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Merge pull request #438 from Hjorthmedh/neuromod_redux2
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Neuromod redux2
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@Hjorthmedh
Hjorthmedh authored Nov 29, 2024
2 parents d6866f0 + 48830da commit f0085d8
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Showing 39 changed files with 42,329 additions and 88,603 deletions.
1 change: 1 addition & 0 deletions examples/notebooks/neuromodulation/data/DA-bath-experiment.json
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"section_x": [0.5, 0.5]
}
},
"use_rxd_neuromodulation": true,
"rxd_enable_extracellular": false,
"bath_application": {
"DA": {
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101 changes: 101 additions & 0 deletions examples/notebooks/neuromodulation/data/SBtab/Compound.tsv
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!!SBtab SBtabVersion='1.0' Document='Nair_2016_optimized' TableName='Compound' TableTitle='Compound' TableType = 'Compound'
!ID !Name !Unit !InitialValue !IsConstant !Assignment !Interpolation !Type !Location !IsInput !Identifiers:UniProt !Identifiers:kegg_compound
S0 AC5 nanomole/liter 700 0 0 0 kinetic Spine 0 P84309 K08045
S1 AC5_ATP nanomole/liter 0 0 0 0 kinetic Spine 0
S2 AC5_Ca nanomole/liter 0 0 0 0 kinetic Spine 0
S3 AC5_Ca_ATP nanomole/liter 0 0 0 0 kinetic Spine 0
S4 AC5_Ca_GaolfGTP nanomole/liter 0 0 0 0 kinetic Spine 0
S5 AC5_Ca_GaolfGTP_ATP nanomole/liter 0 0 0 0 kinetic Spine 0
S6 AC5_GaolfGTP nanomole/liter 0 0 0 0 kinetic Spine 0
S7 AC5_GaolfGTP_ATP nanomole/liter 0 0 0 0 kinetic Spine 0
S8 AMP nanomole/liter 0 1 0 0 kinetic Spine 0 C00020
S9 ATP nanomole/liter 5000000 1 ATP_expression 0 kinetic Spine 0 C00002
S10 B56PP2A nanomole/liter 2000 0 0 0 kinetic Spine 0 P63330 Q76MZ3 Q14738 K03456
S11 B56PP2A_D32p75 nanomole/liter 0 0 0 0 kinetic Spine 0
S12 B56PP2A_pARPP21 nanomole/liter 0 0 0 0 kinetic Spine 0
S13 B56PP2Ap nanomole/liter 0 0 0 0 kinetic Spine 0
S14 B56PP2Ap_D32p75 nanomole/liter 0 0 0 0 kinetic Spine 0
S15 B56PP2Ap_pARPP21 nanomole/liter 0 0 0 0 kinetic Spine 0
S16 B72PP2A nanomole/liter 2000 0 0 0 kinetic Spine 0 P63330 Q76MZ3 B2RXC8
S17 B72PP2A_D32p34 nanomole/liter 0 0 0 0 kinetic Spine 0
S18 B72PP2A_D32p75 nanomole/liter 0 0 0 0 kinetic Spine 0
S19 B72PP2A_pARPP21 nanomole/liter 0 0 0 0 kinetic Spine 0
S20 B72PP2A_Ca_D32p34 nanomole/liter 0 0 0 0 kinetic Spine 0
S21 B72PP2A_Ca_D32p75 nanomole/liter 0 0 0 0 kinetic Spine 0
S22 B72PP2A_Ca nanomole/liter 0 0 0 0 kinetic Spine 0
S23 B72PP2A_Ca_pARPP21 nanomole/liter 0 0 0 0 kinetic Spine 0
S24 Ca nanomole/liter 60 1 Ca_expression 1 kinetic Spine 1
S25 CaM nanomole/liter 9000 0 0 0 kinetic Spine 0 P0DP28 P0DP27 P0DP26 K02183
S26 CaM_Ca2 nanomole/liter 0 0 0 0 kinetic Spine 0
S27 CaM_Ca4 nanomole/liter 0 0 0 0 kinetic Spine 0
S28 CaM_Ca4_pARPP21 nanomole/liter 0 0 0 0 kinetic Spine 0
S29 CaMKII nanomole/liter 20000 0 0 0 kinetic Spine 0 P28652 P11798 K04515
S30 CaMKII_CaM_Ca4 nanomole/liter 0 0 0 0 kinetic Spine 0
S31 CaMKII_CaM nanomole/liter 0 0 0 0 kinetic Spine 0
S32 CaMKII_CaM_Ca2 nanomole/liter 0 0 0 0 kinetic Spine 0
S33 CaMKII_CaM_Ca2_psd nanomole/liter 0 0 0 0 kinetic Spine 0
S34 CaMKII_CaM_psd nanomole/liter 0 0 0 0 kinetic Spine 0
S35 CaMKII_CaM_Ca4_psd nanomole/liter 0 0 0 0 kinetic Spine 0
S36 CaMKII_psd nanomole/liter 0 0 0 0 kinetic Spine 0
S37 cAMP nanomole/liter 0 0 0 0 kinetic Spine 0 C00575
S38 Substrate nanomole/liter 3000 0 0 0 kinetic Spine 0 P23818 P23819 Q9Z2W9 Q9Z2W8 K05197 K05198 K05199 K05200
S39 CDK5 nanomole/liter 1800 0 0 0 kinetic Spine 0 P49615 K02090
S40 CDK5_D32 nanomole/liter 0 0 0 0 kinetic Spine 0
S41 D1R nanomole/liter 2000 0 0 0 kinetic Spine 0 Q61616 K04144
S42 D1R_DA nanomole/liter 0 0 0 0 kinetic Spine 0
S43 D1R_Golf_DA nanomole/liter 0 0 0 0 kinetic Spine 0
S44 D1R_Golf nanomole/liter 0 0 0 0 kinetic Spine 0
S45 D32p34 nanomole/liter 0 0 0 0 kinetic Spine 0
S46 D32p75 nanomole/liter 0 0 0 0 kinetic Spine 0
S47 D32 nanomole/liter 50000 0 0 0 kinetic Spine 0 Q60829 C03758
S48 DA nanomole/liter 20 1 DA_expression 1 kinetic Spine 1 K15494
S49 GaolfGDP nanomole/liter 0 0 0 0 kinetic Spine 0 Q8CGK7 K04633
S50 GaolfGTP nanomole/liter 0 0 0 0 kinetic Spine 0 Q8CGK7 K04633
S51 Gbgolf nanomole/liter 0 0 0 0 kinetic Spine 0 P62874 Q61012 K04548
S52 Golf nanomole/liter 2000 0 0 0 kinetic Spine 0
S53 pCaMKII nanomole/liter 0 0 0 0 kinetic Spine 0
S54 pCaMKII_CaM_Ca4 nanomole/liter 0 0 0 0 kinetic Spine 0
S55 pCaMKII_CaM nanomole/liter 0 0 0 0 kinetic Spine 0
S56 pCaMKII_CaM_Ca2 nanomole/liter 0 0 0 0 kinetic Spine 0
S57 pCaMKII_CaM_Ca2_psd nanomole/liter 0 0 0 0 kinetic Spine 0
S58 pCaMKII_CaM_psd nanomole/liter 0 0 0 0 kinetic Spine 0
S59 pCaMKII_CaM_Ca4_psd nanomole/liter 0 0 0 0 kinetic Spine 0
S60 pCaMKII_psd nanomole/liter 0 0 0 0 kinetic Spine 0
S61 pSubstrate nanomole/liter 0 0 0 0 kinetic Spine 0
S62 PDE4 nanomole/liter 2000 0 0 0 kinetic Spine 0 O89084 Q01063 Q3UEI1 Q9QXI7 K13293
S63 PDE4_cAMP nanomole/liter 0 0 0 0 kinetic Spine 0
S64 PDE10r nanomole/liter 700 0 0 0 kinetic Spine 0 Q8CA95
S65 PDE10r_cAMP nanomole/liter 0 0 0 0 kinetic Spine 0
S66 PDE10c nanomole/liter 0 0 0 0 kinetic Spine 0
S67 PDE10c_cAMP nanomole/liter 0 0 0 0 kinetic Spine 0
S68 PKA nanomole/liter 1200 0 0 0 kinetic Spine 0 K04345
S69 PKAc nanomole/liter 0 0 0 0 kinetic Spine 0 P05132 P68181
S70 PKAc_B56PP2A nanomole/liter 0 0 0 0 kinetic Spine 0
S71 PKAc_D32 nanomole/liter 0 0 0 0 kinetic Spine 0
S72 PKAc_ARPP21 nanomole/liter 0 0 0 0 kinetic Spine 0
S73 PKA_Ca2MP nanomole/liter 0 0 0 0 kinetic Spine 0
S74 PKA_Ca4MP nanomole/liter 0 0 0 0 kinetic Spine 0
S75 PKAc_D32p75 nanomole/liter 0 0 0 0 kinetic Spine 0
S76 PKAreg nanomole/liter 0 0 0 0 kinetic Spine 0 P31324
S77 PP1 nanomole/liter 3000 0 0 0 kinetic Spine 0 P62137 P62141 P63087 K06269
S78 PP1_pCaMKII_psd nanomole/liter 0 0 0 0 kinetic Spine 0
S79 PP1_pSubstrate nanomole/liter 0 0 0 0 kinetic Spine 0
S80 PP1_D32p34 nanomole/liter 0 0 0 0 kinetic Spine 0
S81 CaMKII_CaM_Ca4_psd_CaMKII_CaM_Ca4_psd nanomole/liter 0 0 0 0 kinetic Spine 0
S82 pCaMKII_CaM_Ca4_psd_CaMKII_CaM_Ca4_psd nanomole/liter 0 0 0 0 kinetic Spine 0
S83 CaMKII_CaM_Ca4_CaMKII_CaM_Ca4 nanomole/liter 0 0 0 0 kinetic Spine 0
S84 pCaMKII_CaM_Ca4_CaMKII_CaM_Ca4 nanomole/liter 0 0 0 0 kinetic Spine 0
S85 PP2B nanomole/liter 4000 0 0 0 kinetic Spine 0 P63328 P48453 K04348
S86 PP2Bc nanomole/liter 0 0 0 0 kinetic Spine 0
S87 PP2Bc_D32p34 nanomole/liter 0 0 0 0 kinetic Spine 0
S88 PP2B_CaM nanomole/liter 0 0 0 0 kinetic Spine 0
S89 PP2B_CaM_Ca2 nanomole/liter 0 0 0 0 kinetic Spine 0
S90 pARPP21 nanomole/liter 0 0 0 0 kinetic Spine 0
S91 ARPP21 nanomole/liter 20000 0 0 0 kinetic Spine 0 Q9DCB4 100173450
S92 pCaMKII_psd_Substrate nanomole/liter 0 0 0 0 kinetic Spine 0
S93 pCaMKII_CaM_psd_Substrate nanomole/liter 0 0 0 0 kinetic Spine 0
S94 pCaMKII_CaM_Ca2_psd_Substrate nanomole/liter 0 0 0 0 kinetic Spine 0
S95 pCaMKII_CaM_Ca4_psd_Substrate nanomole/liter 0 0 0 0 kinetic Spine 0
S96 CaMKII_CaM_psd_Substrate nanomole/liter 0 0 0 0 kinetic Spine 0
S97 CaMKII_CaM_Ca2_psd_Substrate nanomole/liter 0 0 0 0 kinetic Spine 0
S98 CaMKII_CaM_Ca4_psd_Substrate nanomole/liter 0 0 0 0 kinetic Spine 0
6 changes: 6 additions & 0 deletions examples/notebooks/neuromodulation/data/SBtab/Constant.tsv
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!!SBtab SBtabVersion='1.0' Document='Nair_2016_optimized' TableName='Constant' TableTitle='Constant' TableType = 'Constant'
!ID !Name !Value !Unit
C0 tau_DA1 34.979 millisecond
C1 tau_DA2 420 millisecond
C2 DA_basal 20 nanomole/liter
C3 Ca_basal 60 nanomole/liter
5 changes: 5 additions & 0 deletions examples/notebooks/neuromodulation/data/SBtab/Expression.tsv
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!!SBtab SBtabVersion='1.0' Document='Nair_2016_optimized' TableName='Expression' TableTitle='Expression' TableType = 'Expression'
!ID !Name !Formula !Unit !Location
EX0 ATP_expression 5000000 nanomole/liter Spine
EX1 Ca_expression 1 nanomole/liter Spine
EX2 DA_expression DA_basal+(1/(1+exp((-10E+10)*(time-DA_start)))*(DA_max/(exp(-tau_DA1*tau_DA2/(tau_DA2-tau_DA1)*log(tau_DA2/tau_DA1)/tau_DA1)-exp(-tau_DA1*tau_DA2/(tau_DA2-tau_DA1)*log(tau_DA2/tau_DA1)/tau_DA2))*(exp(-(time-DA_start)/tau_DA1)-exp(-(time-DA_start)/tau_DA2)))) nanomole/liter Spine
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