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c302_D1_IClamp.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_D1_IClamp">
<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: ['ADAL', 'PVCL']
Cell stimulated: []
Connection: []
Connection numbers overridden: None
Connection numbers scaled: None
Connection polarities override: None
Muscles: ['MDR01']
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_ad = 20 per_s (SRC: BlindGuess, certainty 0.1)
BioParameter: exc_syn_ar = .5 per_s (SRC: BlindGuess, certainty 0.1)
BioParameter: exc_syn_beta = 0.25 per_mV (SRC: BlindGuess, certainty 0.1)
BioParameter: exc_syn_erev = 0 mV (SRC: BlindGuess, certainty 0.1)
BioParameter: exc_syn_vth = -35 mV (SRC: BlindGuess, certainty 0.1)
BioParameter: global_connectivity_power_scaling = 0 (SRC: BlindGuess, certainty 0.1)
BioParameter: inh_syn_ad = 10 per_s (SRC: BlindGuess, certainty 0.1)
BioParameter: inh_syn_ar = .005 per_s (SRC: BlindGuess, certainty 0.1)
BioParameter: inh_syn_beta = 0.5 per_mV (SRC: BlindGuess, certainty 0.1)
BioParameter: inh_syn_erev = -80 mV (SRC: BlindGuess, certainty 0.1)
BioParameter: inh_syn_vth = -55 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 = 4 mS_per_cm2 (SRC: BlindGuess, certainty 0.1)
BioParameter: muscle_k_fast_cond_density = 0.2 mS_per_cm2 (SRC: BlindGuess, certainty 0.1)
BioParameter: muscle_k_slow_cond_density = 4 mS_per_cm2 (SRC: BlindGuess, certainty 0.1)
BioParameter: muscle_leak_cond_density = 0.005 mS_per_cm2 (SRC: BlindGuess, certainty 0.1)
BioParameter: muscle_length = 20 (SRC: BlindGuess, certainty 0.1)
BioParameter: muscle_spike_thresh = -26 mV (SRC: BlindGuess, certainty 0.1)
BioParameter: neuron_ca_boyle_cond_density = 1.6862775772264702 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 = 1.8333751019872582 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 = -26 mV (SRC: BlindGuess, certainty 0.1)
BioParameter: neuron_to_muscle_elec_syn_gbase = 0.0001 nS (SRC: BlindGuess, certainty 0.1)
BioParameter: neuron_to_muscle_exc_syn_conductance = 2 nS (SRC: BlindGuess, certainty 0.1)
BioParameter: neuron_to_muscle_inh_syn_conductance = 0.25 nS (SRC: BlindGuess, certainty 0.1)
BioParameter: neuron_to_neuron_elec_syn_gbase = 0.005 nS (SRC: BlindGuess, certainty 0.1)
BioParameter: neuron_to_neuron_exc_syn_conductance = 2 nS (SRC: BlindGuess, certainty 0.1)
BioParameter: neuron_to_neuron_inh_syn_conductance = 26 nS (SRC: BlindGuess, certainty 0.1)
BioParameter: resistivity = 3 kohm_cm (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 = 0 ms (SRC: KnownError, certainty 0)
BioParameter: unphysiological_offset_current_dur = 2000 ms (SRC: KnownError, certainty 0)
</notes>
<include href="cell_C.xml"/>
<include href="custom_synapses.xml"/>
<include href="cells/ADAL_D.cell.nml"/>
<include href="cells/PVCL_D.cell.nml"/>
<fixedFactorConcentrationModel id="CaPool" ion="ca" restingConc="0 mM" decayConstant="11.5943 ms" rho="0.000238919 mol_per_m_per_A_per_s"/>
<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="0.005 mS_per_cm2" erev="-50 mV" ion="non_specific"/>
<channelDensity id="k_slow_all" ionChannel="k_slow" condDensity="4 mS_per_cm2" erev="-60 mV" ion="k"/>
<channelDensity id="k_fast_all" ionChannel="k_fast" condDensity="0.2 mS_per_cm2" erev="-60 mV" ion="k"/>
<channelDensity id="ca_boyle_all" ionChannel="ca_boyle" condDensity="4 mS_per_cm2" erev="40 mV" ion="ca"/>
<spikeThresh value="-26 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="3 kohm_cm"/>
</intracellularProperties>
</biophysicalProperties>
</cell>
<pulseGenerator id="offset_current" delay="0 ms" duration="2000 ms" amplitude="0 pA"/>
<pulseGenerator id="stim_ADAL_1" delay="100ms" duration="800ms" amplitude="1pA"/>
<pulseGenerator id="stim_PVCL_1" delay="100ms" duration="800ms" amplitude="1pA"/>
<pulseGenerator id="stim_MDR01_1" delay="100ms" duration="800ms" amplitude="1pA"/>
<pulseGenerator id="stim_ADAL_2" delay="1100ms" duration="800ms" amplitude="2pA"/>
<pulseGenerator id="stim_PVCL_2" delay="1100ms" duration="800ms" amplitude="2pA"/>
<pulseGenerator id="stim_MDR01_2" delay="1100ms" duration="800ms" amplitude="2pA"/>
<pulseGenerator id="stim_ADAL_3" delay="2100ms" duration="800ms" amplitude="3pA"/>
<pulseGenerator id="stim_PVCL_3" delay="2100ms" duration="800ms" amplitude="3pA"/>
<pulseGenerator id="stim_MDR01_3" delay="2100ms" duration="800ms" amplitude="3pA"/>
<pulseGenerator id="stim_ADAL_4" delay="3100ms" duration="800ms" amplitude="4pA"/>
<pulseGenerator id="stim_PVCL_4" delay="3100ms" duration="800ms" amplitude="4pA"/>
<pulseGenerator id="stim_MDR01_4" delay="3100ms" duration="800ms" amplitude="4pA"/>
<pulseGenerator id="stim_ADAL_5" delay="4100ms" duration="800ms" amplitude="5pA"/>
<pulseGenerator id="stim_PVCL_5" delay="4100ms" duration="800ms" amplitude="5pA"/>
<pulseGenerator id="stim_MDR01_5" delay="4100ms" duration="800ms" amplitude="5pA"/>
<pulseGenerator id="stim_ADAL_6" delay="5100ms" duration="800ms" amplitude="6pA"/>
<pulseGenerator id="stim_PVCL_6" delay="5100ms" duration="800ms" amplitude="6pA"/>
<pulseGenerator id="stim_MDR01_6" delay="5100ms" duration="800ms" amplitude="6pA"/>
<network id="c302_D1_IClamp">
<property tag="recommended_duration_ms" value="6000"/>
<property tag="recommended_dt_ms" value="0.05"/>
<population id="ADAL" component="ADAL" size="1" type="populationList">
<property tag="color" value="1 0 .4"/>
<property tag="type" value="interneuron"/>
<property tag="receptor" value=""/>
<property tag="neurotransmitter" value="Glutamate"/>
<property tag="OpenWormBackerAssignedName" value="Xabe"/>
<instance id="0">
<location x="0.0" y="0.0" z="0.0"/>
</instance>
</population>
<population id="PVCL" component="PVCL" size="1" type="populationList">
<property tag="color" value="1 0 .4"/>
<property tag="type" value="interneuron"/>
<property tag="receptor" value="PDFR-1; SER-2"/>
<property tag="neurotransmitter" value="Acetylcholine"/>
<property tag="OpenWormBackerAssignedName" value="Ramana Kumar"/>
<instance id="0">
<location x="0.0" y="0.0" z="0.0"/>
</instance>
</population>
<population id="MDR01" component="GenericMuscleCell" size="1" type="populationList">
<property tag="color" value="0 .6 0"/>
<instance id="0">
<location x="-80.0" y="-270.0" z="80.0"/>
</instance>
</population>
<inputList id="Input_ADAL_stim_ADAL_1" population="ADAL" component="stim_ADAL_1">
<input id="0" target="../ADAL/0/ADAL" destination="synapses"/>
</inputList>
<inputList id="Input_PVCL_stim_PVCL_1" population="PVCL" component="stim_PVCL_1">
<input id="0" target="../PVCL/0/PVCL" destination="synapses"/>
</inputList>
<inputList id="Input_MDR01_stim_MDR01_1" population="MDR01" component="stim_MDR01_1">
<input id="0" target="../MDR01/0/GenericMuscleCell" destination="synapses"/>
</inputList>
<inputList id="Input_ADAL_stim_ADAL_2" population="ADAL" component="stim_ADAL_2">
<input id="0" target="../ADAL/0/ADAL" destination="synapses"/>
</inputList>
<inputList id="Input_PVCL_stim_PVCL_2" population="PVCL" component="stim_PVCL_2">
<input id="0" target="../PVCL/0/PVCL" destination="synapses"/>
</inputList>
<inputList id="Input_MDR01_stim_MDR01_2" population="MDR01" component="stim_MDR01_2">
<input id="0" target="../MDR01/0/GenericMuscleCell" destination="synapses"/>
</inputList>
<inputList id="Input_ADAL_stim_ADAL_3" population="ADAL" component="stim_ADAL_3">
<input id="0" target="../ADAL/0/ADAL" destination="synapses"/>
</inputList>
<inputList id="Input_PVCL_stim_PVCL_3" population="PVCL" component="stim_PVCL_3">
<input id="0" target="../PVCL/0/PVCL" destination="synapses"/>
</inputList>
<inputList id="Input_MDR01_stim_MDR01_3" population="MDR01" component="stim_MDR01_3">
<input id="0" target="../MDR01/0/GenericMuscleCell" destination="synapses"/>
</inputList>
<inputList id="Input_ADAL_stim_ADAL_4" population="ADAL" component="stim_ADAL_4">
<input id="0" target="../ADAL/0/ADAL" destination="synapses"/>
</inputList>
<inputList id="Input_PVCL_stim_PVCL_4" population="PVCL" component="stim_PVCL_4">
<input id="0" target="../PVCL/0/PVCL" destination="synapses"/>
</inputList>
<inputList id="Input_MDR01_stim_MDR01_4" population="MDR01" component="stim_MDR01_4">
<input id="0" target="../MDR01/0/GenericMuscleCell" destination="synapses"/>
</inputList>
<inputList id="Input_ADAL_stim_ADAL_5" population="ADAL" component="stim_ADAL_5">
<input id="0" target="../ADAL/0/ADAL" destination="synapses"/>
</inputList>
<inputList id="Input_PVCL_stim_PVCL_5" population="PVCL" component="stim_PVCL_5">
<input id="0" target="../PVCL/0/PVCL" destination="synapses"/>
</inputList>
<inputList id="Input_MDR01_stim_MDR01_5" population="MDR01" component="stim_MDR01_5">
<input id="0" target="../MDR01/0/GenericMuscleCell" destination="synapses"/>
</inputList>
<inputList id="Input_ADAL_stim_ADAL_6" population="ADAL" component="stim_ADAL_6">
<input id="0" target="../ADAL/0/ADAL" destination="synapses"/>
</inputList>
<inputList id="Input_PVCL_stim_PVCL_6" population="PVCL" component="stim_PVCL_6">
<input id="0" target="../PVCL/0/PVCL" destination="synapses"/>
</inputList>
<inputList id="Input_MDR01_stim_MDR01_6" population="MDR01" component="stim_MDR01_6">
<input id="0" target="../MDR01/0/GenericMuscleCell" destination="synapses"/>
</inputList>
</network>
</neuroml>