/
parameters_C1.py
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/
parameters_C1.py
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'''
Parameters C1 for c302 still under developemnt!!
C1 adds analogue synapses... Might be merged into C
Subject to change without notice!!
'''
from neuroml import Cell
from neuroml import Morphology
from neuroml import Point3DWithDiam
from neuroml import Segment
from neuroml import BiophysicalProperties
from neuroml import IntracellularProperties
from neuroml import Resistivity
from neuroml import Species
from neuroml import MembraneProperties
from neuroml import InitMembPotential
from neuroml import SpecificCapacitance
from neuroml import ChannelDensity
from neuroml import SpikeThresh
from neuroml import GradedSynapse
from neuroml import GapJunction
from neuroml import PulseGenerator
from bioparameters import c302ModelPrototype
'''
The values below are a FIRST APPROXIMATION of conductance based neurons for use in a network to
investigate the synaptic connectivity of C elegans
'''
class ParameterisedModel(c302ModelPrototype):
def __init__(self):
self.level = "C"
self.custom_component_types_definitions = 'cell_C.xml'
self.set_default_bioparameters()
def set_default_bioparameters(self):
self.add_bioparameter("cell_length", "230.3459", "BlindGuess", "0.1")
self.add_bioparameter("cell_diameter", "10", "BlindGuess", "0.1")
self.add_bioparameter("initial_memb_pot", "-45 mV", "BlindGuess", "0.1")
self.add_bioparameter("specific_capacitance", "1 uF_per_cm2", "BlindGuess", "0.1")
self.add_bioparameter("spike_thresh", "-20 mV", "BlindGuess", "0.1")
self.add_bioparameter("leak_cond_density", "0.05 mS_per_cm2", "BlindGuess", "0.1")
self.add_bioparameter("leak_erev", "-50 mV", "BlindGuess", "0.1")
self.add_bioparameter("k_slow_cond_density", "0.5 mS_per_cm2", "BlindGuess", "0.1")
self.add_bioparameter("k_slow_erev", "-60 mV", "BlindGuess", "0.1")
self.add_bioparameter("k_fast_cond_density", "0.05 mS_per_cm2", "BlindGuess", "0.1")
self.add_bioparameter("k_fast_erev", "-60 mV", "BlindGuess", "0.1")
self.add_bioparameter("ca_boyle_cond_density", "0.5 mS_per_cm2", "BlindGuess", "0.1")
self.add_bioparameter("ca_boyle_erev", "40 mV", "BlindGuess", "0.1")
self.add_bioparameter("exc_syn_conductance", "8 nS", "BlindGuess", "0.1")
self.add_bioparameter("exc_syn_delta", "5 mV", "BlindGuess", "0.1")
self.add_bioparameter("exc_syn_vth", "0 mV", "BlindGuess", "0.1")
self.add_bioparameter("exc_syn_erev", "0 mV", "BlindGuess", "0.1")
self.add_bioparameter("exc_syn_k", "0.025per_ms", "BlindGuess", "0.1")
self.add_bioparameter("inh_syn_conductance", "8 nS", "BlindGuess", "0.1")
self.add_bioparameter("inh_syn_delta", "5 mV", "BlindGuess", "0.1")
self.add_bioparameter("inh_syn_vth", "0 mV", "BlindGuess", "0.1")
self.add_bioparameter("inh_syn_erev", "-70 mV", "BlindGuess", "0.1")
self.add_bioparameter("inh_syn_k", "0.025per_ms", "BlindGuess", "0.1")
self.add_bioparameter("elec_syn_gbase", "0.3 nS", "BlindGuess", "0.1")
self.add_bioparameter("unphysiological_offset_current", "0.35 nA", "KnownError", "0")
self.add_bioparameter("unphysiological_offset_current_del", "0 ms", "KnownError", "0")
self.add_bioparameter("unphysiological_offset_current_dur", "2000 ms", "KnownError", "0")
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)