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c302_C1_Syns.net.nml
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<neuroml xmlns="http://www.neuroml.org/schema/neuroml2" xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.1.xsd" id="c302_C1_Syns">
<notes>
Parameters and setting used to generate this network:
Data reader: SpreadsheetDataReader
c302 version: 0.9.1
owmeta version: - not installed -
owmeta_core version: - not installed -
Cells: ['URYDL', 'SMDDR', 'VD12', 'VB11', 'AS2', 'AIZL', 'ASHL']
Cell stimulated: []
Connection: []
Connection numbers overridden: None
Connection numbers scaled: None
Connection polarities override: None
Muscles: ['MDL07']
Known BioParameters:
BioParameter: ca_boyle_erev = 40 mV (SRC: BlindGuess, certainty 0.1)
BioParameter: ca_conc_decay_time = 11.5943 ms (SRC: BlindGuess, certainty 0.1)
BioParameter: ca_conc_rho = 0.000238919 mol_per_m_per_A_per_s (SRC: BlindGuess, certainty 0.1)
BioParameter: cell_diameter = 5 (SRC: BlindGuess, certainty 0.1)
BioParameter: exc_syn_delta = 5 mV (SRC: BlindGuess, certainty 0.1)
BioParameter: exc_syn_erev = 0 mV (SRC: BlindGuess, certainty 0.1)
BioParameter: exc_syn_k = 0.025per_ms (SRC: BlindGuess, certainty 0.1)
BioParameter: exc_syn_vth = 0 mV (SRC: BlindGuess, certainty 0.1)
BioParameter: inh_syn_delta = 5 mV (SRC: BlindGuess, certainty 0.1)
BioParameter: inh_syn_erev = -70 mV (SRC: BlindGuess, certainty 0.1)
BioParameter: inh_syn_k = 0.025per_ms (SRC: BlindGuess, certainty 0.1)
BioParameter: inh_syn_vth = 0 mV (SRC: BlindGuess, certainty 0.1)
BioParameter: initial_memb_pot = -45 mV (SRC: BlindGuess, certainty 0.1)
BioParameter: k_fast_erev = -60 mV (SRC: BlindGuess, certainty 0.1)
BioParameter: k_slow_erev = -60 mV (SRC: BlindGuess, certainty 0.1)
BioParameter: leak_erev = -50 mV (SRC: BlindGuess, certainty 0.1)
BioParameter: muscle_ca_boyle_cond_density = 0.0007 S_per_cm2 (SRC: BlindGuess, certainty 0.1)
BioParameter: muscle_k_fast_cond_density = 0.0001 S_per_cm2 (SRC: BlindGuess, certainty 0.1)
BioParameter: muscle_k_slow_cond_density = 0.0006 S_per_cm2 (SRC: BlindGuess, certainty 0.1)
BioParameter: muscle_leak_cond_density = 5e-7 S_per_cm2 (SRC: BlindGuess, certainty 0.1)
BioParameter: muscle_length = 20 (SRC: BlindGuess, certainty 0.1)
BioParameter: muscle_spike_thresh = -20 mV (SRC: BlindGuess, certainty 0.1)
BioParameter: neuron_ca_boyle_cond_density = 3 mS_per_cm2 (SRC: BlindGuess, certainty 0.1)
BioParameter: neuron_k_fast_cond_density = 0.0711643917483308 mS_per_cm2 (SRC: BlindGuess, certainty 0.1)
BioParameter: neuron_k_slow_cond_density = 3 mS_per_cm2 (SRC: BlindGuess, certainty 0.1)
BioParameter: neuron_leak_cond_density = 0.005 mS_per_cm2 (SRC: BlindGuess, certainty 0.1)
BioParameter: neuron_spike_thresh = -20 mV (SRC: BlindGuess, certainty 0.1)
BioParameter: neuron_to_muscle_elec_syn_gbase = 0.00052 nS (SRC: BlindGuess, certainty 0.1)
BioParameter: neuron_to_muscle_exc_syn_conductance = 0.09 nS (SRC: BlindGuess, certainty 0.1)
BioParameter: neuron_to_muscle_inh_syn_conductance = 0.09 nS (SRC: BlindGuess, certainty 0.1)
BioParameter: neuron_to_neuron_elec_syn_gbase = 0.00052 nS (SRC: BlindGuess, certainty 0.1)
BioParameter: neuron_to_neuron_exc_syn_conductance = 0.09 nS (SRC: BlindGuess, certainty 0.1)
BioParameter: neuron_to_neuron_inh_syn_conductance = 0.09 nS (SRC: BlindGuess, certainty 0.1)
BioParameter: specific_capacitance = 1 uF_per_cm2 (SRC: BlindGuess, certainty 0.1)
BioParameter: unphysiological_offset_current = 0 pA (SRC: KnownError, certainty 0)
BioParameter: unphysiological_offset_current_del = 50 ms (SRC: Testing IClamp, certainty 0)
BioParameter: unphysiological_offset_current_dur = 2000 ms (SRC: KnownError, certainty 0)
</notes>
<include href="cell_C.xml"/>
<fixedFactorConcentrationModel id="CaPool" ion="ca" restingConc="0 mM" decayConstant="11.5943 ms" rho="0.000238919 mol_per_m_per_A_per_s"/>
<gapJunction id="neuron_to_neuron_elec_syn" conductance="0.00052 nS"/>
<silentSynapse id="silent"/>
<gradedSynapse id="neuron_to_neuron_inh_syn" conductance="0.09 nS" delta="5 mV" Vth="0 mV" k="0.025per_ms" erev="-70 mV"/>
<gradedSynapse id="neuron_to_neuron_exc_syn" conductance="0.09 nS" delta="5 mV" Vth="0 mV" k="0.025per_ms" erev="0 mV"/>
<gradedSynapse id="neuron_to_muscle_exc_syn" conductance="0.09 nS" delta="5 mV" Vth="0 mV" k="0.025per_ms" erev="0 mV"/>
<cell id="GenericMuscleCell">
<morphology id="morphology_GenericMuscleCell">
<segment id="0" name="soma">
<proximal x="0.0" y="0.0" z="0.0" diameter="5.0"/>
<distal x="0.0" y="20.0" z="0.0" diameter="5.0"/>
</segment>
</morphology>
<biophysicalProperties id="biophys_GenericMuscleCell">
<membraneProperties>
<channelDensity id="Leak_all" ionChannel="Leak" condDensity="5e-7 S_per_cm2" erev="-50 mV" ion="non_specific"/>
<channelDensity id="k_slow_all" ionChannel="k_slow" condDensity="0.0006 S_per_cm2" erev="-60 mV" ion="k"/>
<channelDensity id="k_fast_all" ionChannel="k_fast" condDensity="0.0001 S_per_cm2" erev="-60 mV" ion="k"/>
<channelDensity id="ca_boyle_all" ionChannel="ca_boyle" condDensity="0.0007 S_per_cm2" erev="40 mV" ion="ca"/>
<spikeThresh value="-20 mV"/>
<specificCapacitance value="1 uF_per_cm2"/>
<initMembPotential value="-45 mV"/>
</membraneProperties>
<intracellularProperties>
<species id="ca" concentrationModel="CaPool" ion="ca" initialConcentration="0 mM" initialExtConcentration="2E-6 mol_per_cm3"/>
<resistivity value="0.1 kohm_cm"/>
</intracellularProperties>
</biophysicalProperties>
</cell>
<cell id="GenericNeuronCell">
<morphology id="morphology_GenericNeuronCell">
<segment id="0" name="soma">
<proximal x="0.0" y="0.0" z="0.0" diameter="5.0"/>
<distal x="0.0" y="0.0" z="0.0" diameter="5.0"/>
</segment>
</morphology>
<biophysicalProperties id="biophys_GenericNeuronCell">
<membraneProperties>
<channelDensity id="Leak_all" ionChannel="Leak" condDensity="0.005 mS_per_cm2" erev="-50 mV" ion="non_specific"/>
<channelDensity id="k_slow_all" ionChannel="k_slow" condDensity="3 mS_per_cm2" erev="-60 mV" ion="k"/>
<channelDensity id="k_fast_all" ionChannel="k_fast" condDensity="0.0711643917483308 mS_per_cm2" erev="-60 mV" ion="k"/>
<channelDensity id="ca_boyle_all" ionChannel="ca_boyle" condDensity="3 mS_per_cm2" erev="40 mV" ion="ca"/>
<spikeThresh value="-20 mV"/>
<specificCapacitance value="1 uF_per_cm2"/>
<initMembPotential value="-45 mV"/>
</membraneProperties>
<intracellularProperties>
<species id="ca" concentrationModel="CaPool" ion="ca" initialConcentration="0 mM" initialExtConcentration="2E-6 mol_per_cm3"/>
<resistivity value="0.1 kohm_cm"/>
</intracellularProperties>
</biophysicalProperties>
</cell>
<pulseGenerator id="offset_current" delay="50 ms" duration="2000 ms" amplitude="0 pA"/>
<pulseGenerator id="stim_URYDL_1" delay="500ms" duration="800ms" amplitude="1pA"/>
<pulseGenerator id="stim_VD12_1" delay="500ms" duration="800ms" amplitude="1pA"/>
<pulseGenerator id="stim_AS2_1" delay="500ms" duration="800ms" amplitude="1pA"/>
<pulseGenerator id="stim_AIZL_1" delay="500ms" duration="800ms" amplitude="1pA"/>
<pulseGenerator id="stim_URYDL_2" delay="1900ms" duration="800ms" amplitude="5pA"/>
<pulseGenerator id="stim_VD12_2" delay="1900ms" duration="800ms" amplitude="5pA"/>
<pulseGenerator id="stim_AS2_2" delay="1900ms" duration="800ms" amplitude="5pA"/>
<pulseGenerator id="stim_AIZL_2" delay="1900ms" duration="800ms" amplitude="5pA"/>
<network id="c302_C1_Syns">
<property tag="recommended_duration_ms" value="3600"/>
<property tag="recommended_dt_ms" value="0.05"/>
<population id="AIZL" component="GenericNeuronCell" size="1" type="populationList">
<property tag="color" value="1 0 .4"/>
<property tag="type" value="interneuron"/>
<property tag="receptor" value="MOD-1; NPR-2; SER-2"/>
<property tag="neurotransmitter" value="Glutamate"/>
<instance id="0">
<location x="5.6000004" y="-258.75" z="37.450000000000003"/>
</instance>
</population>
<population id="AS2" component="GenericNeuronCell" size="1" type="populationList">
<property tag="color" value=".5 .4 1"/>
<property tag="type" value="motor"/>
<property tag="receptor" value="ACR-14; ACR-15; CKR-2; DOP-1; DOP-3; LGC-46; NPR-3; UNC-63"/>
<property tag="neurotransmitter" value="Acetylcholine"/>
<property tag="OpenWormBackerAssignedName" value="Geraldine"/>
<instance id="0">
<location x="-1.8750001" y="-203.875" z="-12.725"/>
</instance>
</population>
<population id="ASHL" component="GenericNeuronCell" size="1" type="populationList">
<property tag="color" value="1 .2 1"/>
<property tag="type" value="sensory"/>
<property tag="receptor" value="DCAR-1; DOP-4; NPR-1; NPR-2; NTR-1; NTR-2; OCR-2; OCTR-1; OSM-9; SER-3; SER-5; SRA-6; SRB-6; TMC-1; TRPA-1; TYRA-2; UNC-8"/>
<property tag="neurotransmitter" value="Glutamate"/>
<instance id="0">
<location x="5.55" y="-265.625" z="41.0"/>
</instance>
</population>
<population id="SMDDR" component="GenericNeuronCell" size="1" type="populationList">
<property tag="color" value=".5 .4 1"/>
<property tag="type" value="motor"/>
<property tag="receptor" value="LGC-55; NTR-2"/>
<property tag="neurotransmitter" value="Acetylcholine"/>
<instance id="0">
<location x="-7.4500003" y="-266.25" z="34.100000000000001"/>
</instance>
</population>
<population id="URYDL" component="GenericNeuronCell" size="1" type="populationList">
<property tag="color" value="1 .2 1"/>
<property tag="type" value="sensory"/>
<property tag="receptor" value="LGC-53; PDFR-1; SER-1"/>
<property tag="neurotransmitter" value="Glutamate"/>
<instance id="0">
<location x="4.125" y="-281.425000000000011" z="51.899997999999997"/>
</instance>
</population>
<population id="VB11" component="GenericNeuronCell" size="1" type="populationList">
<property tag="color" value=".5 .4 1"/>
<property tag="type" value="motor; sensory"/>
<property tag="receptor" value="CKR-2; DOP-1; DOP-3; NPR-3"/>
<property tag="neurotransmitter" value="Acetylcholine"/>
<instance id="0">
<location x="-1.8249999" y="262.324999999999989" z="-21.949999999999999"/>
</instance>
</population>
<population id="VD12" component="GenericNeuronCell" size="1" type="populationList">
<property tag="color" value=".5 .4 1"/>
<property tag="type" value="motor"/>
<property tag="receptor" value="DOP-3; MOD-1; NPR-1; SER-2"/>
<property tag="neurotransmitter" value="GABA"/>
<instance id="0">
<location x="-0.75" y="345.5" z="-23.149999999999999"/>
</instance>
</population>
<population id="MDL07" component="GenericMuscleCell" size="1" type="populationList">
<property tag="color" value="0 .6 0"/>
<instance id="0">
<location x="80.0" y="-90.0" z="80.0"/>
</instance>
</population>
<electricalProjection id="NC_AIZL_ASHL_Generic_GJ" presynapticPopulation="AIZL" postsynapticPopulation="ASHL">
<electricalConnectionInstanceW id="0" preCell="../AIZL/0/GenericNeuronCell" postCell="../ASHL/0/GenericNeuronCell" synapse="neuron_to_neuron_elec_syn" weight="1.0"/>
</electricalProjection>
<electricalProjection id="NC_ASHL_AIZL_Generic_GJ" presynapticPopulation="ASHL" postsynapticPopulation="AIZL">
<electricalConnectionInstanceW id="0" preCell="../ASHL/0/GenericNeuronCell" postCell="../AIZL/0/GenericNeuronCell" synapse="neuron_to_neuron_elec_syn" weight="1.0"/>
</electricalProjection>
<continuousProjection id="NC_VD12_VB11_GABA" presynapticPopulation="VD12" postsynapticPopulation="VB11">
<continuousConnectionInstanceW id="0" preCell="../VD12/0/GenericNeuronCell" postCell="../VB11/0/GenericNeuronCell" preComponent="silent" postComponent="neuron_to_neuron_inh_syn" weight="1.0"/>
</continuousProjection>
<continuousProjection id="NC_URYDL_SMDDR_Glutamate" presynapticPopulation="URYDL" postsynapticPopulation="SMDDR">
<continuousConnectionInstanceW id="0" preCell="../URYDL/0/GenericNeuronCell" postCell="../SMDDR/0/GenericNeuronCell" preComponent="silent" postComponent="neuron_to_neuron_exc_syn" weight="1.0"/>
</continuousProjection>
<continuousProjection id="NC_AS2_MDL07_Acetylcholine" presynapticPopulation="AS2" postsynapticPopulation="MDL07">
<continuousConnectionInstanceW id="0" preCell="../AS2/0/GenericNeuronCell" postCell="../MDL07/0/GenericMuscleCell" preComponent="silent" postComponent="neuron_to_muscle_exc_syn" weight="3.0"/>
</continuousProjection>
<inputList id="Input_URYDL_stim_URYDL_1" population="URYDL" component="stim_URYDL_1">
<input id="0" target="../URYDL/0/GenericNeuronCell" destination="synapses"/>
</inputList>
<inputList id="Input_VD12_stim_VD12_1" population="VD12" component="stim_VD12_1">
<input id="0" target="../VD12/0/GenericNeuronCell" destination="synapses"/>
</inputList>
<inputList id="Input_AS2_stim_AS2_1" population="AS2" component="stim_AS2_1">
<input id="0" target="../AS2/0/GenericNeuronCell" destination="synapses"/>
</inputList>
<inputList id="Input_AIZL_stim_AIZL_1" population="AIZL" component="stim_AIZL_1">
<input id="0" target="../AIZL/0/GenericNeuronCell" destination="synapses"/>
</inputList>
<inputList id="Input_URYDL_stim_URYDL_2" population="URYDL" component="stim_URYDL_2">
<input id="0" target="../URYDL/0/GenericNeuronCell" destination="synapses"/>
</inputList>
<inputList id="Input_VD12_stim_VD12_2" population="VD12" component="stim_VD12_2">
<input id="0" target="../VD12/0/GenericNeuronCell" destination="synapses"/>
</inputList>
<inputList id="Input_AS2_stim_AS2_2" population="AS2" component="stim_AS2_2">
<input id="0" target="../AS2/0/GenericNeuronCell" destination="synapses"/>
</inputList>
<inputList id="Input_AIZL_stim_AIZL_2" population="AIZL" component="stim_AIZL_2">
<input id="0" target="../AIZL/0/GenericNeuronCell" destination="synapses"/>
</inputList>
</network>
</neuroml>