-
Notifications
You must be signed in to change notification settings - Fork 22
/
Copy pathc302_C2_Syns.net.nml
261 lines (257 loc) · 18.4 KB
/
c302_C2_Syns.net.nml
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
<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_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 = 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 = 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"/>
<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_inh_syn" conductance="0.29 nS" delta="5 mV" Vth="0 mV" k="0.015per_ms" erev="-70 mV"/>
<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_muscle_exc_syn" conductance="0.10 nS" delta="19 mV" Vth="27 mV" k="1.205per_ms" erev="37 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="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_C2_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>