|
| 1 | +""" |
| 2 | +
|
| 3 | +Parameters W2D: |
| 4 | + Cells: Simple cell with just bias and gain from Worm2D |
| 5 | + Chem Synapses: Continuous transmission of output of one cell to next |
| 6 | + Gap junctions: Electrical connection; current linearly depends on difference in voltages |
| 7 | +
|
| 8 | +ASSESSMENT: |
| 9 | + Useful as tested in a number of 2D worm body models & very few parameters |
| 10 | +
|
| 11 | +""" |
| 12 | + |
| 13 | +from neuroml import PulseGenerator |
| 14 | + |
| 15 | +from neuroml import GapJunction |
| 16 | + |
| 17 | +from c302.bioparameters import c302ModelPrototype |
| 18 | + |
| 19 | + |
| 20 | +class ParameterisedModel(c302ModelPrototype): |
| 21 | + def __init__(self): |
| 22 | + super(ParameterisedModel, self).__init__() |
| 23 | + self.level = "W2D" |
| 24 | + self.custom_component_types_definitions = [ |
| 25 | + "cell_W2D.xml", |
| 26 | + "custom_synapses.xml", |
| 27 | + ] |
| 28 | + |
| 29 | + self.set_default_bioparameters() |
| 30 | + self.print_("Set default parameters for %s" % self.level) |
| 31 | + |
| 32 | + def set_default_bioparameters(self): |
| 33 | + self.add_bioparameter("initial_memb_pot", "-45 mV", "BlindGuess", "0.1") |
| 34 | + |
| 35 | + self.add_bioparameter( |
| 36 | + "neuron_to_neuron_elec_syn_gbase", "1 nS", "BlindGuess", "0.1" |
| 37 | + ) |
| 38 | + self.add_bioparameter( |
| 39 | + "neuron_to_muscle_elec_syn_gbase", "1 nS", "BlindGuess", "0.1" |
| 40 | + ) |
| 41 | + |
| 42 | + self.add_bioparameter( |
| 43 | + "unphysiological_offset_current", "0 pA", "KnownError", "0" |
| 44 | + ) # Can be activated later |
| 45 | + self.add_bioparameter( |
| 46 | + "unphysiological_offset_current_del", "0 ms", "KnownError", "0" |
| 47 | + ) |
| 48 | + self.add_bioparameter( |
| 49 | + "unphysiological_offset_current_dur", "2000 ms", "KnownError", "0" |
| 50 | + ) |
| 51 | + |
| 52 | + def create_models(self): |
| 53 | + self.create_generic_muscle_cell() |
| 54 | + self.create_generic_neuron_cell() |
| 55 | + self.create_offsetcurrent() |
| 56 | + self.create_neuron_to_neuron_syn() |
| 57 | + self.create_neuron_to_muscle_syn() |
| 58 | + |
| 59 | + def create_generic_muscle_cell(self): |
| 60 | + self.generic_muscle_cell = CellW2D(id="GenericMuscleCell") |
| 61 | + |
| 62 | + def create_generic_neuron_cell(self): |
| 63 | + self.generic_neuron_cell = CellW2D(id="GenericNeuronCell") |
| 64 | + |
| 65 | + def create_offsetcurrent(self): |
| 66 | + self.offset_current = PulseGenerator( |
| 67 | + id="offset_current", |
| 68 | + delay=self.get_bioparameter("unphysiological_offset_current_del").value, |
| 69 | + duration=self.get_bioparameter("unphysiological_offset_current_dur").value, |
| 70 | + amplitude=self.get_bioparameter("unphysiological_offset_current").value, |
| 71 | + ) |
| 72 | + |
| 73 | + def create_neuron_to_neuron_syn(self): |
| 74 | + self.neuron_to_neuron_exc_syn = OutputSynapse(id="neuron_to_neuron_w2d") |
| 75 | + |
| 76 | + self.neuron_to_neuron_elec_syn = GapJunction( |
| 77 | + id="neuron_to_neuron_elec_syn", |
| 78 | + conductance=self.get_bioparameter("neuron_to_neuron_elec_syn_gbase").value, |
| 79 | + ) |
| 80 | + |
| 81 | + def create_neuron_to_muscle_syn(self): |
| 82 | + self.neuron_to_muscle_exc_syn = OutputSynapse(id="neuron_to_muscle_w2d") |
| 83 | + |
| 84 | + self.neuron_to_muscle_elec_syn = GapJunction( |
| 85 | + id="neuron_to_muscle_elec_syn", |
| 86 | + conductance=self.get_bioparameter("neuron_to_muscle_elec_syn_gbase").value, |
| 87 | + ) |
| 88 | + |
| 89 | + def get_elec_syn(self, pre_cell, post_cell, type): |
| 90 | + if type == "neuron_to_neuron": |
| 91 | + gbase = self.get_bioparameter("neuron_to_neuron_elec_syn_gbase").value |
| 92 | + conn_id = "neuron_to_neuron_elec_syn" |
| 93 | + |
| 94 | + elif type == "neuron_to_muscle": |
| 95 | + gbase = self.get_bioparameter("neuron_to_muscle_elec_syn_gbase").value |
| 96 | + conn_id = "neuron_to_muscle_elec_syn" |
| 97 | + |
| 98 | + return GapJunction(id=conn_id, conductance=gbase) |
| 99 | + |
| 100 | + def get_exc_syn(self, pre_cell, post_cell, type): |
| 101 | + return self.neuron_to_neuron_exc_syn |
| 102 | + |
| 103 | + def get_inh_syn(self, pre_cell, post_cell, type): |
| 104 | + return self.neuron_to_neuron_exc_syn |
| 105 | + |
| 106 | + |
| 107 | +from c302.bioparameters import NonNeuroMLCustomType |
| 108 | + |
| 109 | + |
| 110 | +class CellW2D(NonNeuroMLCustomType): |
| 111 | + def __init__(self, id): |
| 112 | + self.id = id |
| 113 | + |
| 114 | + |
| 115 | +class OutputSynapse(NonNeuroMLCustomType): |
| 116 | + def __init__(self, id): |
| 117 | + self.id = id |
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