HL23VIP_933.cell.nml 822 KB

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  3. <notes>Cell: HL23VIP exported from NEURON ModelView. Reference: Yao, H. K.; Guet-McCreight, A.; Mazza, F.; Moradi Chameh, H.; Prevot, T. D.; Griffiths, J. D.; Tripathy, S. J.; Valiante, T. A.; Sibille, E. &amp; Hay, E. Reduced inhibition in depression impairs stimulus processing in human cortical microcircuits Cell Reports, Elsevier, 2022, 38</notes>
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  12028. neuroLexId = sao864921383 form a non-overlapping set of all of the segments.
  12029. These segmentGroups correspond to the 'cables' of NeuroML v1.8.1, and map to/from NEURON sections.</notes>
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  12081. <notes>This group contains an unbranched set of segments, and all of the segmentGroups marked with
  12082. neuroLexId = sao864921383 form a non-overlapping set of all of the segments.
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  12108. <notes>This group contains an unbranched set of segments, and all of the segmentGroups marked with
  12109. neuroLexId = sao864921383 form a non-overlapping set of all of the segments.
  12110. These segmentGroups correspond to the 'cables' of NeuroML v1.8.1, and map to/from NEURON sections.</notes>
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  12119. <notes>This group contains an unbranched set of segments, and all of the segmentGroups marked with
  12120. neuroLexId = sao864921383 form a non-overlapping set of all of the segments.
  12121. These segmentGroups correspond to the 'cables' of NeuroML v1.8.1, and map to/from NEURON sections.</notes>
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  12137. neuroLexId = sao864921383 form a non-overlapping set of all of the segments.
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  12154. These segmentGroups correspond to the 'cables' of NeuroML v1.8.1, and map to/from NEURON sections.</notes>
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  14881. <member segment="1322"/>
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  14911. </segmentGroup>
  14912. <segmentGroup id="dend_26" neuroLexId="sao864921383">
  14913. <notes>This group contains an unbranched set of segments, and all of the segmentGroups marked with
  14914. neuroLexId = sao864921383 form a non-overlapping set of all of the segments.
  14915. These segmentGroups correspond to the 'cables' of NeuroML v1.8.1, and map to/from NEURON sections.</notes>
  14916. <member segment="1011"/>
  14917. <member segment="1012"/>
  14918. <member segment="1013"/>
  14919. <member segment="1014"/>
  14920. <member segment="1015"/>
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  14922. <member segment="1017"/>
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  14931. <member segment="1026"/>
  14932. <member segment="1027"/>
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  14934. <member segment="1029"/>
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  14936. <member segment="1031"/>
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  14941. <member segment="1036"/>
  14942. <member segment="1037"/>
  14943. </segmentGroup>
  14944. <segmentGroup id="dend_28" neuroLexId="sao864921383">
  14945. <notes>This group contains an unbranched set of segments, and all of the segmentGroups marked with
  14946. neuroLexId = sao864921383 form a non-overlapping set of all of the segments.
  14947. These segmentGroups correspond to the 'cables' of NeuroML v1.8.1, and map to/from NEURON sections.</notes>
  14948. <property tag="numberInternalDivisions" value="7"/>
  14949. <annotation>
  14950. <property xmlns="http://www.neuroml.org/schema/neuroml2" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xs="http://www.w3.org/2001/XMLSchema" tag="numberInternalDivisions" value="7"/>
  14951. </annotation>
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  15021. <member segment="1254"/>
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  15023. <member segment="1256"/>
  15024. <member segment="1257"/>
  15025. <member segment="1258"/>
  15026. <member segment="1259"/>
  15027. <member segment="1260"/>
  15028. <member segment="1261"/>
  15029. <member segment="1262"/>
  15030. <member segment="1263"/>
  15031. <member segment="1264"/>
  15032. <member segment="1265"/>
  15033. <member segment="1266"/>
  15034. <member segment="1267"/>
  15035. <member segment="1268"/>
  15036. <member segment="1269"/>
  15037. <member segment="1270"/>
  15038. <member segment="1271"/>
  15039. <member segment="1272"/>
  15040. <member segment="1273"/>
  15041. <member segment="1274"/>
  15042. <member segment="1275"/>
  15043. <member segment="1276"/>
  15044. <member segment="1277"/>
  15045. <member segment="1278"/>
  15046. <member segment="1279"/>
  15047. <member segment="1280"/>
  15048. <member segment="1281"/>
  15049. <member segment="1282"/>
  15050. <member segment="1283"/>
  15051. <member segment="1284"/>
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  15054. <member segment="1287"/>
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  15057. <member segment="1290"/>
  15058. <member segment="1291"/>
  15059. <member segment="1292"/>
  15060. <member segment="1293"/>
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  15065. <member segment="1298"/>
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  15067. <member segment="1300"/>
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  15069. <member segment="1302"/>
  15070. <member segment="1303"/>
  15071. <member segment="1304"/>
  15072. <member segment="1305"/>
  15073. </segmentGroup>
  15074. <segmentGroup id="dend_27" neuroLexId="sao864921383">
  15075. <notes>This group contains an unbranched set of segments, and all of the segmentGroups marked with
  15076. neuroLexId = sao864921383 form a non-overlapping set of all of the segments.
  15077. These segmentGroups correspond to the 'cables' of NeuroML v1.8.1, and map to/from NEURON sections.</notes>
  15078. <property tag="numberInternalDivisions" value="9"/>
  15079. <annotation>
  15080. <property xmlns="http://www.neuroml.org/schema/neuroml2" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xs="http://www.w3.org/2001/XMLSchema" tag="numberInternalDivisions" value="9"/>
  15081. </annotation>
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  15158. <member segment="1114"/>
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  15164. <member segment="1120"/>
  15165. <member segment="1121"/>
  15166. <member segment="1122"/>
  15167. <member segment="1123"/>
  15168. <member segment="1124"/>
  15169. <member segment="1125"/>
  15170. <member segment="1126"/>
  15171. <member segment="1127"/>
  15172. <member segment="1128"/>
  15173. <member segment="1129"/>
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  15197. <member segment="1153"/>
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  15211. <member segment="1167"/>
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  15213. <member segment="1169"/>
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  15228. <member segment="1184"/>
  15229. </segmentGroup>
  15230. <segmentGroup id="soma_group" neuroLexId="GO:0043025">
  15231. <notes>Default soma segment group for the cell</notes>
  15232. <include segmentGroup="soma_0"/>
  15233. </segmentGroup>
  15234. <segmentGroup id="axon_group" neuroLexId="GO:0030424">
  15235. <notes>Default axon segment group for the cell</notes>
  15236. <include segmentGroup="axon_0"/>
  15237. <include segmentGroup="axon_1"/>
  15238. </segmentGroup>
  15239. <segmentGroup id="dendrite_group" neuroLexId="GO:0030425">
  15240. <notes>Default dendrite segment group for the cell</notes>
  15241. <include segmentGroup="dend_0"/>
  15242. <include segmentGroup="dend_1"/>
  15243. <include segmentGroup="dend_2"/>
  15244. <include segmentGroup="dend_3"/>
  15245. <include segmentGroup="dend_4"/>
  15246. <include segmentGroup="dend_5"/>
  15247. <include segmentGroup="dend_6"/>
  15248. <include segmentGroup="dend_7"/>
  15249. <include segmentGroup="dend_8"/>
  15250. <include segmentGroup="dend_9"/>
  15251. <include segmentGroup="dend_10"/>
  15252. <include segmentGroup="dend_11"/>
  15253. <include segmentGroup="dend_12"/>
  15254. <include segmentGroup="dend_13"/>
  15255. <include segmentGroup="dend_14"/>
  15256. <include segmentGroup="dend_15"/>
  15257. <include segmentGroup="dend_16"/>
  15258. <include segmentGroup="dend_17"/>
  15259. <include segmentGroup="dend_18"/>
  15260. <include segmentGroup="dend_19"/>
  15261. <include segmentGroup="dend_20"/>
  15262. <include segmentGroup="dend_21"/>
  15263. <include segmentGroup="dend_22"/>
  15264. <include segmentGroup="dend_23"/>
  15265. <include segmentGroup="dend_24"/>
  15266. <include segmentGroup="dend_25"/>
  15267. <include segmentGroup="dend_26"/>
  15268. <include segmentGroup="dend_27"/>
  15269. <include segmentGroup="dend_28"/>
  15270. <include segmentGroup="dend_29"/>
  15271. <include segmentGroup="dend_30"/>
  15272. <include segmentGroup="dend_31"/>
  15273. <include segmentGroup="dend_32"/>
  15274. <include segmentGroup="dend_33"/>
  15275. <include segmentGroup="dend_34"/>
  15276. <include segmentGroup="dend_35"/>
  15277. <include segmentGroup="dend_36"/>
  15278. <include segmentGroup="dend_37"/>
  15279. <include segmentGroup="dend_38"/>
  15280. <include segmentGroup="dend_39"/>
  15281. <include segmentGroup="dend_40"/>
  15282. <include segmentGroup="dend_41"/>
  15283. <include segmentGroup="dend_42"/>
  15284. <include segmentGroup="dend_43"/>
  15285. <include segmentGroup="dend_44"/>
  15286. <include segmentGroup="dend_45"/>
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  15289. <include segmentGroup="dend_48"/>
  15290. <include segmentGroup="dend_49"/>
  15291. <include segmentGroup="dend_50"/>
  15292. <include segmentGroup="dend_51"/>
  15293. <include segmentGroup="dend_52"/>
  15294. </segmentGroup>
  15295. <segmentGroup id="all">
  15296. <include segmentGroup="axon_0"/>
  15297. <include segmentGroup="axon_1"/>
  15298. <include segmentGroup="dend_0"/>
  15299. <include segmentGroup="dend_1"/>
  15300. <include segmentGroup="dend_2"/>
  15301. <include segmentGroup="dend_3"/>
  15302. <include segmentGroup="dend_4"/>
  15303. <include segmentGroup="dend_5"/>
  15304. <include segmentGroup="dend_6"/>
  15305. <include segmentGroup="dend_7"/>
  15306. <include segmentGroup="dend_8"/>
  15307. <include segmentGroup="dend_9"/>
  15308. <include segmentGroup="dend_10"/>
  15309. <include segmentGroup="dend_11"/>
  15310. <include segmentGroup="dend_12"/>
  15311. <include segmentGroup="dend_13"/>
  15312. <include segmentGroup="dend_14"/>
  15313. <include segmentGroup="dend_15"/>
  15314. <include segmentGroup="dend_16"/>
  15315. <include segmentGroup="dend_17"/>
  15316. <include segmentGroup="dend_18"/>
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  15318. <include segmentGroup="dend_20"/>
  15319. <include segmentGroup="dend_21"/>
  15320. <include segmentGroup="dend_22"/>
  15321. <include segmentGroup="dend_23"/>
  15322. <include segmentGroup="dend_24"/>
  15323. <include segmentGroup="dend_25"/>
  15324. <include segmentGroup="dend_26"/>
  15325. <include segmentGroup="dend_27"/>
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  15328. <include segmentGroup="dend_30"/>
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  15330. <include segmentGroup="dend_32"/>
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  15332. <include segmentGroup="dend_34"/>
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  15349. <include segmentGroup="dend_51"/>
  15350. <include segmentGroup="dend_52"/>
  15351. <include segmentGroup="soma_0"/>
  15352. </segmentGroup>
  15353. </morphology>
  15354. <biophysicalProperties id="biophys">
  15355. <membraneProperties>
  15356. <channelDensity id="pas" ionChannel="pas" condDensity="2.5756438955642182e-05 S_per_cm2" erev="-79.74132024971513 mV" ion="non_specific"/>
  15357. <channelDensity id="Ih" ionChannel="Ih" condDensity="4.274951616063423e-05 S_per_cm2" erev="-45 mV" ion="hcn"/>
  15358. <channelDensity id="NaTg_somatic" ionChannel="NaTg_VIP_somatic" condDensity="0.11491205828369114 S_per_cm2" erev="50 mV" segmentGroup="soma_group" ion="na"/>
  15359. <channelDensity id="Nap_somatic" ionChannel="Nap" condDensity="0.0001895305240694194 S_per_cm2" erev="50 mV" segmentGroup="soma_group" ion="na"/>
  15360. <channelDensity id="K_P_somatic" ionChannel="K_P" condDensity="0.0009925418924114282 S_per_cm2" erev="-85 mV" segmentGroup="soma_group" ion="k"/>
  15361. <channelDensity id="K_T_somatic" ionChannel="K_T" condDensity="0.009051981253674193 S_per_cm2" erev="-85 mV" segmentGroup="soma_group" ion="k"/>
  15362. <channelDensity id="Kv3_1_somatic" ionChannel="Kv3_1" condDensity="0.31215653649208114 S_per_cm2" erev="-85 mV" segmentGroup="soma_group" ion="k"/>
  15363. <channelDensity id="Im_somatic" ionChannel="Im" condDensity="0.0003679378262289559 S_per_cm2" erev="-85 mV" segmentGroup="soma_group" ion="k"/>
  15364. <channelDensity id="SK_somatic" ionChannel="SK" condDensity="0.1655502166633749 S_per_cm2" erev="-85 mV" segmentGroup="soma_group" ion="k"/>
  15365. <channelDensity id="NaTg_axonal" ionChannel="NaTg_VIP_axonal" condDensity="0.20112200814143477 S_per_cm2" erev="50 mV" segmentGroup="axon_group" ion="na"/>
  15366. <channelDensity id="Nap_axonal" ionChannel="Nap" condDensity="0.0006248906854665301 S_per_cm2" erev="50 mV" segmentGroup="axon_group" ion="na"/>
  15367. <channelDensity id="K_P_axonal" ionChannel="K_P" condDensity="0.26489876414660096 S_per_cm2" erev="-85 mV" segmentGroup="axon_group" ion="k"/>
  15368. <channelDensity id="K_T_axonal" ionChannel="K_T" condDensity="0.014364427062274185 S_per_cm2" erev="-85 mV" segmentGroup="axon_group" ion="k"/>
  15369. <channelDensity id="Kv3_1_axonal" ionChannel="Kv3_1" condDensity="0.0011201608191112877 S_per_cm2" erev="-85 mV" segmentGroup="axon_group" ion="k"/>
  15370. <channelDensity id="Im_axonal" ionChannel="Im" condDensity="0.00013891465461042372 S_per_cm2" erev="-85 mV" segmentGroup="axon_group" ion="k"/>
  15371. <channelDensity id="SK_axonal" ionChannel="SK" condDensity="0.7027792087501376 S_per_cm2" erev="-85 mV" segmentGroup="axon_group" ion="k"/>
  15372. <channelDensityNernst id="Ca_HVA_somatic" ionChannel="Ca_HVA" condDensity="4.384846294634834e-05 S_per_cm2" segmentGroup="soma_group" ion="ca"/>
  15373. <channelDensityNernst id="Ca_LVA_somatic" ionChannel="Ca_LVA" condDensity="0.0034472458995879864 S_per_cm2" segmentGroup="soma_group" ion="ca"/>
  15374. <channelDensityNernst id="Ca_HVA_axonal" ionChannel="Ca_HVA" condDensity="2.819397237794038e-05 S_per_cm2" segmentGroup="axon_group" ion="ca"/>
  15375. <channelDensityNernst id="Ca_LVA_axonal" ionChannel="Ca_LVA" condDensity="0.010354001513952075 S_per_cm2" segmentGroup="axon_group" ion="ca"/>
  15376. <specificCapacitance value="2 uF_per_cm2"/>
  15377. <initMembPotential value="-80mV"/>
  15378. </membraneProperties>
  15379. <intracellularProperties>
  15380. <species id="ca" concentrationModel="CaDynamics_E2_NML2_VIP_somatic" ion="ca" initialConcentration="1e-4 mM" initialExtConcentration="2.0E-6 mol_per_cm3" segmentGroup="soma_group"/>
  15381. <species id="ca" concentrationModel="CaDynamics_E2_NML2_VIP_axonal" ion="ca" initialConcentration="1e-4 mM" initialExtConcentration="2.0E-6 mol_per_cm3" segmentGroup="axon_group"/>
  15382. <resistivity value="0.1 kohm_cm"/>
  15383. </intracellularProperties>
  15384. </biophysicalProperties>
  15385. </cell>
  15386. </neuroml>