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c302_C2_Muscles.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_C2_Muscles">
<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: ['AS1', 'AS10', 'AS11', 'AS2', 'AS3', 'AS4', 'AS5', 'AS6', 'AS7', 'AS8', 'AS9', 'AVFL', 'AVFR', 'AVKR', 'AVL', 'CEPVL', 'CEPVR', 'DA1', 'DA2', 'DA3', 'DA4', 'DA5', 'DA6', 'DA7', 'DA8', 'DA9', 'DB1', 'DB2', 'DB3', 'DB4', 'DB5', 'DB6', 'DB7', 'DD1', 'DD2', 'DD3', 'DD4', 'DD5', 'DD6', 'DVB', 'HSNL', 'HSNR', 'IL1DL', 'IL1DR', 'IL1L', 'IL1R', 'IL1VL', 'IL1VR', 'PDA', 'PDB', 'PVNL', 'PVNR', 'RID', 'RIML', 'RIMR', 'RIVL', 'RIVR', 'RMDDL', 'RMDDR', 'RMDL', 'RMDR', 'RMDVL', 'RMDVR', 'RMED', 'RMEL', 'RMER', 'RMEV', 'RMFL', 'RMGL', 'RMGR', 'RMHL', 'RMHR', 'SMBDL', 'SMBDR', 'SMBVL', 'SMBVR', 'SMDDL', 'SMDDR', 'SMDVL', 'SMDVR', 'URADL', 'URADR', 'URAVL', 'URAVR', 'VA1', 'VA10', 'VA11', 'VA12', 'VA2', 'VA3', 'VA4', 'VA5', 'VA6', 'VA7', 'VA8', 'VA9', 'VB1', 'VB10', 'VB11', 'VB2', 'VB3', 'VB4', 'VB5', 'VB6', 'VB7', 'VB8', 'VB9', 'VC1', 'VC2', 'VC3', 'VC4', 'VC5', 'VC6', 'VD1', 'VD10', 'VD11', 'VD12', 'VD13', 'VD2', 'VD3', 'VD4', 'VD5', 'VD6', 'VD7', 'VD8', 'VD9', 'AVAL', 'AVAR', 'AVBL', 'AVBR', 'AVDL', 'AVDR', 'PVCL', 'PVCR']
Cell stimulated: ['AVBL', 'AVBR']
Connection: []
Connection numbers overridden: None
Connection numbers scaled: None
Connection polarities override: None
Muscles: All muscles
Known BioParameters:
BioParameter: ca_boyle_erev = 10 mV (SRC: BlindGuess, certainty 0.1)
BioParameter: ca_conc_decay_time = 13.811870945509265 ms (SRC: BlindGuess, certainty 0.1)
BioParameter: ca_conc_decay_time_muscle = 60.811870945509265 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: ca_conc_rho_muscle = 0.002238919 mol_per_m_per_A_per_s (SRC: BlindGuess, certainty 0.1)
BioParameter: cell_diameter = 5 (SRC: BlindGuess, certainty 0.1)
BioParameter: initial_memb_pot = -60 mV (SRC: BlindGuess, certainty 0.1)
BioParameter: k_fast_erev = -70 mV (SRC: BlindGuess, certainty 0.1)
BioParameter: k_slow_erev = -60 mV (SRC: BlindGuess, certainty 0.1)
BioParameter: leak_erev = -60 mV (SRC: BlindGuess, certainty 0.1)
BioParameter: muscle_ca_boyle_cond_density = 0.812775772264702 mS_per_cm2 (SRC: BlindGuess, certainty 0.1)
BioParameter: muscle_ca_boyle_erev = 0 mV (SRC: BlindGuess, certainty 0.1)
BioParameter: muscle_initial_memb_pot = -28 mV (SRC: BlindGuess, certainty 0.1)
BioParameter: muscle_k_fast_cond_density = 0.042711643917483308 mS_per_cm2 (SRC: BlindGuess, certainty 0.1)
BioParameter: muscle_k_fast_erev = -30 mV (SRC: BlindGuess, certainty 0.1)
BioParameter: muscle_k_slow_cond_density = 0.45833751019872582 mS_per_cm2 (SRC: BlindGuess, certainty 0.1)
BioParameter: muscle_k_slow_erev = -30 mV (SRC: BlindGuess, certainty 0.1)
BioParameter: muscle_leak_cond_density = 0.002 mS_per_cm2 (SRC: BlindGuess, certainty 0.1)
BioParameter: muscle_leak_erev = -20 mV (SRC: BlindGuess, certainty 0.1)
BioParameter: muscle_length = 20 (SRC: BlindGuess, certainty 0.1)
BioParameter: muscle_specific_capacitance = 1 uF_per_cm2 (SRC: BlindGuess, certainty 0.1)
BioParameter: muscle_spike_thresh = -10 mV (SRC: BlindGuess, certainty 0.1)
BioParameter: muscle_to_muscle_elec_syn_gbase = 0 nS (SRC: BlindGuess, certainty 0.1)
BioParameter: neuron_ca_boyle_cond_density = 1.812775772264702 mS_per_cm2 (SRC: BlindGuess, certainty 0.1)
BioParameter: neuron_k_fast_cond_density = 0.042711643917483308 mS_per_cm2 (SRC: BlindGuess, certainty 0.1)
BioParameter: neuron_k_slow_cond_density = 0.45833751019872582 mS_per_cm2 (SRC: BlindGuess, certainty 0.1)
BioParameter: neuron_leak_cond_density = 0.002 mS_per_cm2 (SRC: BlindGuess, certainty 0.1)
BioParameter: neuron_spike_thresh = -55 mV (SRC: BlindGuess, certainty 0.1)
BioParameter: neuron_to_motor_delayed_elec_syn_gbase = 0.01252 nS (SRC: BlindGuess, certainty 0.1)
BioParameter: neuron_to_motor_delayed_elec_syn_mu = -30 (SRC: BlindGuess, certainty 0.1)
BioParameter: neuron_to_motor_delayed_elec_syn_sigma = 0.4 (SRC: BlindGuess, certainty 0.1)
BioParameter: neuron_to_motor_delayed_elec_syn_weight = 1 (SRC: BlindGuess, certainty 0.1)
BioParameter: neuron_to_muscle_elec_syn_gbase = 0.00152 nS (SRC: BlindGuess, certainty 0.1)
BioParameter: neuron_to_muscle_exc_syn_conductance = 0.10 nS (SRC: BlindGuess, certainty 0.1)
BioParameter: neuron_to_muscle_exc_syn_delta = 19 mV (SRC: BlindGuess, certainty 0.1)
BioParameter: neuron_to_muscle_exc_syn_erev = 37 mV (SRC: BlindGuess, certainty 0.1)
BioParameter: neuron_to_muscle_exc_syn_k = 1.205per_ms (SRC: BlindGuess, certainty 0.1)
BioParameter: neuron_to_muscle_exc_syn_mu = 5 mV (SRC: BlindGuess, certainty 0.1)
BioParameter: neuron_to_muscle_exc_syn_sigma = 0.5 per_mV (SRC: BlindGuess, certainty 0.1)
BioParameter: neuron_to_muscle_exc_syn_vth = 27 mV (SRC: BlindGuess, certainty 0.1)
BioParameter: neuron_to_muscle_exc_syn_weight = 1 (SRC: BlindGuess, certainty 0.1)
BioParameter: neuron_to_muscle_inh_syn_conductance = 1.29 nS (SRC: BlindGuess, certainty 0.1)
BioParameter: neuron_to_muscle_inh_syn_delta = 5 mV (SRC: BlindGuess, certainty 0.1)
BioParameter: neuron_to_muscle_inh_syn_erev = -35 mV (SRC: BlindGuess, certainty 0.1)
BioParameter: neuron_to_muscle_inh_syn_k = 0.025per_ms (SRC: BlindGuess, certainty 0.1)
BioParameter: neuron_to_muscle_inh_syn_vth = 0 mV (SRC: BlindGuess, certainty 0.1)
BioParameter: neuron_to_neuron_elec_syn_gbase = 0.01252 nS (SRC: BlindGuess, certainty 0.1)
BioParameter: neuron_to_neuron_elec_syn_weight = 1 (SRC: BlindGuess, certainty 0.1)
BioParameter: neuron_to_neuron_exc_syn_conductance = 0.49 nS (SRC: BlindGuess, certainty 0.1)
BioParameter: neuron_to_neuron_exc_syn_delta = 5 mV (SRC: BlindGuess, certainty 0.1)
BioParameter: neuron_to_neuron_exc_syn_erev = -10 mV (SRC: BlindGuess, certainty 0.1)
BioParameter: neuron_to_neuron_exc_syn_k = 0.5per_ms (SRC: BlindGuess, certainty 0.1)
BioParameter: neuron_to_neuron_exc_syn_vth = 00 mV (SRC: BlindGuess, certainty 0.1)
BioParameter: neuron_to_neuron_inh_syn_conductance = 0.29 nS (SRC: BlindGuess, certainty 0.1)
BioParameter: neuron_to_neuron_inh_syn_delta = 5 mV (SRC: BlindGuess, certainty 0.1)
BioParameter: neuron_to_neuron_inh_syn_erev = -70 mV (SRC: BlindGuess, certainty 0.1)
BioParameter: neuron_to_neuron_inh_syn_k = 0.015per_ms (SRC: BlindGuess, certainty 0.1)
BioParameter: neuron_to_neuron_inh_syn_vth = 0 mV (SRC: BlindGuess, certainty 0.1)
BioParameter: specific_capacitance = 5 uF_per_cm2 (SRC: BlindGuess, certainty 0.1)
BioParameter: unphysiological_offset_current = 5pA (SRC: Testing IClamp, certainty 0)
BioParameter: unphysiological_offset_current_del = 50 ms (SRC: Testing IClamp, certainty 0)
BioParameter: unphysiological_offset_current_dur = 900 ms (SRC: Testing IClamp, certainty 0)
</notes>
<include href="cell_C.xml"/>
<include href="custom_muscle_components.xml"/>
<include href="custom_synapses.xml"/>
<fixedFactorConcentrationModel id="CaPool" ion="ca" restingConc="0 mM" decayConstant="13.811870945509265 ms" rho="0.000238919 mol_per_m_per_A_per_s"/>
<fixedFactorConcentrationModel id="CaPoolMuscle" ion="ca" restingConc="0 mM" decayConstant="60.811870945509265 ms" rho="0.002238919 mol_per_m_per_A_per_s"/>
<gapJunction id="neuron_to_neuron_elec_syn" conductance="0.01252 nS"/>
<silentSynapse id="silent"/>
<gradedSynapse id="neuron_to_neuron_exc_syn" conductance="0.49 nS" delta="5 mV" Vth="00 mV" k="0.5per_ms" erev="-10 mV"/>
<gradedSynapse id="neuron_to_neuron_inh_syn" conductance="0.29 nS" delta="5 mV" Vth="0 mV" k="0.015per_ms" erev="-70 mV"/>
<gradedSynapse id="neuron_to_muscle_exc_syn" conductance="0.10 nS" delta="19 mV" Vth="27 mV" k="1.205per_ms" erev="37 mV"/>
<gradedSynapse id="neuron_to_muscle_inh_syn" conductance="1.29 nS" delta="5 mV" Vth="0 mV" k="0.025per_ms" erev="-35 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="0.002 mS_per_cm2" erev="-20 mV" ion="non_specific"/>
<channelDensity id="k_slow_all" ionChannel="k_slow_muscle" condDensity="0.45833751019872582 mS_per_cm2" erev="-30 mV" ion="k"/>
<channelDensity id="k_fast_all" ionChannel="k_fast_muscle" condDensity="0.042711643917483308 mS_per_cm2" erev="-30 mV" ion="k"/>
<channelDensity id="ca_boyle_all" ionChannel="ca_boyle_muscle" condDensity="0.812775772264702 mS_per_cm2" erev="0 mV" ion="ca"/>
<spikeThresh value="-10 mV"/>
<specificCapacitance value="1 uF_per_cm2"/>
<initMembPotential value="-28 mV"/>
</membraneProperties>
<intracellularProperties>
<species id="ca" concentrationModel="CaPoolMuscle" 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="0.002 mS_per_cm2" erev="-60 mV" ion="non_specific"/>
<channelDensity id="k_slow_all" ionChannel="k_slow" condDensity="0.45833751019872582 mS_per_cm2" erev="-60 mV" ion="k"/>
<channelDensity id="k_fast_all" ionChannel="k_fast" condDensity="0.042711643917483308 mS_per_cm2" erev="-70 mV" ion="k"/>
<channelDensity id="ca_boyle_all" ionChannel="ca_boyle" condDensity="1.812775772264702 mS_per_cm2" erev="10 mV" ion="ca"/>
<spikeThresh value="-55 mV"/>
<specificCapacitance value="5 uF_per_cm2"/>
<initMembPotential value="-60 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="900 ms" amplitude="5pA"/>
<network id="c302_C2_Muscles">
<property tag="recommended_duration_ms" value="1000"/>
<property tag="recommended_dt_ms" value="0.05"/>
<population id="AS1" 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="Kottbusser Tor"/>
<instance id="0">
<location x="-0.275" y="-229.038000000000011" z="4.738"/>
</instance>
</population>
<population id="AS10" 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"/>
<instance id="0">
<location x="-1.9" y="278.25" z="-24.0"/>
</instance>
</population>
<population id="AS11" 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"/>
<instance id="0">
<location x="-1.8750001" y="315.699999999999989" z="-26.124998000000001"/>
</instance>
</population>
<population id="AS2" component="GenericNeuronCell" size="1" type="populationList">
<property tag="color" value=".5 .4 1"/>
<property tag="type" value="motor"/>
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