species([cyt, mem, ecs], name='x', charge=1)
ki, ko, nai, nao, xi, xo = k[cyt], k[ecs], na[cyt], na[ecs], x[cyt], x[ecs]
# gates
ngate = rxd.Species([cyt, mem], name='ngate', initial=0.24458654944007166)
mgate = rxd.Species([cyt, mem], name='mgate', initial=0.028905534475191907)
gserca = 0.3913 gleak = 6.020 kserca = 0.1 kip3 = 0.15 kact = 0.4 ip3rtau = 2000 h.CVode().active(1) h.cvode.atol(1e-10) # define the regions for the rxd cyt = rxd.Region(h.allsec(), nrn_region='i', geometry=rxd.FractionalVolume(fc, surface_fraction=1)) er = rxd.Region(h.allsec(), geometry=rxd.FractionalVolume(fe)) cyt_er_membrane = rxd.Region(h.allsec(), geometry=rxd.FixedPerimeter(1)) # the species and other states ca = rxd.Species([cyt, er], d=caDiff, name='ca', charge=2, initial=cac_init) ip3 = rxd.Species(cyt, d=ip3Diff, initial=ip3_init) ip3r_gate_state = rxd.State(cyt_er_membrane, initial=0.8) h_gate = ip3r_gate_state[cyt_er_membrane] # pumps and channels between ER and Cytosol serca = rxd.MultiCompartmentReaction(ca[cyt]>ca[er], gserca/((kserca / (1000. * ca[cyt])) ** 2 + 1), membrane=cyt_er_membrane, custom_dynamics=True) leak = rxd.MultiCompartmentReaction(ca[er]!=ca[cyt], gleak, gleak, membrane=cyt_er_membrane) minf = ip3[cyt] * 1000. * ca[cyt] / (ip3[cyt] + kip3) / (1000. * ca[cyt] + kact) k = gip3r * (minf * h_gate) ** 3 ip3r = rxd.MultiCompartmentReaction(ca[er]!=ca[cyt], k, k, membrane=cyt_er_membrane) ip3rg = rxd.Rate(h_gate, (1. / (1 + 1000. * ca[cyt] / (0.3)) - h_gate) / ip3rtau)
mem = rxd.Region(h.allsec(), name='cell_mem', geometry=rxd.membrane())
# extracellular
ecs = rxd.Extracellular(-100, -100, -100, 100, 100, 100, dx=100)
# Who?
def init(ics, ecs):
return lambda nd: ecs if isinstance(nd, rxd.node.NodeExtracellular
) else ics
# ions
k = rxd.Species([cyt, mem, ecs],
name='k',
d=1e3,
charge=1,
initial=init(54.4, 2.5),
ecs_boundary_conditions=2.5)
na = rxd.Species([cyt, mem, ecs],
name='na',
d=1e3,
charge=1,
initial=init(10.0, 140.0),
ecs_boundary_conditions=140)
x = rxd.Species([cyt, mem, ecs], name='x', charge=1)
ki, ko, nai, nao, xi, xo = k[cyt], k[ecs], na[cyt], na[ecs], x[cyt], x[ecs]
# gates
ngate = rxd.State([cyt, mem], name='ngate', initial=0.24458654944007166)
fe = 0.3
caCYT_init = 0.1
cyt = rxd.Region(h.allsec(),
name='cyt',
nrn_region='i',
geometry=rxd.FractionalVolume(fc, surface_fraction=1))
er = rxd.Region(h.allsec(), name='er', geometry=rxd.FractionalVolume(fe / 2.))
cyt_er_membrane = rxd.Region(h.allsec(),
name='mem',
geometry=rxd.ScalableBorder(
1, on_cell_surface=False))
ca = rxd.Species([cyt, er], d=caDiff, name="ca", charge=2, initial=caCYT_init)
ip3 = rxd.Species(cyt, d=ip3Diff, name="ip3", initial=ip3_init)
ip3r_gate_state = rxd.Species(cyt_er_membrane, name="gate", initial=0.8)
h_gate = ip3r_gate_state[cyt_er_membrane]
minf = ip3[cyt] * rescale_v * v * ca[cyt] / (ip3[cyt] + kip3) / (
rescale_v * v * ca[cyt] + kact)
k = gip3r * (minf * h_gate)**3
ip3r = rxd.MultiCompartmentReaction(ca[er],
ca[cyt],
k,
k,
membrane=cyt_er_membrane)
serca = rxd.MultiCompartmentReaction(ca[cyt],
# extracellular
ecs = rxd.Extracellular(-100, -100, -100, 100, 100, 100, dx=100)
# Who?
def init(ics, ecs):
return lambda nd: ecs if isinstance(nd, rxd.node.NodeExtracellular
) else ics
# ions
k = rxd.Species(
[cyt, mem, ecs],
name="k",
d=1e3,
charge=1,
initial=init(54.4, 2.5),
ecs_boundary_conditions=2.5,
)
na = rxd.Species(
[cyt, mem, ecs],
name="na",
d=1e3,
charge=1,
initial=init(10.0, 140.0),
ecs_boundary_conditions=140,
)
x = rxd.Species([cyt, mem, ecs], name="x", charge=1)
ki, ko, nai, nao, xi, xo = k[cyt], k[ecs], na[cyt], na[ecs], x[cyt], x[ecs]
dend2 = h.Section()
dend2.diam = 2
dend2.nseg = 101
dend2.L = 50
dend2.connect(dend1)
diff_constant = 1
h.cvode_active(True)
r = rxd.Region(h.allsec(), dx=0.25)
rxd.set_solve_type([dend1], dimension=3)
ca = rxd.Species(
r,
d=diff_constant,
atolscale=0.1,
initial=lambda node: 1 if (0.8 < node.x and node.segment in dend1) or
(node.x < 0.2 and node.segment in dend2) else 0,
)
bistable_reaction = rxd.Rate(ca, -ca * (1 - ca) * (0.01 - ca))
h.finitialize()
for i in range(2):
h.fadvance()
rxd.nthread(2)
for i in range(2, 4):
h.fadvance()
rxd.nthread(3)
for i in range(4, 6):
h.fadvance()
rxd.nthread(4)
# membrane
mem = rxd.Region(h.allsec(), name="cell_mem", geometry=rxd.membrane())
# extracellular
ecs = rxd.Extracellular(xl, yl, zl, xh, yh, zh, dx=50)
# Who?
def init(ics, ecs):
return lambda nd: ecs if isinstance(nd, rxd.node.NodeExtracellular) else ics
# ions
k = rxd.Species([cyt, mem, ecs], name="k", d=1, charge=1, initial=init(54.4, 2.5))
na = rxd.Species([cyt, mem, ecs], name="na", d=1, charge=1, initial=init(10.0, 140.0))
x = rxd.Species([cyt, mem, ecs], name="x", charge=1)
ki, ko, nai, nao, xi, xo = k[cyt], k[ecs], na[cyt], na[ecs], x[cyt], x[ecs]
# gates
ngate = rxd.Species([cyt, mem], name="ngate", initial=0.24458654944007166)
mgate = rxd.Species([cyt, mem], name="mgate", initial=0.028905534475191907)
hgate = rxd.Species([cyt, mem], name="hgate", initial=0.7540796658225246)
# mycellA parameter
pA = rxd.Parameter(
[cyt, mem],
name="paramA",
from neuron import h, crxd as rxd, gui from neuron.crxd import initializer h.CVode().active(1) rxdsec = [h.Section(), h.Section()] cyt = rxd.Region(rxdsec) er = rxd.Region(rxdsec) ca = rxd.Species([cyt, er]) caextrude = rxd.Rate(ca, 1) # test for forced initialization before model fully described initializer._do_init() ip3 = rxd.Species(cyt) h.tstop = 1000 h.run()
def __init__(self):
self.soma = h.Section(name='soma', cell=self)
self.soma.pt3dclear()
self.soma.pt3dadd(x, y, z + somaR, 2.0 * somaR)
self.soma.pt3dadd(x, y, z - somaR, 2.0 * somaR)
self.dend = h.Section(name='dend', cell=self)
self.dend.pt3dclear()
self.dend.pt3dadd(x, y, z - somaR, 2.0 * dendR)
self.dend.pt3dadd(x, y, z - somaR - dendL, 2.0 * dendR)
self.dend.nseg = 10
self.dend.connect(self.soma, 1, 0)
self.all = [self.soma, self.dend]
#---------------soma----------------
# for mechanism_s in ['h','hNa','hha2', 'IA','kadcr','borgka','Ih','Ihvip', 'kap', 'km' ,'pas', 'Nafcr', 'kdrcr', 'IKscr', 'iCcr', 'kadcr']:
# self.soma.insert(mechanism_s)
for mechanism_s in [
'extracellular', 'h', 'hNa', 'hha2', 'IA', 'Ih', 'Nasoma',
'km', 'Ksoma', 'pas', 'k_ion', 'na_ion', 'kap', 'nap', 'kdrcr',
'Nafcr', 'IKscr'
]:
self.soma.insert(mechanism_s)
self.soma(0.5).IA.gkAbar = 0.0165
self.soma(0.5).Ih.gkhbar = 0.00035 * 0.1
self.soma(0.5).Nasoma.gnasoma = 0.0107 * 1.2
self.soma(0.5).Nasoma.gl = 1 / Rm
self.soma(0.5).Nasoma.el = -67
self.soma(0.5).Ksoma.gksoma = 0.0319 * 1.5
#print(self.soma.psection())
self.n_Ksoma = h.Vector().record(self.soma(0.5).Ksoma._ref_n)
self.h_Nasoma = h.Vector().record(self.soma(0.5).Nasoma._ref_h)
self.m_Nasoma = h.Vector().record(self.soma(0.5).Nasoma._ref_m)
self.soma(0.5).h.ghdbar = 0.00005
self.soma(0.5).h.vhalfl = -73
self.soma(0.5).Ih.gkhbar = 0.00035 * 0.1
self.soma(0.5).km.gbar = 0.06
#self.soma(0.5).borgka.gkabar = 0.00015*4*0.5
#self.soma(0.5).kadcr.gkabar = 0.003
self.soma(0.5).hha2.gnabar = 0.007
self.soma(0.5).hha2.gkbar = 0.007 / 10
self.soma(0.5).hha2.gl = 0
self.soma(0.5).hha2.el = -70
#self.soma(0.5).pas.g = 1/Rm
#self.soma(0.5).pas.e = -70
self.soma(0.5).Nafcr.gnafbar = 0.015
self.soma(0.5).kdrcr.gkdrbar = 0.018
self.soma(0.5).IKscr.gKsbar = 0.000725
#self.soma(0.5).iCcr.gkcbar = 0.00003
#self.soma(0.5).kadcr.gkabar = 0.003
#print(self.soma.psection())
#self.n_Ksoma = h.Vector().record(self.soma(0.5).Ksoma._ref_n)
#self.h_Nasoma = h.Vector().record(self.soma(0.5).Nasoma._ref_h)
#self.m_Nasoma = h.Vector().record(self.soma(0.5).Nasoma._ref_m)
self.somaV = h.Vector()
self.somaV.record(self.soma(0.5)._ref_v)
#---------------dend----------------
for mechanism_d in [
'Nadend', 'Kdend', 'hha_old', 'h', 'hNa', 'IA', 'kap', 'pas',
'Nafcr', 'kdrcr', 'nap', 'k_ion', 'na_ion', 'Ihvip', 'kad'
]:
self.dend.insert(mechanism_d)
self.dend(0.5).IA.gkAbar = 0.004 * 1.2
#self.dend1(0.5).Ih.gkhbar = 0.00035*0.1
self.dend(0.5).Nadend.gnadend = 2 * 0.0117
self.dend(0.5).Nadend.gl = 1 / Rm
self.dend(0.5).Nadend.el = -65
self.dend(0.5).Kdend.gkdend = 20 * 0.023
self.dend(0.5).h.ghdbar = 0.00005 * 4
self.dend(0.5).h.vhalfl = -81
self.dend(0.5).IA.gkAbar = 0.004 * 1.2
self.dend(0.5).kad.gkabar = 0
#self.dend(0.5).km.gbar = 0.06
#self.dend(0.5).borgka.gkabar = 0.00015*4*0.5
self.dend(0.5).hha_old.gnabar = 0.007
self.dend(0.5).hha_old.gkbar = 0.007 / 8.065
self.dend(0.5).hha_old.el = -70
self.dend(0.5).hha_old.gl = 0
#self.dend(0.5).pas.g = 1/20000
#self.dend(0.5).pas.e = -70
self.dend(0.5).Nafcr.gnafbar = 0.018 * 5
self.dend(0.5).kdrcr.gkdrbar = 0.018 * 0.5
#self.Dn_Kdend = h.Vector().record(self.dend(0.5).Kdend._ref_n)
#self.Dh_Nadend = h.Vector().record(self.dend(0.5).Nadend._ref_h)
#self.Dm_Nadend = h.Vector().record(self.dend(0.5).Nadend._ref_m)
self.dendV = h.Vector()
self.dendV.record(self.dend(0.5)._ref_v)
self.k_vec = h.Vector().record(self.soma(0.5)._ref_ik)
self.na_vec = h.Vector().record(self.soma(0.5)._ref_ina)
self.na_concentration = h.Vector().record(self.soma(0.5)._ref_nai)
self.k_concentration = h.Vector().record(self.soma(0.5)._ref_ki)
self.v_vec = h.Vector().record(self.soma(0.5)._ref_vext[0])
for sec in self.all:
Ra = 150
cm = 1.2
self.cyt = rxd.Region(self.all,
name='cyt',
nrn_region='i',
dx=1.0,
geometry=rxd.FractionalVolume(
0.9, surface_fraction=1.0))
self.na = rxd.Species([self.cyt],
name='na',
charge=1,
d=1.0,
initial=14)
self.k = rxd.Species([self.cyt],
name='k',
charge=1,
d=1.0,
initial=120)
self.k_i = self.k[self.cyt]
# enable extracellular RxD
rxd.options.enable.extracellular = True
# simulation parameters
dx = 1.0 # voxel size
L = 9.0 # length of initial cube
Lecs = 21.0 # lengths of ECS
# define the extracellular region
extracellular = rxd.Extracellular(-Lecs/2., -Lecs/2., -Lecs/2.,
Lecs/2., Lecs/2., Lecs/2., dx=dx,
volume_fraction=0.2, tortuosity=lambda x,y,z: 1.6)
# define the extracellular species
k_rxd = rxd.Species(extracellular, name='k', d=2.62, charge=1,
initial=lambda nd: 1.0 if abs(nd.x3d) <= L/2. and
abs(nd.y3d) <= L/2. and abs(nd.z3d) <= L/2. else 0.0)
# copy of the initial state to plot (figure 4a upper panel)
states_init = k_rxd[extracellular].states3d.copy()
# record the concentration at (0,0,0)
ecs_vec = h.Vector()
ecs_vec.record(k_rxd[extracellular].node_by_location(0, 0, 0)._ref_value)
# record the time
t_vec = h.Vector()
t_vec.record(h._ref_t)
h.finitialize()
h.dt = 0.1
h.continuerun(100) #run the simulation
# the extracellular space
ecs = rxd.Extracellular(-55,
-55,
-55,
55,
55,
55,
dx=10,
volume_fraction=0.2,
tortuosity=1.6)
# Who?
x = rxd.Species([cyt, org, cyt_org_membrane, ecs],
name='x',
d=1.0,
charge=1,
initial=0)
Xcyt = x[cyt]
Xorg = x[org]
# What? - produce X in cell 1
# parameter to limit production to cell 1
cell1_param = rxd.Parameter(org,
initial=lambda node: 1.0
if node.segment.sec == cell1 else 0)
# production with a rate following Michaels Menton kinetics
createX = rxd.Rate(Xorg, cell1_param[org] * 1.0 / (10.0 + Xorg))
# leak between organelles and cytosol
Dcab = 0 # create sections soma = h.Section(name="soma") dend = h.Section(name="dend") soma.L=100 soma.diam=1 soma.nseg=101 dend.L=100 dend.diam=1 dend.nseg=101 soma.connect(dend) r = rxd.Region(h.allsec()) Ca = rxd.Species(r, name='Ca', d=Dca) Buf = rxd.Species(r, name='Buf', d=Db) CaBuf = rxd.Species(r, name='CaBuf', d=Dcab) buffering = rxd.Reaction(Ca[r] + Buf[r], CaBuf[r], kf, kb) # # set initial concentrations to ca0, b0, cab0 in soma, # and to 0.001 in dend # Ca.initial = lambda node: (ca0 if node.sec._sec==soma else 0.001) Buf.initial = lambda node: (b0 if node.sec._sec==soma else 0.001) CaBuf.initial = lambda node:(cab0 if node.sec._sec==soma else 0.001)
stim1.amp = 10
ecs = rxd.Extracellular(-Lx / 2.0,
-Ly / 2.0,
-Lz / 2.0,
Lx / 2.0,
Ly / 2.0,
Lz / 2.0,
dx=20,
volume_fraction=alpha,
tortuosity=tort)
k = rxd.Species(ecs,
name='k',
d=2.62,
charge=1,
initial=lambda nd: 3
if nd.x3d**2 + nd.y3d**2 + nd.z3d**2 < r0**2 else 3,
ecs_boundary_conditions=3)
na = rxd.Species(ecs,
name='na',
d=1.78,
charge=1,
initial=135,
ecs_boundary_conditions=135)
ca = rxd.Species(ecs,
name='ca',
d=0.08,
charge=2,
from neuron import h, crxd as rxd
h.load_file("stdrun.hoc")
cell = h.Section(name="cell")
r = rxd.Region([cell])
def Declare_Parameters(**kwargs):
"""helper function enabling clean declaration of parameters in top namespace"""
for key, value in kwargs.items():
globals()[key] = rxd.Parameter(r, name=key, initial=value)
def Declare_Species(**kwargs):
"""helper function enabling clean declaration of species in top namespace"""
for key, value in kwargs.items():
globals()[key] = rxd.Species(r, name=key, initial=value)
k3 = rxd.Parameter(r, name="k3", initial=1.2)
k4 = rxd.Parameter(r, name="k4", initial=0.6)
P2 = rxd.Species(r, name="P2", initial=0.0614368)
T2 = rxd.Species(r, name="T2", initial=0.0145428)
C = rxd.Species(r, name="C", initial=0.207614)
h.finitialize(-65)
h.continuerun(72)
def Declare_Species(**kwargs):
"""helper function enabling clean declaration of species in top namespace"""
for key, value in kwargs.items():
globals()[key] = rxd.Species(r, name=key, initial=value)
mem = rxd.Region(h.allsec(), name="cell_mem", geometry=rxd.membrane())
# extracellular
ecs = rxd.Extracellular(-100, -100, -100, 100, 100, 100, dx=33)
# Who?
def init(ics, ecs):
return lambda nd: ecs if isinstance(nd, rxd.node.NodeExtracellular
) else ics
# ions
k = rxd.Species([cyt, mem],
name="k",
d=1,
charge=1,
initial=54.4,
represents="CHEBI:29103")
kecs = rxd.Parameter([ecs],
name="k",
value=2.5,
charge=1,
represents="CHEBI:29103")
na = rxd.Species([cyt, mem],
name="na",
d=1,
charge=1,
initial=10.0,
represents="CHEBI:29101")
def _addSpecies(self, params):
from .. import sim
for label, param in params.items():
# regions
if 'regions' not in param:
print(' Error creating Species %s: "regions" parameter was missing'%(label))
continue
if not isinstance(param['regions'], list):
param['regions'] = [param['regions']]
try:
nrnRegions = [self.rxd['regions'][region]['hObj'] for region in param['regions'] if self.rxd['regions'][region]['hObj'] != None]
except:
print(' Error creating Species %s: could not find regions %s'%(label, param['regions']))
# d
if 'd' not in param:
param['d'] = 0
# charge
if 'charge' not in param:
param['charge'] = 0
# initial
if 'initial' not in param:
param['initial'] = None
if isinstance(param['initial'], basestring): # string-based func
funcStr = self._replaceRxDStr(param['initial'], constants=True, regions=True, species=False)
# create final function dynamically from string
importStr = ' from neuron import crxd as rxd \n from netpyne import sim'
afterDefStr = 'sim.net.rxd["species"]["%s"]["initialFunc"] = initial' % (label)
funcStr = 'def initial (node): \n%s \n return %s \n%s' % (importStr, funcStr, afterDefStr) # convert to lambda function
try:
exec(funcStr, {'rxd': rxd}, {'sim': sim})
initial = sim.net.rxd["species"][label]["initialFunc"]
except:
print(' Error creating Species %s: cannot evaluate "initial" expression -- "%s"'%(label, param['initial']))
continue
else:
initial = param['initial']
# ecs boundary condition
if 'ecs_boundary_conditions' not in param:
param['ecs_boundary_conditions'] = None
# atolscale
if 'atolscale' not in param:
param['atolscale'] = 1
if 'name' not in param:
name = label
else:
name = param['name']
# call rxd method to create Species
if nrnRegions: self.rxd['species'][label]['hObj'] = rxd.Species(regions=nrnRegions,
d=param['d'],
charge=param['charge'],
initial=initial,
atolscale=param['atolscale'],
name=name,
ecs_boundary_conditions=param['ecs_boundary_conditions'])
else: self.rxd['species'][label]['hObj'] = None
print(' Created Species %s'%(label))
# Where? -- define the extracellular space
ecs = rxd.Extracellular(-Lx / 2.0,
-Ly / 2.0,
-Lz / 2.0,
Lx / 2.0,
Ly / 2.0,
Lz / 2.0,
dx=10,
volume_fraction=alpha,
tortuosity=tort)
# What? -- define the species
k = rxd.Species(ecs,
name='k',
d=2.62,
charge=1,
initial=lambda nd: 40
if nd.x3d**2 + nd.y3d**2 + nd.z3d**2 < r0**2 else 3.5,
ecs_boundary_conditions=3.5)
na = rxd.Species(ecs,
name='na',
d=1.78,
charge=1,
initial=133.574,
ecs_boundary_conditions=133.574)
if args.buffer:
# Additional species are used for a phenomenological model of astrocytic
# buffering
kb = 0.0008
mem = rxd.Region(h.allsec(), name='cell_mem', geometry=rxd.membrane())
# extracellular
ecs = rxd.Extracellular(-100, -100, -100, 100, 100, 100, dx=33)
# Who?
def init(ics, ecs):
return lambda nd: ecs if isinstance(nd, rxd.node.NodeExtracellular
) else ics
# ions
k = rxd.Species([cyt, mem],
name='k',
d=1,
charge=1,
initial=54.4,
represents='CHEBI:29103')
kecs = rxd.Parameter([ecs],
name='k',
value=2.5,
charge=1,
represents='CHEBI:29103')
na = rxd.Species([cyt, mem],
name='na',
d=1,
charge=1,
initial=10.0,
represents='CHEBI:29101')
'''
print(3)
ecs = rxd.Extracellular(-Lx / 2.0,
-Ly / 2.0,
-Lz / 2.0,
Lx / 2.0,
Ly / 2.0,
Lz / 2.0,
dx=20,
volume_fraction=alpha,
tortuosity=tort)
k = rxd.Species(ecs,
name='k',
d=2.62,
charge=1,
initial=1,
ecs_boundary_conditions=1)
na = rxd.Species(ecs,
name='na',
d=1.78,
charge=1,
initial=145,
ecs_boundary_conditions=145)
ca = rxd.Species(ecs,
name='ca',
d=0.08,
charge=2,
initial=25,
name = __main__.__file__
if name[-3 :] == '.py':
name = name[: -3]
h.load_file('stdrun.hoc')
dend = h.Section()
dend.diam = 2
dend.nseg = 101
dend.L = 100
rxd.set_solve_type(dimension=3)
diff_constant = 1
r = rxd.Region(h.allsec(),dx=0.5)
ca = rxd.Species(r, d=diff_constant, initial=lambda node:
1 if 0.4 < node.x < 0.6 else 0)
h.finitialize()
initial_amount = (numpy.array(ca.nodes.concentration) * numpy.array(ca.nodes.volume)).sum()
for t in [25, 50, 75, 100, 125]:
h.continuerun(t)
pyplot.plot([nd.x for nd in ca.nodes], ca.nodes.concentration)
final_amount = (numpy.array(ca.nodes.concentration) * numpy.array(ca.nodes.volume)).sum()
print("initial {}\tfinal {}\tdiff {}".format(initial_amount, final_amount, initial_amount - final_amount))
pyplot.tight_layout()
pyplot.savefig('{0}.png'.format(name))
pyplot.show()
# somaB.nseg = 11
# Where?
# intracellular
cyt = rxd.Region(h.allsec(), name='cyt', nrn_region='i')
# membrane
mem = rxd.Region(h.allsec(), name='cell_mem', geometry=rxd.membrane())
# extracellular
ecs = rxd.Extracellular(-100, -100, -100, 100, 100, 100, dx=33)
# Who? ions & gates
# intracellular sodium & potassium
na = rxd.Species([cyt, mem], name='na', d=1, charge=1, initial=10)
k = rxd.Species([cyt, mem], name='k', d=1, charge=1, initial=54.4)
# extracellular parameters provide a constant concentration for the Nernst potential and reactions.
kecs = rxd.Parameter(ecs, name='k_ecs', charge=1, value=2.5)
naecs = rxd.Parameter(ecs, name='na_ecs', charge=1, value=140)
# an undistinguished charged ion for the leak current
x = rxd.Species([cyt, mem, ecs], name='x', charge=1)
# define the various species and parameters on the intracellular and extracellular regions
ki, ko, nai, nao, xi, xo = k[cyt], kecs[ecs], na[cyt], naecs[ecs], x[cyt], x[
ecs]
# the gating states
ngate = rxd.State([cyt, mem], name='ngate', initial=0.24458654944007166)
results['species'] = set(my_species)
results['name'] = sec.hname()
results['hoc_internal_name'] = sec.hoc_internal_name()
results['cell'] = sec.cell()
#all_active_reactions = [r() for r in rxd_module._all_reactions if r() is not None]
return results
if __name__ == '__main__':
from pprint import pprint
from neuron import h, rxd
soma = h.Section(name='soma')
soma.insert('hh')
soma.insert('pas')
soma.nseg = 3
iclamp = h.IClamp(soma(0.3))
gaba = h.ExpSyn(soma(0.7))
dend = h.Section(name='dend')
dend.connect(soma)
cyt = rxd.Region([dend], name='cyt', nrn_region='i')
er = rxd.Region([dend], name='er')
na = rxd.Species(cyt, name='na', charge=1)
ca = rxd.Species([cyt, er], name='ca', charge=2)
h.finitialize(-65)
pprint(psection(soma))
print('\n')
pprint(psection(dend))
from neuron import h, crxd as rxd
h.load_file('stdrun.hoc')
soma = h.Section(name='soma')
r = rxd.Region([soma])
soma.nseg = 5
c = rxd.Species(r, initial=1.0)
assert (len(c.nodes) == 5)
soma.nseg = 3
assert (len(c.nodes) == 3)
soma.nseg = 7
assert (len(c[r].nodes) == 7)
h.tstop = 100
h.run()
# the extracellular space
ecs = rxd.Extracellular(-55,
-55,
-55,
55,
55,
55,
dx=10,
volume_fraction=0.2,
tortuosity=1.6)
# Who?
x = rxd.Species(
[cyt, org, cyt_org_membrane, cyt_ecs_membrane, ecs],
name="x",
d=1.0,
charge=1,
initial=0,
)
Xcyt = x[cyt]
Xorg = x[org]
Xecs = x[ecs]
# What? - produce X in cell 1
# parameter to limit production to cell 1
cell1_param = rxd.Parameter(org,
initial=lambda node: 1.0
if node.segment.sec == cell1 else 0)
# production with a rate following Michaels Menton kinetics
createX = rxd.Rate(Xorg, cell1_param[org] * 1.0 / (10.0 + Xorg))
from neuron import h, crxd as rxd
from matplotlib import pyplot
h.load_file('stdrun.hoc')
cell = h.Section(name='cell')
r = rxd.Region([cell])
def Declare_Parameters(**kwargs):
'''helper function enabling clean declaration of parameters in top namespace'''
for key, value in kwargs.items():
globals()[key] = rxd.Parameter(r, name=key, initial=value)
def Declare_Species(**kwargs):
'''helper function enabling clean declaration of species in top namespace'''
for key, value in kwargs.items():
globals()[key] = rxd.Species(r, name=key, initial=value)
k3 = rxd.Parameter(r, name='k3', initial=1.2)
k4 = rxd.Parameter(r, name='k4', initial=0.6)
P2 = rxd.Species(r, name='P2', initial=0.0614368)
T2 = rxd.Species(r, name='T2', initial=0.0145428)
C = rxd.Species(r, name='C', initial=0.207614)
h.finitialize(-65)
h.continuerun(72)
