def create_models(self):
self.generic_cell = Cell(id = "GenericCell")
morphology = Morphology()
morphology.id = "morphology_"+self.generic_cell.id
self.generic_cell.morphology = morphology
prox_point = Point3DWithDiam(x="0", y="0", z="0", diameter=self.get_bioparameter("cell_diameter").value)
dist_point = Point3DWithDiam(x="0", y="0", z=self.get_bioparameter("cell_length").value, diameter=self.get_bioparameter("cell_diameter").value)
segment = Segment(id="0",
name="soma",
proximal = prox_point,
distal = dist_point)
morphology.segments.append(segment)
self.generic_cell.biophysical_properties = BiophysicalProperties(id="biophys_"+self.generic_cell.id)
mp = MembraneProperties()
self.generic_cell.biophysical_properties.membrane_properties = mp
mp.init_memb_potentials.append(InitMembPotential(value=self.get_bioparameter("initial_memb_pot").value))
mp.specific_capacitances.append(SpecificCapacitance(value=self.get_bioparameter("specific_capacitance").value))
mp.spike_threshes.append(SpikeThresh(value=self.get_bioparameter("spike_thresh").value))
mp.channel_densities.append(ChannelDensity(cond_density=self.get_bioparameter("leak_cond_density").value,
id="Leak_all",
ion_channel="Leak",
erev=self.get_bioparameter("leak_erev").value,
ion="non_specific"))
mp.channel_densities.append(ChannelDensity(cond_density=self.get_bioparameter("k_slow_cond_density").value,
id="k_slow_all",
ion_channel="k_slow",
erev=self.get_bioparameter("k_slow_erev").value,
ion="k"))
mp.channel_densities.append(ChannelDensity(cond_density=self.get_bioparameter("k_fast_cond_density").value,
id="k_fast_all",
ion_channel="k_fast",
erev=self.get_bioparameter("k_fast_erev").value,
ion="k"))
mp.channel_densities.append(ChannelDensity(cond_density=self.get_bioparameter("ca_boyle_cond_density").value,
id="ca_boyle_all",
ion_channel="ca_boyle",
erev=self.get_bioparameter("ca_boyle_erev").value,
ion="ca"))
ip = IntracellularProperties()
self.generic_cell.biophysical_properties.intracellular_properties = ip
# NOTE: resistivity/axial resistance not used for single compartment cell models, so value irrelevant!
ip.resistivities.append(Resistivity(value="0.1 kohm_cm"))
# NOTE: Ca reversal potential not calculated by Nernst, so initial_ext_concentration value irrelevant!
species = Species(id="ca",
ion="ca",
concentration_model="CaPool",
initial_concentration="0 mM",
initial_ext_concentration="2E-6 mol_per_cm3")
ip.species.append(species)
self.exc_syn = GradedSynapse(id="exc_syn",
conductance = self.get_bioparameter("exc_syn_conductance").value,
delta = self.get_bioparameter("exc_syn_delta").value,
Vth = self.get_bioparameter("exc_syn_vth").value,
erev = self.get_bioparameter("exc_syn_erev").value,
k = self.get_bioparameter("exc_syn_k").value)
self.inh_syn = GradedSynapse(id="inh_syn",
conductance = self.get_bioparameter("inh_syn_conductance").value,
delta = self.get_bioparameter("inh_syn_delta").value,
Vth = self.get_bioparameter("inh_syn_vth").value,
erev = self.get_bioparameter("inh_syn_erev").value,
k = self.get_bioparameter("inh_syn_k").value)
self.elec_syn = GapJunction(id="elec_syn",
conductance = self.get_bioparameter("elec_syn_gbase").value)
self.offset_current = PulseGenerator(id="offset_current",
delay=self.get_bioparameter("unphysiological_offset_current_del").value,
duration=self.get_bioparameter("unphysiological_offset_current_dur").value,
amplitude=self.get_bioparameter("unphysiological_offset_current").value)
def create_generic_neuron_cell(self):
self.generic_neuron_cell = Cell(id="GenericNeuronCell")
morphology = Morphology()
morphology.id = "morphology_" + self.generic_neuron_cell.id
self.generic_neuron_cell.morphology = morphology
prox_point = Point3DWithDiam(
x="0",
y="0",
z="0",
diameter=self.get_bioparameter("cell_diameter").value)
dist_point = Point3DWithDiam(
x="0",
y="0",
z="0",
diameter=self.get_bioparameter("cell_diameter").value)
segment = Segment(id="0",
name="soma",
proximal=prox_point,
distal=dist_point)
morphology.segments.append(segment)
self.generic_neuron_cell.biophysical_properties = BiophysicalProperties(
id="biophys_" + self.generic_neuron_cell.id)
mp = MembraneProperties()
self.generic_neuron_cell.biophysical_properties.membrane_properties = mp
mp.init_memb_potentials.append(
InitMembPotential(
value=self.get_bioparameter("initial_memb_pot").value))
mp.specific_capacitances.append(
SpecificCapacitance(value=self.get_bioparameter(
"neuron_specific_capacitance").value))
mp.spike_threshes.append(
SpikeThresh(
value=self.get_bioparameter("neuron_spike_thresh").value))
mp.channel_densities.append(
ChannelDensity(cond_density=self.get_bioparameter(
"neuron_leak_cond_density").value,
id="Leak_all",
ion_channel="Leak",
erev=self.get_bioparameter("leak_erev").value,
ion="non_specific"))
mp.channel_densities.append(
ChannelDensity(cond_density=self.get_bioparameter(
"neuron_k_slow_cond_density").value,
id="k_slow_all",
ion_channel="k_slow",
erev=self.get_bioparameter("k_slow_erev").value,
ion="k"))
'''
mp.channel_densities.append(ChannelDensity(cond_density=self.get_bioparameter("neuron_k_fast_cond_density").value,
id="k_fast_all",
ion_channel="k_fast",
erev=self.get_bioparameter("k_fast_erev").value,
ion="k"))'''
mp.channel_densities.append(
ChannelDensity(cond_density=self.get_bioparameter(
"neuron_ca_simple_cond_density").value,
id="ca_simple_all",
ion_channel="ca_simple",
erev=self.get_bioparameter("ca_simple_erev").value,
ion="ca"))
ip = IntracellularProperties()
self.generic_neuron_cell.biophysical_properties.intracellular_properties = ip
# NOTE: resistivity/axial resistance not used for single compartment cell models, so value irrelevant!
ip.resistivities.append(Resistivity(value="0.1 kohm_cm"))
# NOTE: Ca reversal potential not calculated by Nernst, so initial_ext_concentration value irrelevant!
species = Species(id="ca",
ion="ca",
concentration_model="CaPool",
initial_concentration="0 mM",
initial_ext_concentration="2E-6 mol_per_cm3")
ip.species.append(species)
def create_neuron_cell(self, cell_name, morphology):
cell = Cell(id=cell_name)
cell.notes = "Cell model created by c302 with custom electrical parameters"
cell.morphology = morphology
cell.biophysical_properties = BiophysicalProperties(id="biophys_" +
cell.id)
mp = MembraneProperties()
cell.biophysical_properties.membrane_properties = mp
mp.init_memb_potentials.append(
InitMembPotential(
value=self.get_bioparameter("initial_memb_pot").value))
mp.specific_capacitances.append(
SpecificCapacitance(
value=self.get_bioparameter("specific_capacitance").value))
mp.spike_threshes.append(
SpikeThresh(
value=self.get_bioparameter("neuron_spike_thresh").value))
mp.channel_densities.append(
ChannelDensity(cond_density=self.get_bioparameter(
"neuron_leak_cond_density").value,
id="Leak_all",
ion_channel="Leak",
erev=self.get_bioparameter("leak_erev").value,
ion="non_specific"))
mp.channel_densities.append(
ChannelDensity(cond_density=self.get_bioparameter(
"neuron_k_slow_cond_density").value,
id="k_slow_all",
ion_channel="k_slow",
erev=self.get_bioparameter("k_slow_erev").value,
ion="k"))
mp.channel_densities.append(
ChannelDensity(cond_density=self.get_bioparameter(
"neuron_k_fast_cond_density").value,
id="k_fast_all",
ion_channel="k_fast",
erev=self.get_bioparameter("k_fast_erev").value,
ion="k"))
mp.channel_densities.append(
ChannelDensity(cond_density=self.get_bioparameter(
"neuron_ca_boyle_cond_density").value,
id="ca_boyle_all",
ion_channel="ca_boyle",
erev=self.get_bioparameter("ca_boyle_erev").value,
ion="ca"))
ip = IntracellularProperties()
cell.biophysical_properties.intracellular_properties = ip
# NOTE: resistivity/axial resistance not used for single compartment cell models, so value irrelevant!
ip.resistivities.append(
Resistivity(value=self.get_bioparameter("resistivity").value))
# NOTE: Ca reversal potential not calculated by Nernst, so initial_ext_concentration value irrelevant!
species = Species(id="ca",
ion="ca",
concentration_model="CaPool",
initial_concentration="0 mM",
initial_ext_concentration="2E-6 mol_per_cm3")
ip.species.append(species)
return cell
