HL23SST_828.cell.nml 925 KB

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  3. <notes>Cell: HL23SST 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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  13416. neuroLexId = sao864921383 form a non-overlapping set of all of the segments.
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  13432. These segmentGroups correspond to the 'cables' of NeuroML v1.8.1, and map to/from NEURON sections.</notes>
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  13437. neuroLexId = sao864921383 form a non-overlapping set of all of the segments.
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  13490. These segmentGroups correspond to the 'cables' of NeuroML v1.8.1, and map to/from NEURON sections.</notes>
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  14085. neuroLexId = sao864921383 form a non-overlapping set of all of the segments.
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  15234. neuroLexId = sao864921383 form a non-overlapping set of all of the segments.
  15235. These segmentGroups correspond to the 'cables' of NeuroML v1.8.1, and map to/from NEURON sections.</notes>
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  15288. neuroLexId = sao864921383 form a non-overlapping set of all of the segments.
  15289. These segmentGroups correspond to the 'cables' of NeuroML v1.8.1, and map to/from NEURON sections.</notes>
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  15440. neuroLexId = sao864921383 form a non-overlapping set of all of the segments.
  15441. These segmentGroups correspond to the 'cables' of NeuroML v1.8.1, and map to/from NEURON sections.</notes>
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  15471. These segmentGroups correspond to the 'cables' of NeuroML v1.8.1, and map to/from NEURON sections.</notes>
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  16884. <segmentGroup id="dend_44" neuroLexId="sao864921383">
  16885. <notes>This group contains an unbranched set of segments, and all of the segmentGroups marked with
  16886. neuroLexId = sao864921383 form a non-overlapping set of all of the segments.
  16887. These segmentGroups correspond to the 'cables' of NeuroML v1.8.1, and map to/from NEURON sections.</notes>
  16888. <member segment="2556"/>
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  16922. </segmentGroup>
  16923. <segmentGroup id="dend_43" neuroLexId="sao864921383">
  16924. <notes>This group contains an unbranched set of segments, and all of the segmentGroups marked with
  16925. neuroLexId = sao864921383 form a non-overlapping set of all of the segments.
  16926. These segmentGroups correspond to the 'cables' of NeuroML v1.8.1, and map to/from NEURON sections.</notes>
  16927. <property tag="numberInternalDivisions" value="3"/>
  16928. <annotation>
  16929. <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="3"/>
  16930. </annotation>
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  16980. </segmentGroup>
  16981. <segmentGroup id="dend_29" neuroLexId="sao864921383">
  16982. <notes>This group contains an unbranched set of segments, and all of the segmentGroups marked with
  16983. neuroLexId = sao864921383 form a non-overlapping set of all of the segments.
  16984. These segmentGroups correspond to the 'cables' of NeuroML v1.8.1, and map to/from NEURON sections.</notes>
  16985. <member segment="1929"/>
  16986. <member segment="1930"/>
  16987. <member segment="1931"/>
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  16989. <member segment="1933"/>
  16990. <member segment="1934"/>
  16991. <member segment="1935"/>
  16992. </segmentGroup>
  16993. <segmentGroup id="dend_28" neuroLexId="sao864921383">
  16994. <notes>This group contains an unbranched set of segments, and all of the segmentGroups marked with
  16995. neuroLexId = sao864921383 form a non-overlapping set of all of the segments.
  16996. These segmentGroups correspond to the 'cables' of NeuroML v1.8.1, and map to/from NEURON sections.</notes>
  16997. <member segment="1900"/>
  16998. <member segment="1901"/>
  16999. <member segment="1902"/>
  17000. <member segment="1903"/>
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  17020. <member segment="1923"/>
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  17022. <member segment="1925"/>
  17023. <member segment="1926"/>
  17024. <member segment="1927"/>
  17025. <member segment="1928"/>
  17026. </segmentGroup>
  17027. <segmentGroup id="dend_53" neuroLexId="sao864921383">
  17028. <notes>This group contains an unbranched set of segments, and all of the segmentGroups marked with
  17029. neuroLexId = sao864921383 form a non-overlapping set of all of the segments.
  17030. These segmentGroups correspond to the 'cables' of NeuroML v1.8.1, and map to/from NEURON sections.</notes>
  17031. <member segment="3146"/>
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  17049. <member segment="3164"/>
  17050. </segmentGroup>
  17051. <segmentGroup id="dend_52" neuroLexId="sao864921383">
  17052. <notes>This group contains an unbranched set of segments, and all of the segmentGroups marked with
  17053. neuroLexId = sao864921383 form a non-overlapping set of all of the segments.
  17054. These segmentGroups correspond to the 'cables' of NeuroML v1.8.1, and map to/from NEURON sections.</notes>
  17055. <property tag="numberInternalDivisions" value="5"/>
  17056. <annotation>
  17057. <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="5"/>
  17058. </annotation>
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  17161. </segmentGroup>
  17162. <segmentGroup id="basal_dendrite_group" neuroLexId="GO:0030425">
  17163. <notes>Basal dendrites</notes>
  17164. <include segmentGroup="dend_0"/>
  17165. <include segmentGroup="dend_1"/>
  17166. <include segmentGroup="dend_2"/>
  17167. <include segmentGroup="dend_3"/>
  17168. <include segmentGroup="dend_4"/>
  17169. <include segmentGroup="dend_5"/>
  17170. <include segmentGroup="dend_6"/>
  17171. <include segmentGroup="dend_7"/>
  17172. <include segmentGroup="dend_8"/>
  17173. <include segmentGroup="dend_9"/>
  17174. <include segmentGroup="dend_10"/>
  17175. <include segmentGroup="dend_11"/>
  17176. <include segmentGroup="dend_12"/>
  17177. <include segmentGroup="dend_13"/>
  17178. <include segmentGroup="dend_14"/>
  17179. <include segmentGroup="dend_15"/>
  17180. <include segmentGroup="dend_16"/>
  17181. <include segmentGroup="dend_17"/>
  17182. <include segmentGroup="dend_18"/>
  17183. <include segmentGroup="dend_19"/>
  17184. <include segmentGroup="dend_20"/>
  17185. <include segmentGroup="dend_21"/>
  17186. <include segmentGroup="dend_22"/>
  17187. <include segmentGroup="dend_23"/>
  17188. <include segmentGroup="dend_24"/>
  17189. <include segmentGroup="dend_25"/>
  17190. <include segmentGroup="dend_26"/>
  17191. <include segmentGroup="dend_27"/>
  17192. <include segmentGroup="dend_28"/>
  17193. <include segmentGroup="dend_29"/>
  17194. <include segmentGroup="dend_30"/>
  17195. <include segmentGroup="dend_31"/>
  17196. <include segmentGroup="dend_32"/>
  17197. <include segmentGroup="dend_33"/>
  17198. <include segmentGroup="dend_34"/>
  17199. <include segmentGroup="dend_35"/>
  17200. <include segmentGroup="dend_36"/>
  17201. <include segmentGroup="dend_37"/>
  17202. <include segmentGroup="dend_38"/>
  17203. <include segmentGroup="dend_39"/>
  17204. <include segmentGroup="dend_40"/>
  17205. <include segmentGroup="dend_41"/>
  17206. <include segmentGroup="dend_42"/>
  17207. <include segmentGroup="dend_43"/>
  17208. <include segmentGroup="dend_44"/>
  17209. <include segmentGroup="dend_45"/>
  17210. <include segmentGroup="dend_46"/>
  17211. <include segmentGroup="dend_47"/>
  17212. <include segmentGroup="dend_48"/>
  17213. <include segmentGroup="dend_49"/>
  17214. <include segmentGroup="dend_50"/>
  17215. <include segmentGroup="dend_51"/>
  17216. <include segmentGroup="dend_52"/>
  17217. <include segmentGroup="dend_53"/>
  17218. <include segmentGroup="dend_54"/>
  17219. </segmentGroup>
  17220. <segmentGroup id="myelin_group">
  17221. <notes>Myelin group</notes>
  17222. <include segmentGroup="myelin_0"/>
  17223. </segmentGroup>
  17224. <segmentGroup id="all_minus_myelin">
  17225. <notes>All without myelin</notes>
  17226. <include segmentGroup="axon_0"/>
  17227. <include segmentGroup="axon_1"/>
  17228. <include segmentGroup="dend_0"/>
  17229. <include segmentGroup="dend_1"/>
  17230. <include segmentGroup="dend_2"/>
  17231. <include segmentGroup="dend_3"/>
  17232. <include segmentGroup="dend_4"/>
  17233. <include segmentGroup="dend_5"/>
  17234. <include segmentGroup="dend_6"/>
  17235. <include segmentGroup="dend_7"/>
  17236. <include segmentGroup="dend_8"/>
  17237. <include segmentGroup="dend_9"/>
  17238. <include segmentGroup="dend_10"/>
  17239. <include segmentGroup="dend_11"/>
  17240. <include segmentGroup="dend_12"/>
  17241. <include segmentGroup="dend_13"/>
  17242. <include segmentGroup="dend_14"/>
  17243. <include segmentGroup="dend_15"/>
  17244. <include segmentGroup="dend_16"/>
  17245. <include segmentGroup="dend_17"/>
  17246. <include segmentGroup="dend_18"/>
  17247. <include segmentGroup="dend_19"/>
  17248. <include segmentGroup="dend_20"/>
  17249. <include segmentGroup="dend_21"/>
  17250. <include segmentGroup="dend_22"/>
  17251. <include segmentGroup="dend_23"/>
  17252. <include segmentGroup="dend_24"/>
  17253. <include segmentGroup="dend_25"/>
  17254. <include segmentGroup="dend_26"/>
  17255. <include segmentGroup="dend_27"/>
  17256. <include segmentGroup="dend_28"/>
  17257. <include segmentGroup="dend_29"/>
  17258. <include segmentGroup="dend_30"/>
  17259. <include segmentGroup="dend_31"/>
  17260. <include segmentGroup="dend_32"/>
  17261. <include segmentGroup="dend_33"/>
  17262. <include segmentGroup="dend_34"/>
  17263. <include segmentGroup="dend_35"/>
  17264. <include segmentGroup="dend_36"/>
  17265. <include segmentGroup="dend_37"/>
  17266. <include segmentGroup="dend_38"/>
  17267. <include segmentGroup="dend_39"/>
  17268. <include segmentGroup="dend_40"/>
  17269. <include segmentGroup="dend_41"/>
  17270. <include segmentGroup="dend_42"/>
  17271. <include segmentGroup="dend_43"/>
  17272. <include segmentGroup="dend_44"/>
  17273. <include segmentGroup="dend_45"/>
  17274. <include segmentGroup="dend_46"/>
  17275. <include segmentGroup="dend_47"/>
  17276. <include segmentGroup="dend_48"/>
  17277. <include segmentGroup="dend_49"/>
  17278. <include segmentGroup="dend_50"/>
  17279. <include segmentGroup="dend_51"/>
  17280. <include segmentGroup="dend_52"/>
  17281. <include segmentGroup="dend_53"/>
  17282. <include segmentGroup="dend_54"/>
  17283. <include segmentGroup="soma_0"/>
  17284. </segmentGroup>
  17285. <segmentGroup id="soma_group" neuroLexId="GO:0043025">
  17286. <notes>Default soma segment group for the cell</notes>
  17287. <include segmentGroup="soma_0"/>
  17288. </segmentGroup>
  17289. <segmentGroup id="axon_group" neuroLexId="GO:0030424">
  17290. <notes>Default axon segment group for the cell</notes>
  17291. <include segmentGroup="axon_0"/>
  17292. <include segmentGroup="axon_1"/>
  17293. </segmentGroup>
  17294. <segmentGroup id="dendrite_group" neuroLexId="GO:0030425">
  17295. <notes>Default dendrite segment group for the cell</notes>
  17296. <include segmentGroup="basal_dendrite_group"/>
  17297. </segmentGroup>
  17298. <segmentGroup id="all">
  17299. <include segmentGroup="axon_0"/>
  17300. <include segmentGroup="axon_1"/>
  17301. <include segmentGroup="dend_0"/>
  17302. <include segmentGroup="dend_1"/>
  17303. <include segmentGroup="dend_2"/>
  17304. <include segmentGroup="dend_3"/>
  17305. <include segmentGroup="dend_4"/>
  17306. <include segmentGroup="dend_5"/>
  17307. <include segmentGroup="dend_6"/>
  17308. <include segmentGroup="dend_7"/>
  17309. <include segmentGroup="dend_8"/>
  17310. <include segmentGroup="dend_9"/>
  17311. <include segmentGroup="dend_10"/>
  17312. <include segmentGroup="dend_11"/>
  17313. <include segmentGroup="dend_12"/>
  17314. <include segmentGroup="dend_13"/>
  17315. <include segmentGroup="dend_14"/>
  17316. <include segmentGroup="dend_15"/>
  17317. <include segmentGroup="dend_16"/>
  17318. <include segmentGroup="dend_17"/>
  17319. <include segmentGroup="dend_18"/>
  17320. <include segmentGroup="dend_19"/>
  17321. <include segmentGroup="dend_20"/>
  17322. <include segmentGroup="dend_21"/>
  17323. <include segmentGroup="dend_22"/>
  17324. <include segmentGroup="dend_23"/>
  17325. <include segmentGroup="dend_24"/>
  17326. <include segmentGroup="dend_25"/>
  17327. <include segmentGroup="dend_26"/>
  17328. <include segmentGroup="dend_27"/>
  17329. <include segmentGroup="dend_28"/>
  17330. <include segmentGroup="dend_29"/>
  17331. <include segmentGroup="dend_30"/>
  17332. <include segmentGroup="dend_31"/>
  17333. <include segmentGroup="dend_32"/>
  17334. <include segmentGroup="dend_33"/>
  17335. <include segmentGroup="dend_34"/>
  17336. <include segmentGroup="dend_35"/>
  17337. <include segmentGroup="dend_36"/>
  17338. <include segmentGroup="dend_37"/>
  17339. <include segmentGroup="dend_38"/>
  17340. <include segmentGroup="dend_39"/>
  17341. <include segmentGroup="dend_40"/>
  17342. <include segmentGroup="dend_41"/>
  17343. <include segmentGroup="dend_42"/>
  17344. <include segmentGroup="dend_43"/>
  17345. <include segmentGroup="dend_44"/>
  17346. <include segmentGroup="dend_45"/>
  17347. <include segmentGroup="dend_46"/>
  17348. <include segmentGroup="dend_47"/>
  17349. <include segmentGroup="dend_48"/>
  17350. <include segmentGroup="dend_49"/>
  17351. <include segmentGroup="dend_50"/>
  17352. <include segmentGroup="dend_51"/>
  17353. <include segmentGroup="dend_52"/>
  17354. <include segmentGroup="dend_53"/>
  17355. <include segmentGroup="dend_54"/>
  17356. <include segmentGroup="myelin_0"/>
  17357. <include segmentGroup="soma_0"/>
  17358. </segmentGroup>
  17359. </morphology>
  17360. <biophysicalProperties id="biophys">
  17361. <membraneProperties>
  17362. <channelDensity id="pas" ionChannel="pas" condDensity="0.0000232 S_per_cm2" erev="-81.5 mV" segmentGroup="all_minus_myelin" ion="non_specific"/>
  17363. <channelDensity id="NaTg_somatic" ionChannel="NaTg_SST_somatic" condDensity="0.127 S_per_cm2" erev="50 mV" segmentGroup="soma_group" ion="na"/>
  17364. <channelDensity id="Ih_somatic" ionChannel="Ih" condDensity="0.0000431 S_per_cm2" erev="-45 mV" segmentGroup="soma_group" ion="hcn"/>
  17365. <channelDensity id="K_P_somatic" ionChannel="K_P" condDensity="0.0111 S_per_cm2" erev="-85 mV" segmentGroup="soma_group" ion="k"/>
  17366. <channelDensity id="K_T_somatic" ionChannel="K_T" condDensity="0.00000 S_per_cm2" erev="-85 mV" segmentGroup="soma_group" ion="k"/>
  17367. <channelDensity id="Kv3_1_somatic" ionChannel="Kv3_1" condDensity="0.871 S_per_cm2" erev="-85 mV" segmentGroup="soma_group" ion="k"/>
  17368. <channelDensity id="Im_somatic" ionChannel="Im" condDensity="0.000158 S_per_cm2" erev="-85 mV" segmentGroup="soma_group" ion="k"/>
  17369. <channelDensity id="SK_somatic" ionChannel="SK" condDensity="0.00 S_per_cm2" erev="-85 mV" segmentGroup="soma_group" ion="k"/>
  17370. <channelDensity id="Ih_basal" ionChannel="Ih" condDensity="0.0000949 S_per_cm2" erev="-45 mV" segmentGroup="basal_dendrite_group" ion="hcn"/>
  17371. <channelDensity id="NaTg_axonal" ionChannel="NaTg_SST_axonal" condDensity="0.343 S_per_cm2" erev="50 mV" segmentGroup="axon_group" ion="na"/>
  17372. <channelDensity id="Nap_axonal" ionChannel="Nap" condDensity="0.000444 S_per_cm2" erev="50 mV" segmentGroup="axon_group" ion="na"/>
  17373. <channelDensity id="K_P_axonal" ionChannel="K_P" condDensity="0.0295 S_per_cm2" erev="-85 mV" segmentGroup="axon_group" ion="k"/>
  17374. <channelDensity id="K_T_axonal" ionChannel="K_T" condDensity="0.023 S_per_cm2" erev="-85 mV" segmentGroup="axon_group" ion="k"/>
  17375. <channelDensity id="Kv3_1_axonal" ionChannel="Kv3_1" condDensity="0.984 S_per_cm2" erev="-85 mV" segmentGroup="axon_group" ion="k"/>
  17376. <channelDensity id="Im_axonal" ionChannel="Im" condDensity="0.000317 S_per_cm2" erev="-85 mV" segmentGroup="axon_group" ion="k"/>
  17377. <channelDensity id="SK_axonal" ionChannel="SK" condDensity="0.00113 S_per_cm2" erev="-85 mV" segmentGroup="axon_group" ion="k"/>
  17378. <channelDensity id="Ih_axonal" ionChannel="Ih" condDensity="0.00001 S_per_cm2" erev="-45 mV" segmentGroup="axon_group" ion="hcn"/>
  17379. <channelDensityNernst id="Ca_HVA_somatic" ionChannel="Ca_HVA" condDensity="0.00355 S_per_cm2" segmentGroup="soma_group" ion="ca"/>
  17380. <channelDensityNernst id="Ca_LVA_somatic" ionChannel="Ca_LVA" condDensity="0.00314 S_per_cm2" segmentGroup="soma_group" ion="ca"/>
  17381. <channelDensityNernst id="Ca_HVA_axonal" ionChannel="Ca_HVA" condDensity="0.00145 S_per_cm2" segmentGroup="axon_group" ion="ca"/>
  17382. <channelDensityNernst id="Ca_LVA_axonal" ionChannel="Ca_LVA" condDensity="0.0627 S_per_cm2" segmentGroup="axon_group" ion="ca"/>
  17383. <specificCapacitance value="1 uF_per_cm2" segmentGroup="all_minus_myelin"/>
  17384. <specificCapacitance value="0.02 uF_per_cm2" segmentGroup="myelin_group"/>
  17385. <specificCapacitance value="1 uF_per_cm2" segmentGroup="basal_dendrite_group"/>
  17386. <initMembPotential value="-80mV"/>
  17387. </membraneProperties>
  17388. <intracellularProperties>
  17389. <species id="ca" concentrationModel="CaDynamics_E2_NML2_SST_somatic" ion="ca" initialConcentration="1e-4 mM" initialExtConcentration="2.0E-6 mol_per_cm3" segmentGroup="soma_group"/>
  17390. <species id="ca" concentrationModel="CaDynamics_E2_NML2_SST_axonal" ion="ca" initialConcentration="1e-4 mM" initialExtConcentration="2.0E-6 mol_per_cm3" segmentGroup="axon_group"/>
  17391. <resistivity value="0.1 kohm_cm" segmentGroup="all_minus_myelin"/>
  17392. <resistivity value="0.1 kohm_cm" segmentGroup="myelin_group"/>
  17393. </intracellularProperties>
  17394. </biophysicalProperties>
  17395. </cell>
  17396. </neuroml>