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Commit 566e6046 authored by Rui Ribeiro's avatar Rui Ribeiro
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pre-release

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SI/Gi_parameters.csv 0 → 100644
+ 68
− 0
View file @ 566e6046
Parameter,Value,Unit
time_in,0,s
time_out,0,s
L_init,0.01,uM
R_init,2,uM
Gi_init,3,uM
AC5_init,0.7,uM
Ca_cytos_free,0.06,uM
ATP_init,5000,uM
PDE4_init,2,uM
PDE10_init,1,uM
PKA_init,1.2,uM
RL_kon,100.0,uM-1*s-1
RL_koff,200,s-1
RL_Gi_kon,6600.0,uM-1*s-1
RL_Gi_koff,200,s-1
RL_Gi_decay,60,s-1
GaiGTP_decay,30,s-1
Gi_formation,100,s-1
AC5_ATP_kon,0.1,uM-1*s-1
AC5_ATP_koff,1,s-1
AC5_basal,1,uM-1*s-1
AC5_reverse_basal,0.0004,
AC5_Ca_kon,1.0,uM-1*s-1
AC5_Ca_koff,0.9,s-1
AC5_Ca_ATP_kon,0.075,uM-1*s-1
AC5_Ca_ATP_koff,1,s-1
AC5_Ca_ATP_to_cAMP,0.5,uM-1*s-1
AC5_Ca_ATP_to_cAMP_reverse,0.00015,
AC5_ATP_Ca_kon,1.0,uM-1*s-1
AC5_ATP_Ca_koff,0.9,s-1
AC5_GaiGTP_kon,50000,uM-1*s-1
AC5_GaiGTP_koff,5,s-1
AC5_GaiGTP_ATP_kon,0.0625,uM-1*s-1
AC5_GaiGTP_ATP_koff,1,s-1
AC5_ATP_GaiGTP_kon,50000,uM-1*s-1
AC5_ATP_GaiGTP_koff,5,s-1
AC5_GaiGTP_ATP_to_cAMP,0.25,uM-1*s-1
AC5_GaiGTP_ATP_to_cAMP_reverse,0.00105,
AC5_GaiGTP_decay,30,s-1
AC5_GaiGTP_decay_koff,30,s-1
AC5_Ca_GaiGTP_kon,50000,uM-1*s-1
AC5_Ca_GaiGTP_koff,5,s-1
AC5_Ca_GaiGTP_ATP_kon,0.0563,uM-1*s-1
AC5_Ca_GaiGTP_ATP_koff,1,s-1
AC5_Ca_ATP_GaiGTP_kon,50000,uM-1*s-1
AC5_Ca_ATP_GaiGTP_koff,5,s-1
AC5_Ca_GaiGTP_ATP_to_cAMP,0.125,uM-1*s-1
AC5_Ca_GaiGTP_ATP_to_cAMP_reverse,2.81E-5,s-1
AC5_Ca_GaiGTP_decay,30,s-1
AC5_Ca_GaiGTP_ATP_decay,30,s-1
PDE4_cAMP_kon,10.0,uM-1*s-1
PDE4_cAMP_koff,1,s-1
PDE4_cAMP_to_AMP,2,s-1
PDE10_2cAMP_kon,0.001,uM-1*s-1
PDE10_2cAMP_koff,9,s-1
PDE10_cAMP_kon,100.0,uM-1*s-1
PDE10_cAMP_koff,2,s-1
PDE10_2cAMP_cAMP_kon,130.0,uM-1*s-1
PDE10_2cAMP_cAMP_koff,2,s-1
PDE10_cAMP_decay,3,s-1
PDE10_2cAMP_cAMP_decay,10,s-1
PKA_cAMP2_kon,0.26,uM-1*s-1
PKA_cAMP2_koff,1,s-1
PKA_cAMP4_kon,0.346,uM-1*s-1
PKA_cAMP4_koff,1,s-1
PKA_activation,10000.0,uM-1*s-1
PKA_activation_reverse,0.025,s-1
SI/Gi_pathway_parameters.md deleted 100644 → 0
+ 0
− 39
View file @ d06784b0
| Reaction number | Reaction | Foward parameters names | Reverse parameters names | Foward default values (1/(nM*s)) | Reverse default values (1/s) |
|:---------------:|:------------------------------------------:|:------------------------:|:---------------------------------:|:--------------------------------:|:----------------------------:|
| 1 | DA + D2R <-> D2RDA | RL_kon | RL_koff | 0.1 | 200 |
| 3 | D2RDA + Gi <-> D2RDAGi | RL_Gi_kon | RL_Gi_koff | 6.6 | 200 |
| 9 | D2RDAGi -> GaiGTP + D2RDA + Gbgi | | RL_Gi_decay | | 60 |
| 13 | GaolfGTP -> GaolfGDP | | GaiGTP_decay | | 30 |
| 14 | GaolfGDP + Gbgolf -> Golf | | Gi_formation | | 100 |
| 16 | AC5 + Ca <-> AC5Ca | AC5_Ca_kon | AC5_Ca_koff | 0.001 | 0.9 |
| 21 | AC5 + ATP <-> [AC5*ATP] | AC5_ATP_kon | AC5_ATP_koff | 0.0001 | 1 |
| 22 | [AC5*ATP] -> cAMP + AC5 | | AC5_basal | | 1 |
| 23 | cAMP + AC5 -> [AC5*ATP] | | AC5_reverse_basal | | 0.0004 |
| 24 | AC5Ca + ATP <-> [AC5Ca*ATP] | AC5_Ca_ATP_kon | AC5_Ca_ATP_koff | 7.50E-05 | 1 |
| 25 | [AC5Ca*ATP] -> cAMP + AC5Ca | | AC5_Ca_ATP_to_cAMP | | 0.5 |
| 26 | cAMP + AC5Ca -> [AC5Ca*ATP] | | AC5_Ca_ATP_to_cAMP_reverse | | 0.00015 |
| 30 | Ca + [AC5*ATP] <-> [AC5Ca*ATP] | AC5_ATP_Ca_kon | AC5_ATP_Ca_koff | 0.001 | 0.9 |
| 37 | GaiGTP + AC5 <-> AC5GaiGTP | AC5_GaiGTP_kon | AC5_GaiGTP_koff | 50 | 5 |
| 38 | ATP + AC5GaiGTP <-> [AC5GaiGTP*ATP] | AC5_GaiGTP_ATP_kon | AC5_GaiGTP_ATP_koff | 6.25E-05 | 1 |
| 39 | [AC5*ATP] + GaiGTP <-> [AC5GaiGTP*ATP] | AC5_ATP_GaiGTP_kon | AC5_ATP_GaiGTP_koff | 50 | 5 |
| 40 | [AC5GaiGTP*ATP] -> cAMP + AC5GaiGTP | | AC5_GaiGTP_ATP_to_cAMP | | 0.25 |
| 41 | cAMP + AC5GaiGTP -> [AC5GaiGTP*ATP] | | AC5_GaiGTP_ATP_to_cAMP_reverse | | 0.00105 |
| 42 | AC5GaiGTP -> AC5 + GaiGDP | | AC5_GaiGTP_decay | | 30 |
| 43 | [AC5GaiGTP*ATP] -> [AC5*ATP] + GaiGDP | | AC5_GaiGTP_decay_koff | | 30 |
| 55 | GaiGTP + AC5Ca <-> AC5CaGaiGTP | AC5_Ca_GaiGTP_kon | AC5_Ca_GaiGTP_koff | 50 | 5 |
| 56 | AC5CaGaiGTP + ATP <-> [AC5CaGaiGTP*ATP] | AC5_Ca_GaiGTP_ATP_kon | AC5_Ca_GaiGTP_ATP_koff | 5.63E-05 | 1 |
| 57 | [AC5Ca*ATP] + GaiGTP <-> [AC5CaGaiGTP*ATP] | AC5_Ca_ATP_GaiGTP_kon | AC5_Ca_ATP_GaiGTP_koff | 50 | 5 |
| 58 | [AC5CaGaiGTP*ATP] -> cAMP + AC5CaGaiGTP | | AC5_Ca_GaiGTP_ATP_to_cAMP | | 0.125 |
| 59 | cAMP + AC5CaGaiGTP -> [AC5CaGaiGTP*ATP] | | AC5_Ca_GaiGTP_ATP_to_cAMP_reverse | | 2.81E-05 |
| 60 | AC5CaGaiGTP -> AC5Ca + GaiGDP | | AC5_Ca_GaiGTP_decay | | 30 |
| 61 | [AC5CaGaiGTP*ATP] -> [AC5Ca*ATP] + GaiGDP | | AC5_Ca_GaiGTP_ATP_decay | | 30 |
| 73 | cAMP + PDE4 <-> [PDE4*cAMP] | PDE104_cAMP_kon | PDE4_cAMP_koff | 0.01 | 1 |
| 74 | PDE10 + 2 cAMP <-> PDE10c | PDE10_2cAMP_kon | PDE10_2cAMP_koff | 1.00E-06 | 9 |
| 75 | [PDE4*cAMP] -> PDE4 + AMP | | PDE4_cAMP_to_AMP | | 2 |
| 76 | cAMP + PDE10 <-> [PDE10*cAMP] | PDE10_cAMP_kon | PDE10_cAMP_koff | 0.1 | 2 |
| 77 | cAMP + PDE10c <-> [PDE10c*cAMP] | PDE10_2cAMP_cAMP_kon | PDE10_2cAMP_cAMP_koff | 0.13 | 2 |
| 78 | [PDE10*cAMP] -> PDE10 + AMP | | PDE10_cAMP_decay | | 3 |
| 79 | [PDE10c*cAMP] -> PDE10c + AMP | | PDE10_2cAMP_cAMP_decay | | 10 |
| 80 | cAMP + PKA <-> PKAcAMP2 | PKA_cAMP2_kon | PKA_cAMP2_koff | 0.00026 | 1 |
| 81 | cAMP + PKAcAMP2 <-> PKAcAMP4 | PKA_cAMP4_kon | PKA_cAMP4_koff | 0.000346 | 1 |
| 82 | PKAcAMP4 <-> PKAc + PKAreg | PKA_activation | PKA_activation_reverse | 10 | 0.025 |
SI/Gi_pathway_parameters.csv → SI/Gi_reactions.csv
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View file @ 566e6046
Reaction number,Reaction,Forward parameters names,Reverse parameters names,Forward default values (1/(nM*s)),Reverse default values (1/s) Reaction number,Reaction,Forward parameters names,Reverse parameters names,Forward default values (1/(uM*s)),Reverse default values (1/s)
1,DA + D2R <-> D2RDA,RL_kon,RL_koff,0.1,200 1,L + R <-> LR,RL_kon,RL_koff,100.0,200
3,D2RDA + Gi <-> D2RDAGi,RL_Gi_kon,RL_Gi_koff,6.6,200 3,LR + Gi <-> D2RDAGi,RL_Gi_kon,RL_Gi_koff,6600.0,200
9,D2RDAGi -> GaiGTP + D2RDA + Gbgi,,RL_Gi_decay,,60 9,LRGi -> GaiGTP + LR + Gbgi,,RL_Gi_decay,,60
13,GaolfGTP -> GaolfGDP,,GaiGTP_decay,,30 13,GaolfGTP -> GaolfGDP,,GaiGTP_decay,,30
14,GaolfGDP + Gbgolf -> Golf,,Gi_formation,,100 14,GaolfGDP + Gbgolf -> Golf,,Gi_formation,,100
16,AC5 + Ca <-> AC5Ca,AC5_Ca_kon,AC5_Ca_koff,0.001,0.9 16,AC5 + Ca <-> AC5Ca,AC5_Ca_kon,AC5_Ca_koff,1.0,0.9
21,AC5 + ATP <-> [AC5*ATP],AC5_ATP_kon,AC5_ATP_koff,0.0001,1 21,AC5 + ATP <-> [AC5*ATP],AC5_ATP_kon,AC5_ATP_koff,0.1,1
22,[AC5*ATP] -> cAMP + AC5,,AC5_basal,,1 22,[AC5*ATP] -> cAMP + AC5,,AC5_basal,,1
23,cAMP + AC5 -> [AC5*ATP],,AC5_reverse_basal,,0.0004 23,cAMP + AC5 -> [AC5*ATP],,AC5_reverse_basal,,0.0004
24,AC5Ca + ATP <-> [AC5Ca*ATP],AC5_Ca_ATP_kon,AC5_Ca_ATP_koff,7.50E-05,1 24,AC5Ca + ATP <-> [AC5Ca*ATP],AC5_Ca_ATP_kon,AC5_Ca_ATP_koff,0.075,1
25,[AC5Ca*ATP] -> cAMP + AC5Ca,,AC5_Ca_ATP_to_cAMP,,0.5 25,[AC5Ca*ATP] -> cAMP + AC5Ca,,AC5_Ca_ATP_to_cAMP,,0.5
26,cAMP + AC5Ca -> [AC5Ca*ATP],,AC5_Ca_ATP_to_cAMP_reverse,,0.00015 26,cAMP + AC5Ca -> [AC5Ca*ATP],,AC5_Ca_ATP_to_cAMP_reverse,,0.00015
30,Ca + [AC5*ATP] <-> [AC5Ca*ATP],AC5_ATP_Ca_kon,AC5_ATP_Ca_koff,0.001,0.9 30,Ca + [AC5*ATP] <-> [AC5Ca*ATP],AC5_ATP_Ca_kon,AC5_ATP_Ca_koff,1.0,0.9
37,GaiGTP + AC5 <-> AC5GaiGTP,AC5_GaiGTP_kon,AC5_GaiGTP_koff,50,5 37,GaiGTP + AC5 <-> AC5GaiGTP,AC5_GaiGTP_kon,AC5_GaiGTP_koff,5000,5
38,ATP + AC5GaiGTP <-> [AC5GaiGTP*ATP],AC5_GaiGTP_ATP_kon,AC5_GaiGTP_ATP_koff,6.25E-05,1 38,ATP + AC5GaiGTP <-> [AC5GaiGTP*ATP],AC5_GaiGTP_ATP_kon,AC5_GaiGTP_ATP_koff,0.0625,1
39,[AC5*ATP] + GaiGTP <-> [AC5GaiGTP*ATP],AC5_ATP_GaiGTP_kon,AC5_ATP_GaiGTP_koff,50,5 39,[AC5*ATP] + GaiGTP <-> [AC5GaiGTP*ATP],AC5_ATP_GaiGTP_kon,AC5_ATP_GaiGTP_koff,50000,5
40,[AC5GaiGTP*ATP] -> cAMP + AC5GaiGTP,,AC5_GaiGTP_ATP_to_cAMP,,0.25 40,[AC5GaiGTP*ATP] -> cAMP + AC5GaiGTP,,AC5_GaiGTP_ATP_to_cAMP,,0.25
41,cAMP + AC5GaiGTP -> [AC5GaiGTP*ATP],,AC5_GaiGTP_ATP_to_cAMP_reverse,,0.00105 41,cAMP + AC5GaiGTP -> [AC5GaiGTP*ATP],,AC5_GaiGTP_ATP_to_cAMP_reverse,,0.00105
42,AC5GaiGTP -> AC5 + GaiGDP,,AC5_GaiGTP_decay,,30 42,AC5GaiGTP -> AC5 + GaiGDP,,AC5_GaiGTP_decay,,30
43,[AC5GaiGTP*ATP] -> [AC5*ATP] + GaiGDP,,AC5_GaiGTP_decay_koff,,30 43,[AC5GaiGTP*ATP] -> [AC5*ATP] + GaiGDP,,AC5_GaiGTP_decay_koff,,30
55,GaiGTP + AC5Ca <-> AC5CaGaiGTP,AC5_Ca_GaiGTP_kon,AC5_Ca_GaiGTP_koff,50,5 55,GaiGTP + AC5Ca <-> AC5CaGaiGTP,AC5_Ca_GaiGTP_kon,AC5_Ca_GaiGTP_koff,50000,5
56,AC5CaGaiGTP + ATP <-> [AC5CaGaiGTP*ATP],AC5_Ca_GaiGTP_ATP_kon,AC5_Ca_GaiGTP_ATP_koff,5.63E-05,1 56,AC5CaGaiGTP + ATP <-> [AC5CaGaiGTP*ATP],AC5_Ca_GaiGTP_ATP_kon,AC5_Ca_GaiGTP_ATP_koff,0.0563,1
57,[AC5Ca*ATP] + GaiGTP <-> [AC5CaGaiGTP*ATP],AC5_Ca_ATP_GaiGTP_kon,AC5_Ca_ATP_GaiGTP_koff,50,5 57,[AC5Ca*ATP] + GaiGTP <-> [AC5CaGaiGTP*ATP],AC5_Ca_ATP_GaiGTP_kon,AC5_Ca_ATP_GaiGTP_koff,50000,5
58,[AC5CaGaiGTP*ATP] -> cAMP + AC5CaGaiGTP,,AC5_Ca_GaiGTP_ATP_to_cAMP,,0.125 58,[AC5CaGaiGTP*ATP] -> cAMP + AC5CaGaiGTP,,AC5_Ca_GaiGTP_ATP_to_cAMP,,0.125
59,cAMP + AC5CaGaiGTP -> [AC5CaGaiGTP*ATP],,AC5_Ca_GaiGTP_ATP_to_cAMP_reverse,,2.81E-05 59,cAMP + AC5CaGaiGTP -> [AC5CaGaiGTP*ATP],,AC5_Ca_GaiGTP_ATP_to_cAMP_reverse,,2.81E-05
60,AC5CaGaiGTP -> AC5Ca + GaiGDP,,AC5_Ca_GaiGTP_decay,,30 60,AC5CaGaiGTP -> AC5Ca + GaiGDP,,AC5_Ca_GaiGTP_decay,,30
61,[AC5CaGaiGTP*ATP] -> [AC5Ca*ATP] + GaiGDP,,AC5_Ca_GaiGTP_ATP_decay,,30 61,[AC5CaGaiGTP*ATP] -> [AC5Ca*ATP] + GaiGDP,,AC5_Ca_GaiGTP_ATP_decay,,30
73,cAMP + PDE4 <-> [PDE4*cAMP],PDE104_cAMP_kon,PDE4_cAMP_koff,0.01,1 73,cAMP + PDE4 <-> [PDE4*cAMP],PDE104_cAMP_kon,PDE4_cAMP_koff,10.0,1
74,PDE10 + 2 cAMP <-> PDE10c,PDE10_2cAMP_kon,PDE10_2cAMP_koff,1.00E-06,9 74,PDE10 + 2 cAMP <-> PDE10c,PDE10_2cAMP_kon,PDE10_2cAMP_koff,0.001,9
75,[PDE4*cAMP] -> PDE4 + AMP,,PDE4_cAMP_to_AMP,,2 75,[PDE4*cAMP] -> PDE4 + AMP,,PDE4_cAMP_to_AMP,,2
76,cAMP + PDE10 <-> [PDE10*cAMP],PDE10_cAMP_kon,PDE10_cAMP_koff,0.1,2 76,cAMP + PDE10 <-> [PDE10*cAMP],PDE10_cAMP_kon,PDE10_cAMP_koff,100.0,2
77,cAMP + PDE10c <-> [PDE10c*cAMP],PDE10_2cAMP_cAMP_kon,PDE10_2cAMP_cAMP_koff,0.13,2 77,cAMP + PDE10c <-> [PDE10c*cAMP],PDE10_2cAMP_cAMP_kon,PDE10_2cAMP_cAMP_koff,130.0,2
78,[PDE10*cAMP] -> PDE10 + AMP,,PDE10_cAMP_decay,,3 78,[PDE10*cAMP] -> PDE10 + AMP,,PDE10_cAMP_decay,,3
79,[PDE10c*cAMP] -> PDE10c + AMP,,PDE10_2cAMP_cAMP_decay,,10 79,[PDE10c*cAMP] -> PDE10c + AMP,,PDE10_2cAMP_cAMP_decay,,10
80,cAMP + PKA <-> PKAcAMP2,PKA_cAMP2_kon,PKA_cAMP2_koff,0.00026,1 80,cAMP + PKA <-> PKAcAMP2,PKA_cAMP2_kon,PKA_cAMP2_koff,0.26,1
81,cAMP + PKAcAMP2 <-> PKAcAMP4,PKA_cAMP4_kon,PKA_cAMP4_koff,0.000346,1 81,cAMP + PKAcAMP2 <-> PKAcAMP4,PKA_cAMP4_kon,PKA_cAMP4_koff,0.346,1
82,PKAcAMP4 <-> PKAc + PKAreg,PKA_activation,PKA_activation_reverse,10,0.025 82,PKAcAMP4 <-> PKAc + PKAreg,PKA_activation,PKA_activation_reverse,10000.0,0.025
SI/Gq_parameters.csv 0 → 100644
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− 0
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Parameter,Value,Unit
time_in,0,s
time_out,0,s
Gq_a_GDP_init:0.0027739,uM
Gq_a_GDP_init:6.4172E-4,uM
Gq_bg_init:0.0037173,uM
RGS4_init:0.019994,uM
RGS4_Gq_a_GTP_init:6.4168E-6,uM
Ca_init:0.1,uM
PLCb_init:0.090022,uM
PLCb_Gq_a_GTP_init:1.4492E-4,uM
PLCb_Ca_init:0.0093825,uM
PLCb_Ca_Gq_a_GTP_init:1.5038E-4,uM
PIP2_init:2.6578,uM
IP3_init:0.21952,uM
DAG_init:0.055555,uM
R_Gq_trimer_init:0,uM
R_L_Gq_trimer_init:0,uM
Gq_trimer_init:0.61869,uM
RL_kon:1.00,uM-1*s-1
RL_koff:0.0046,s-1
Gqa_Gqbg_kon:6.0,uM-1*s-1
Gqa_Gqbg_koff:0.0001,s-1
RL_Gq_decay:0.04,s-1
RGS4_Gq_a_GTP_kon:20.83,uM-1*s-1
RGS4_Gq_a_GTP_koff:33.32,s-1
RGS4_Gq_a_GTP_decay:8.33,s-1
Gq_a_GTP_decay:0.01,s-1
Gq_a_GTP_PLCb_kon:2.52,uM-1*s-1
Gq_a_GTP_PLCb_off:1.00,s-1
Gq_a_GTP_PLCb_Ca_kon:30.0,uM-1*s-1
Gq_a_GTP_PLCb_Ca_koff:1.00,s-1
Gq_a_GTP_PLCb_Ca_decay:0.013,s-1
PLCb_Ca_kon:3.00,uM-1*s-1
PLCb_Ca_koff:1.00,s-1
PLCb_Ca_Gq_a_GTP_kon:25.2,uM-1*s-1
PLCb_Ca_Gq_a_GTP_koff:1.00,s-1
DAG_decay:0.15,s-1
SI/Gq_reactions.csv 0 → 100644
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− 0
View file @ 566e6046
Reaction number,Reaction,Forward parameters names,Reverse parameter names,Forward default (1/(nM*s)),Reverse default (1/s)
SI/Gs_parameters.csv
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− 38
View file @ 566e6046
Reaction number,Reaction,Forward parameters names,Reverse parameter names,Forward default (1/(nM*s)), Reverse default (1/s) Parameter,Value,Unit
1,D1R + DA <-> D1RDA,RL_kon,RL_koff,0.005,5 time_in,0,s
3,D1RDA + Golf <-> D1RDAGolf,RL_Golf_kon,RL_Golf_koff,0.003,5 time_out,0,s
9,D1RDAGolf -> Gbgolf + D1RDA + GaolfGTP,,RL_Golf_decay,,15 L_init,0.01,uM
10,GaolfGTP -> GaolfGDP,,GaolfGTP_decay,,30 R_init,2,uM
11,GaolfGDP + Gbgolf -> Golf,,Golf_formation,,100 Golf_init,2,uM
15,AC5 + GaolfGTP <-> AC5GaolfGTP,AC5_GaolfGTP_kon,AC5_GaolfGTP_koff,0.2,0.1 AC5_init,0.7,uM
16,AC5 + Ca <-> AC5Ca,AC5_Ca_kon,AC5_GaolfGTP_koff,0.001,0.9 Ca_init,0.06,uM
17,AC5Ca + GaolfGTP <-> AC5CaGaolfGTP,AC5_Ca_GaolfGTP_kon,AC5_Ca_GaolfGTP_koff,0.2,0.1 ATP_init,5000,uM
18,AC5GaolfGTP + ATP <-> [AC5GaolfGTP*ATP],AC5_GaolfGTP_ATP_i_koff,AC5_GaolfGTP_ATP_i_koff,0.00105,1 PDE4_init,2,uM
19,[AC5GaolfGTP*ATP] -> cAMP + AC5GaolfGTP,,cAMP_formation,,20 PDE10_init,0.7,uM
20,cAMP + AC5GaolfGTP -> [AC5GaolfGTP*ATP],,cAMP_reverse,,0.084 PKA_init,1.2,uM
21,AC5 + ATP <-> [AC5*ATP],AC5_ATP_kon,AC5_ATP_koff,0.0001,1 RL_kon,5.0,uM-1*s-1
22,[AC5*ATP] -> cAMP + AC5,,AC5_basal,,1 RL_koff,5,s-1
23,cAMP + AC5 -> [AC5*ATP],,AC5_reverse_basal,,0.0004 RL_Golf_kon,3.0,uM-1*s-1
24,AC5Ca + ATP <-> [AC5Ca*ATP],AC5_Ca_ATP_kon,AC5_Ca_ATP_koff,7.50E-05,1 RL_Golf_koff,5.0,s-1
25,[AC5Ca*ATP] -> cAMP + AC5Ca,,AC5_Ca_ATP_to_cAMP,,0.5 RL_Golf_decay,15,s-1
26,cAMP + AC5Ca -> [AC5Ca*ATP],,AC5_Ca_ATP_to_cAMP_reverse,,0.00015 GaolfGTP_decay,30,s-1
27,GaolfGTP + [AC5*ATP] <-> [AC5GaolfGTP*ATP],AC5_GaolfGTP_ATP_a_koff,AC5_GaolfGTP_ATP_a_koff,0.2,0.1 Golf_formation,100,s-1
28,AC5GaolfGTP -> AC5 + GaolfGDP,,AC5_GaolfGTP_decay,,0.2 AC5_ATP_kon,0.1,uM-1*s-1
29,[AC5GaolfGTP*ATP] -> [AC5*ATP] + GaolfGDP,,AC5_GaolfGTP_ATP_decay,,0.2 AC5_ATP_koff,1,uM-1*s-1
30,Ca + [AC5*ATP] <-> [AC5Ca*ATP],AC5_ATP_Ca_kon,AC5_ATP_Ca_koff,0.001,0.9 AC5_basal,1,s-1
31,AC5CaGaolfGTP + ATP <-> [AC5CaGaolfGTP*ATP],AC5_Ca_GaolfGTP_ATP_kon,AC5_Ca_GaolfGTP_ATP_koff,0.00055,1 AC5_reverse_basal,0.0004,s-1
32,GaolfGTP + [AC5Ca*ATP] <-> [AC5CaGaolfGTP*ATP],AC5_CA_ATP_GaolfGTP_kon,AC5_CA_ATP_GaolfGTP_koff,0.2,0.1 AC5_Ca_kon,1.0,uM-1*s-1
33,[AC5CaGaolfGTP*ATP] -> cAMP + AC5CaGaolfGTP,,AC5_Ca_GaolfGTP_ATP_to_cAMP,,10 AC5_Ca_koff,0.9,s-1
34,cAMP + AC5CaGaolfGTP -> [AC5CaGaolfGTP*ATP],,AC5_Ca_GaolfGTP_ATP_to_cAMP_reverse,,0.022 AC5_Ca_ATP_kon,0.075,uM-1*s-1
35,AC5CaGaolfGTP -> AC5Ca + GaolfGDP,,AC5_Ca_GaolfGTP_decay,,0.2 AC5_Ca_ATP_koff,1,s-1
36,[AC5CaGaolfGTP*ATP] -> [AC5Ca*ATP] + GaolfGDP,,AC5_Ca_GaolfGTP_ATP_decay,,0.2 AC5_Ca_ATP_to_cAMP,0.5,s-1
73,cAMP + PDE4 <-> [PDE4*cAMP],PDE4_cAMP_kon,PDE4_cAMP_koff,0.01,1 AC5_Ca_ATP_to_cAMP_reverse,0.00015,s-1
74,[PDE4*cAMP] -> PDE4 + AMP,,PDE4_cAMP_to_AMP,,2 AC5_ATP_Ca_kon,1.0,uM-1*s-1
75,PDE10 + 2 cAMP <-> PDE10c,PDE10_2cAMP_kon,PDE10_2cAMP_koff,1.00E-06,9 AC5_ATP_Ca_koff,0.9,
76,cAMP + PDE10 <-> [PDE10*cAMP],PDE10_cAMP_kon,PDE10_cAMP_koff,0.1,2 AC5_GaolfGTP_kon,200.0,uM-1*s-1
77,cAMP + PDE10c <-> [PDE10c*cAMP],PDE10_2cAMP_cAMP_kon,PDE10_2cAMP_cAMP_koff,0.13,2 AC5_GaolfGTP_koff,0.1,
78,[PDE10*cAMP] -> PDE10 + AMP,,PDE10_cAMP_decay,,3 AC5_GaolfGTP_ATP_i_kon,1.05,uM-1*s-1
79,[PDE10c*cAMP] -> PDE10c + AMP,,PDE10_2cAMP_cAMP_decay,,10 AC5_GaolfGTP_ATP_i_koff,1,
80,cAMP + PKA <-> PKAcAMP2,PKA_cAMP2_kon,PKA_cAMP2_koff,0.00026,1 cAMP_formation,20,s-1
81,cAMP + PKAcAMP2 <-> PKAcAMP4,PKA_cAMP4_kon,PKA_cAMP4_koff,0.000346,1 cAMP_reverse,0.084,s-1
82,PKAcAMP4 <-> PKAc + PKAreg,PKA_activation,PKA_activation_reverse,10,0.01 AC5_GaolfGTP_ATP_a_kon,200.0,uM-1*s-1
AC5_GaolfGTP_ATP_a_koff,0.1,
AC5_GaolfGTP_decay,0.2,s-1
AC5_GaolfGTP_ATP_decay,0.2,s-1
AC5_Ca_GaolfGTP_kon,200.0,uM-1*s-1
AC5_Ca_GaolfGTP_koff,0.1,s-1
AC5_Ca_GaolfGTP_ATP_kon,0.55,uM-1*s-1
AC5_Ca_GaolfGTP_ATP_koff,1,s-1
AC5_CA_ATP_GaolfGTP_kon,200.0,uM-1*s-1
AC5_CA_ATP_GaolfGTP_koff,0.1,s-1
AC5_Ca_GaolfGTP_ATP_to_cAMP,10,s-1
AC5_Ca_GaolfGTP_ATP_to_cAMP_reverse,0.022,s-1
AC5_Ca_GaolfGTP_decay,0.2,s-1
AC5_Ca_GaolfGTP_ATP_decay,0.2,s-1
PDE4_cAMP_kon,10.0,uM-1*s-1
PDE4_cAMP_koff,1,s-1
PDE4_cAMP_to_AMP,2,s-1
PDE10_2cAMP_kon,0.001,uM-1*s-1
PDE10_2cAMP_koff,9,s-1
PDE10_cAMP_kon,100.0,uM-1*s-1
PDE10_cAMP_koff,2,s-1
PDE10_2cAMP_cAMP_kon,130.0,uM-1*s-1
PDE10_2cAMP_cAMP_koff,2,s-1
PDE10_cAMP_decay,3,s-1
PDE10_2cAMP_cAMP_decay,10,s-1
PKA_cAMP2_kon,0.25999999999999995,uM-1*s-1
PKA_cAMP2_koff,1,s-1
PKA_cAMP4_kon,0.34600000000000003,uM-1*s-1
PKA_cAMP4_koff,1,s-1
PKA_activation,10000.0,uM-1*s-1
PKA_activation_reverse,0.01,s-1
SI/Gs_reactions.csv 0 → 100644
+ 38
− 0
View file @ 566e6046
Reaction number,Reaction,Forward parameters names,Reverse parameter names,Forward default (1/(uM*s)),Reverse default (1/s)
1,R + L <-> RL,RL_kon,RL_koff,5.0,5
3,RL + Golf <-> RLGolf,RL_Golf_kon,RL_Golf_koff,3.0,5
9,RLGolf -> Gbgolf + RL + GaolfGTP,,RL_Golf_decay,,15
10,GaolfGTP -> GaolfGDP,,GaolfGTP_decay,,30
11,GaolfGDP + Gbgolf -> Golf,,Golf_formation,,100
15,AC5 + GaolfGTP <-> AC5GaolfGTP,AC5_GaolfGTP_kon,AC5_GaolfGTP_koff,200.0,0.1
16,AC5 + Ca <-> AC5Ca,AC5_Ca_kon,AC5_GaolfGTP_koff,1.0,0.9
17,AC5Ca + GaolfGTP <-> AC5CaGaolfGTP,AC5_Ca_GaolfGTP_kon,AC5_Ca_GaolfGTP_koff,200.0,0.1
18,AC5GaolfGTP + ATP <-> [AC5GaolfGTP*ATP],AC5_GaolfGTP_ATP_i_koff,AC5_GaolfGTP_ATP_i_koff,1.05,1
19,[AC5GaolfGTP*ATP] -> cAMP + AC5GaolfGTP,,cAMP_formation,,20
20,cAMP + AC5GaolfGTP -> [AC5GaolfGTP*ATP],,cAMP_reverse,,0.084
21,AC5 + ATP <-> [AC5*ATP],AC5_ATP_kon,AC5_ATP_koff,0.1,1
22,[AC5*ATP] -> cAMP + AC5,,AC5_basal,,1
23,cAMP + AC5 -> [AC5*ATP],,AC5_reverse_basal,,0.0004
24,AC5Ca + ATP <-> [AC5Ca*ATP],AC5_Ca_ATP_kon,AC5_Ca_ATP_koff,0.075,1
25,[AC5Ca*ATP] -> cAMP + AC5Ca,,AC5_Ca_ATP_to_cAMP,,0.5
26,cAMP + AC5Ca -> [AC5Ca*ATP],,AC5_Ca_ATP_to_cAMP_reverse,,0.00015
27,GaolfGTP + [AC5*ATP] <-> [AC5GaolfGTP*ATP],AC5_GaolfGTP_ATP_a_kon,AC5_GaolfGTP_ATP_a_koff,200.0,0.1
28,AC5GaolfGTP -> AC5 + GaolfGDP,,AC5_GaolfGTP_decay,,0.2
29,[AC5GaolfGTP*ATP] -> [AC5*ATP] + GaolfGDP,,AC5_GaolfGTP_ATP_decay,,0.2
30,Ca + [AC5*ATP] <-> [AC5Ca*ATP],AC5_ATP_Ca_kon,AC5_ATP_Ca_koff,1.0,0.9
31,AC5CaGaolfGTP + ATP <-> [AC5CaGaolfGTP*ATP],AC5_Ca_GaolfGTP_ATP_kon,AC5_Ca_GaolfGTP_ATP_koff,0.55,1
32,GaolfGTP + [AC5Ca*ATP] <-> [AC5CaGaolfGTP*ATP],AC5_CA_ATP_GaolfGTP_kon,AC5_CA_ATP_GaolfGTP_koff,200.0,0.1
33,[AC5CaGaolfGTP*ATP] -> cAMP + AC5CaGaolfGTP,,AC5_Ca_GaolfGTP_ATP_to_cAMP,,10
34,cAMP + AC5CaGaolfGTP -> [AC5CaGaolfGTP*ATP],,AC5_Ca_GaolfGTP_ATP_to_cAMP_reverse,,0.022
35,AC5CaGaolfGTP -> AC5Ca + GaolfGDP,,AC5_Ca_GaolfGTP_decay,,0.2
36,[AC5CaGaolfGTP*ATP] -> [AC5Ca*ATP] + GaolfGDP,,AC5_Ca_GaolfGTP_ATP_decay,,0.2
73,cAMP + PDE4 <-> [PDE4*cAMP],PDE4_cAMP_kon,PDE4_cAMP_koff,10.0,1
74,[PDE4*cAMP] -> PDE4 + AMP,,PDE4_cAMP_to_AMP,,2
75,PDE10 + 2 cAMP <-> PDE10c,PDE10_2cAMP_kon,PDE10_2cAMP_koff,0.001,9
76,cAMP + PDE10 <-> [PDE10*cAMP],PDE10_cAMP_kon,PDE10_cAMP_koff,100.0,2
77,cAMP + PDE10c <-> [PDE10c*cAMP],PDE10_2cAMP_cAMP_kon,PDE10_2cAMP_cAMP_koff,130.0,2
78,[PDE10*cAMP] -> PDE10 + AMP,,PDE10_cAMP_decay,,3
79,[PDE10c*cAMP] -> PDE10c + AMP,,PDE10_2cAMP_cAMP_decay,,10
80,cAMP + PKA <-> PKAcAMP2,PKA_cAMP2_kon,PKA_cAMP2_koff,0.26,1
81,cAMP + PKAcAMP2 <-> PKAcAMP4,PKA_cAMP4_kon,PKA_cAMP4_koff,0.346,1
82,PKAcAMP4 <-> PKAc + PKAreg,PKA_activation,PKA_activation_reverse,10000.0,0.01
src/lib/pathways/Gi_parameters.csv
+ 20
− 20
View file @ 566e6046
...@@ -10,59 +10,59 @@ ATP_init,5000,uM ...@@ -10,59 +10,59 @@ ATP_init,5000,uM
PDE4_init,2,uM PDE4_init,2,uM
PDE10_init,1,uM PDE10_init,1,uM
PKA_init,1.2,uM PKA_init,1.2,uM
RL_kon,0.1*1E3,uM-1*s-1 RL_kon,100.0,uM-1*s-1
RL_koff,200,s-1 RL_koff,200,s-1
RL_Gi_kon,6.6*1E3,uM-1*s-1 RL_Gi_kon,6600.0,uM-1*s-1
RL_Gi_koff,200,s-1 RL_Gi_koff,200,s-1
RL_Gi_decay,60,s-1 RL_Gi_decay,60,s-1
GaiGTP_decay,30,s-1 GaiGTP_decay,30,s-1
Gi_formation,100,s-1 Gi_formation,100,s-1
AC5_ATP_kon,0.0001*1E3,uM-1*s-1 AC5_ATP_kon,0.1,uM-1*s-1
AC5_ATP_koff,1,s-1 AC5_ATP_koff,1,s-1
AC5_basal,1,uM-1*s-1 AC5_basal,1,uM-1*s-1
AC5_reverse_basal,0.0004, AC5_reverse_basal,0.0004,
AC5_Ca_kon,0.001*1E3,uM-1*s-1 AC5_Ca_kon,1.0,uM-1*s-1
AC5_Ca_koff,0.9,s-1 AC5_Ca_koff,0.9,s-1
AC5_Ca_ATP_kon,7.50E-5*1E3,uM-1*s-1 AC5_Ca_ATP_kon,0.075,uM-1*s-1
AC5_Ca_ATP_koff,1,s-1 AC5_Ca_ATP_koff,1,s-1
AC5_Ca_ATP_to_cAMP,0.5,uM-1*s-1 AC5_Ca_ATP_to_cAMP,0.5,uM-1*s-1
AC5_Ca_ATP_to_cAMP_reverse,0.00015, AC5_Ca_ATP_to_cAMP_reverse,0.00015,
AC5_ATP_Ca_kon,0.001*1E3,uM-1*s-1 AC5_ATP_Ca_kon,1.0,uM-1*s-1
AC5_ATP_Ca_koff,0.9,s-1 AC5_ATP_Ca_koff,0.9,s-1
AC5_GaiGTP_kon,50*1E3,uM-1*s-1 AC5_GaiGTP_kon,50000,uM-1*s-1
AC5_GaiGTP_koff,5,s-1 AC5_GaiGTP_koff,5,s-1
AC5_GaiGTP_ATP_kon,6.25E-5*1E3,uM-1*s-1 AC5_GaiGTP_ATP_kon,0.0625,uM-1*s-1
AC5_GaiGTP_ATP_koff,1,s-1 AC5_GaiGTP_ATP_koff,1,s-1
AC5_ATP_GaiGTP_kon,50*1E3,uM-1*s-1 AC5_ATP_GaiGTP_kon,50000,uM-1*s-1
AC5_ATP_GaiGTP_koff,5,s-1 AC5_ATP_GaiGTP_koff,5,s-1
AC5_GaiGTP_ATP_to_cAMP,0.25,uM-1*s-1 AC5_GaiGTP_ATP_to_cAMP,0.25,uM-1*s-1
AC5_GaiGTP_ATP_to_cAMP_reverse,0.00105, AC5_GaiGTP_ATP_to_cAMP_reverse,0.00105,
AC5_GaiGTP_decay,30,s-1 AC5_GaiGTP_decay,30,s-1
AC5_GaiGTP_decay_koff,30,s-1 AC5_GaiGTP_decay_koff,30,s-1
AC5_Ca_GaiGTP_kon,50*1E3,uM-1*s-1 AC5_Ca_GaiGTP_kon,50000,uM-1*s-1
AC5_Ca_GaiGTP_koff,5,s-1 AC5_Ca_GaiGTP_koff,5,s-1
AC5_Ca_GaiGTP_ATP_kon,5.63E-5*1E3,uM-1*s-1 AC5_Ca_GaiGTP_ATP_kon,0.0563,uM-1*s-1
AC5_Ca_GaiGTP_ATP_koff,1,s-1 AC5_Ca_GaiGTP_ATP_koff,1,s-1
AC5_Ca_ATP_GaiGTP_kon,50*1E3,uM-1*s-1 AC5_Ca_ATP_GaiGTP_kon,50000,uM-1*s-1
AC5_Ca_ATP_GaiGTP_koff,5,s-1 AC5_Ca_ATP_GaiGTP_koff,5,s-1
AC5_Ca_GaiGTP_ATP_to_cAMP,0.125,uM-1*s-1 AC5_Ca_GaiGTP_ATP_to_cAMP,0.125,uM-1*s-1
AC5_Ca_GaiGTP_ATP_to_cAMP_reverse,2.81E-5, AC5_Ca_GaiGTP_ATP_to_cAMP_reverse,2.81E-5,s-1
AC5_Ca_GaiGTP_decay,30,s-1 AC5_Ca_GaiGTP_decay,30,s-1
AC5_Ca_GaiGTP_ATP_decay,30,s-1 AC5_Ca_GaiGTP_ATP_decay,30,s-1
PDE4_cAMP_kon,0.01*1E3,uM-1*s-1 PDE4_cAMP_kon,10.0,uM-1*s-1
PDE4_cAMP_koff,1,s-1 PDE4_cAMP_koff,1,s-1
PDE4_cAMP_to_AMP,2,s-1 PDE4_cAMP_to_AMP,2,s-1
PDE10_2cAMP_kon,1.0E-6*1E3, PDE10_2cAMP_kon,0.001,uM-1*s-1
PDE10_2cAMP_koff,9,s-1 PDE10_2cAMP_koff,9,s-1
PDE10_cAMP_kon,0.1*1E3, PDE10_cAMP_kon,100.0,uM-1*s-1
PDE10_cAMP_koff,2,s-1 PDE10_cAMP_koff,2,s-1
PDE10_2cAMP_cAMP_kon,0.13*1E3, PDE10_2cAMP_cAMP_kon,130.0,uM-1*s-1
PDE10_2cAMP_cAMP_koff,2,s-1 PDE10_2cAMP_cAMP_koff,2,s-1
PDE10_cAMP_decay,3,s-1 PDE10_cAMP_decay,3,s-1
PDE10_2cAMP_cAMP_decay,10,s-1 PDE10_2cAMP_cAMP_decay,10,s-1
PKA_cAMP2_kon,0.00026*1E3,uM-1*s-1 PKA_cAMP2_kon,0.26,uM-1*s-1
PKA_cAMP2_koff,1,s-1 PKA_cAMP2_koff,1,s-1
PKA_cAMP4_kon,0.000346*1E3,uM-1*s-1 PKA_cAMP4_kon,0.346,uM-1*s-1
PKA_cAMP4_koff,1,s-1 PKA_cAMP4_koff,1,s-1
PKA_activation,10*1E3,uM-1*s-1 PKA_activation,10000.0,uM-1*s-1
PKA_activation_reverse,0.025,s-1 PKA_activation_reverse,0.025,s-1
src/lib/pathways/Gi_reactions.csv
+ 20
− 20
View file @ 566e6046
Reaction number,Reaction,Forward parameters names,Reverse parameters names,Forward default values (1/(nM*s)),Reverse default values (1/s) Reaction number,Reaction,Forward parameters names,Reverse parameters names,Forward default values (1/(uM*s)),Reverse default values (1/s)
1,L + R <-> LR,RL_kon,RL_koff,0.1,200 1,L + R <-> LR,RL_kon,RL_koff,100.0,200
3,LR + Gi <-> D2RDAGi,RL_Gi_kon,RL_Gi_koff,6.6,200 3,LR + Gi <-> D2RDAGi,RL_Gi_kon,RL_Gi_koff,6600.0,200
9,LRGi -> GaiGTP + LR + Gbgi,,RL_Gi_decay,,60 9,LRGi -> GaiGTP + LR + Gbgi,,RL_Gi_decay,,60
13,GaolfGTP -> GaolfGDP,,GaiGTP_decay,,30 13,GaolfGTP -> GaolfGDP,,GaiGTP_decay,,30
14,GaolfGDP + Gbgolf -> Golf,,Gi_formation,,100 14,GaolfGDP + Gbgolf -> Golf,,Gi_formation,,100
16,AC5 + Ca <-> AC5Ca,AC5_Ca_kon,AC5_Ca_koff,0.001,0.9 16,AC5 + Ca <-> AC5Ca,AC5_Ca_kon,AC5_Ca_koff,1.0,0.9
21,AC5 + ATP <-> [AC5*ATP],AC5_ATP_kon,AC5_ATP_koff,0.0001,1 21,AC5 + ATP <-> [AC5*ATP],AC5_ATP_kon,AC5_ATP_koff,0.1,1
22,[AC5*ATP] -> cAMP + AC5,,AC5_basal,,1 22,[AC5*ATP] -> cAMP + AC5,,AC5_basal,,1
23,cAMP + AC5 -> [AC5*ATP],,AC5_reverse_basal,,0.0004 23,cAMP + AC5 -> [AC5*ATP],,AC5_reverse_basal,,0.0004
24,AC5Ca + ATP <-> [AC5Ca*ATP],AC5_Ca_ATP_kon,AC5_Ca_ATP_koff,7.50E-05,1 24,AC5Ca + ATP <-> [AC5Ca*ATP],AC5_Ca_ATP_kon,AC5_Ca_ATP_koff,0.075,1
25,[AC5Ca*ATP] -> cAMP + AC5Ca,,AC5_Ca_ATP_to_cAMP,,0.5 25,[AC5Ca*ATP] -> cAMP + AC5Ca,,AC5_Ca_ATP_to_cAMP,,0.5
26,cAMP + AC5Ca -> [AC5Ca*ATP],,AC5_Ca_ATP_to_cAMP_reverse,,0.00015 26,cAMP + AC5Ca -> [AC5Ca*ATP],,AC5_Ca_ATP_to_cAMP_reverse,,0.00015
30,Ca + [AC5*ATP] <-> [AC5Ca*ATP],AC5_ATP_Ca_kon,AC5_ATP_Ca_koff,0.001,0.9 30,Ca + [AC5*ATP] <-> [AC5Ca*ATP],AC5_ATP_Ca_kon,AC5_ATP_Ca_koff,1.0,0.9
37,GaiGTP + AC5 <-> AC5GaiGTP,AC5_GaiGTP_kon,AC5_GaiGTP_koff,50,5 37,GaiGTP + AC5 <-> AC5GaiGTP,AC5_GaiGTP_kon,AC5_GaiGTP_koff,5000,5
38,ATP + AC5GaiGTP <-> [AC5GaiGTP*ATP],AC5_GaiGTP_ATP_kon,AC5_GaiGTP_ATP_koff,6.25E-05,1 38,ATP + AC5GaiGTP <-> [AC5GaiGTP*ATP],AC5_GaiGTP_ATP_kon,AC5_GaiGTP_ATP_koff,0.0625,1
39,[AC5*ATP] + GaiGTP <-> [AC5GaiGTP*ATP],AC5_ATP_GaiGTP_kon,AC5_ATP_GaiGTP_koff,50,5 39,[AC5*ATP] + GaiGTP <-> [AC5GaiGTP*ATP],AC5_ATP_GaiGTP_kon,AC5_ATP_GaiGTP_koff,50000,5
40,[AC5GaiGTP*ATP] -> cAMP + AC5GaiGTP,,AC5_GaiGTP_ATP_to_cAMP,,0.25 40,[AC5GaiGTP*ATP] -> cAMP + AC5GaiGTP,,AC5_GaiGTP_ATP_to_cAMP,,0.25
41,cAMP + AC5GaiGTP -> [AC5GaiGTP*ATP],,AC5_GaiGTP_ATP_to_cAMP_reverse,,0.00105 41,cAMP + AC5GaiGTP -> [AC5GaiGTP*ATP],,AC5_GaiGTP_ATP_to_cAMP_reverse,,0.00105
42,AC5GaiGTP -> AC5 + GaiGDP,,AC5_GaiGTP_decay,,30 42,AC5GaiGTP -> AC5 + GaiGDP,,AC5_GaiGTP_decay,,30
43,[AC5GaiGTP*ATP] -> [AC5*ATP] + GaiGDP,,AC5_GaiGTP_decay_koff,,30 43,[AC5GaiGTP*ATP] -> [AC5*ATP] + GaiGDP,,AC5_GaiGTP_decay_koff,,30
55,GaiGTP + AC5Ca <-> AC5CaGaiGTP,AC5_Ca_GaiGTP_kon,AC5_Ca_GaiGTP_koff,50,5 55,GaiGTP + AC5Ca <-> AC5CaGaiGTP,AC5_Ca_GaiGTP_kon,AC5_Ca_GaiGTP_koff,50000,5
56,AC5CaGaiGTP + ATP <-> [AC5CaGaiGTP*ATP],AC5_Ca_GaiGTP_ATP_kon,AC5_Ca_GaiGTP_ATP_koff,5.63E-05,1 56,AC5CaGaiGTP + ATP <-> [AC5CaGaiGTP*ATP],AC5_Ca_GaiGTP_ATP_kon,AC5_Ca_GaiGTP_ATP_koff,0.0563,1
57,[AC5Ca*ATP] + GaiGTP <-> [AC5CaGaiGTP*ATP],AC5_Ca_ATP_GaiGTP_kon,AC5_Ca_ATP_GaiGTP_koff,50,5 57,[AC5Ca*ATP] + GaiGTP <-> [AC5CaGaiGTP*ATP],AC5_Ca_ATP_GaiGTP_kon,AC5_Ca_ATP_GaiGTP_koff,50000,5
58,[AC5CaGaiGTP*ATP] -> cAMP + AC5CaGaiGTP,,AC5_Ca_GaiGTP_ATP_to_cAMP,,0.125 58,[AC5CaGaiGTP*ATP] -> cAMP + AC5CaGaiGTP,,AC5_Ca_GaiGTP_ATP_to_cAMP,,0.125
59,cAMP + AC5CaGaiGTP -> [AC5CaGaiGTP*ATP],,AC5_Ca_GaiGTP_ATP_to_cAMP_reverse,,2.81E-05 59,cAMP + AC5CaGaiGTP -> [AC5CaGaiGTP*ATP],,AC5_Ca_GaiGTP_ATP_to_cAMP_reverse,,2.81E-05
60,AC5CaGaiGTP -> AC5Ca + GaiGDP,,AC5_Ca_GaiGTP_decay,,30 60,AC5CaGaiGTP -> AC5Ca + GaiGDP,,AC5_Ca_GaiGTP_decay,,30
61,[AC5CaGaiGTP*ATP] -> [AC5Ca*ATP] + GaiGDP,,AC5_Ca_GaiGTP_ATP_decay,,30 61,[AC5CaGaiGTP*ATP] -> [AC5Ca*ATP] + GaiGDP,,AC5_Ca_GaiGTP_ATP_decay,,30
73,cAMP + PDE4 <-> [PDE4*cAMP],PDE104_cAMP_kon,PDE4_cAMP_koff,0.01,1 73,cAMP + PDE4 <-> [PDE4*cAMP],PDE104_cAMP_kon,PDE4_cAMP_koff,10.0,1
74,PDE10 + 2 cAMP <-> PDE10c,PDE10_2cAMP_kon,PDE10_2cAMP_koff,1.00E-06,9 74,PDE10 + 2 cAMP <-> PDE10c,PDE10_2cAMP_kon,PDE10_2cAMP_koff,0.001,9
75,[PDE4*cAMP] -> PDE4 + AMP,,PDE4_cAMP_to_AMP,,2 75,[PDE4*cAMP] -> PDE4 + AMP,,PDE4_cAMP_to_AMP,,2
76,cAMP + PDE10 <-> [PDE10*cAMP],PDE10_cAMP_kon,PDE10_cAMP_koff,0.1,2 76,cAMP + PDE10 <-> [PDE10*cAMP],PDE10_cAMP_kon,PDE10_cAMP_koff,100.0,2
77,cAMP + PDE10c <-> [PDE10c*cAMP],PDE10_2cAMP_cAMP_kon,PDE10_2cAMP_cAMP_koff,0.13,2 77,cAMP + PDE10c <-> [PDE10c*cAMP],PDE10_2cAMP_cAMP_kon,PDE10_2cAMP_cAMP_koff,130.0,2
78,[PDE10*cAMP] -> PDE10 + AMP,,PDE10_cAMP_decay,,3 78,[PDE10*cAMP] -> PDE10 + AMP,,PDE10_cAMP_decay,,3
79,[PDE10c*cAMP] -> PDE10c + AMP,,PDE10_2cAMP_cAMP_decay,,10 79,[PDE10c*cAMP] -> PDE10c + AMP,,PDE10_2cAMP_cAMP_decay,,10
80,cAMP + PKA <-> PKAcAMP2,PKA_cAMP2_kon,PKA_cAMP2_koff,0.00026,1 80,cAMP + PKA <-> PKAcAMP2,PKA_cAMP2_kon,PKA_cAMP2_koff,0.26,1
81,cAMP + PKAcAMP2 <-> PKAcAMP4,PKA_cAMP4_kon,PKA_cAMP4_koff,0.000346,1 81,cAMP + PKAcAMP2 <-> PKAcAMP4,PKA_cAMP4_kon,PKA_cAMP4_koff,0.346,1
82,PKAcAMP4 <-> PKAc + PKAreg,PKA_activation,PKA_activation_reverse,10,0.025 82,PKAcAMP4 <-> PKAc + PKAreg,PKA_activation,PKA_activation_reverse,10000.0,0.025
src/lib/pathways/Gs_parameters.csv
+ 20
− 20
View file @ 566e6046
...@@ -10,59 +10,59 @@ ATP_init,5000,uM ...@@ -10,59 +10,59 @@ ATP_init,5000,uM
PDE4_init,2,uM PDE4_init,2,uM
PDE10_init,0.7,uM PDE10_init,0.7,uM
PKA_init,1.2,uM PKA_init,1.2,uM
RL_kon,5.0,nM-1*s-1 RL_kon,5.0,uM-1*s-1
RL_koff,5,s-1 RL_koff,5,s-1
RL_Golf_kon,3.0,nM-1*s-1 RL_Golf_kon,3.0,uM-1*s-1
RL_Golf_koff,5.0,s-1 RL_Golf_koff,5.0,s-1
RL_Golf_decay,15,s-1 RL_Golf_decay,15,s-1
GaolfGTP_decay,30,s-1 GaolfGTP_decay,30,s-1
Golf_formation,100,s-1 Golf_formation,100,s-1
AC5_ATP_kon,0.1,nM-1*s-1 AC5_ATP_kon,0.1,uM-1*s-1
AC5_ATP_koff,1,nM-1*s-1 AC5_ATP_koff,1,uM-1*s-1
AC5_basal,1,s-1 AC5_basal,1,s-1
AC5_reverse_basal,0.0004,s-1 AC5_reverse_basal,0.0004,s-1
AC5_Ca_kon,1.0,nM-1*s-1 AC5_Ca_kon,1.0,uM-1*s-1
AC5_Ca_koff,0.9,s-1 AC5_Ca_koff,0.9,s-1
AC5_Ca_ATP_kon,0.075,nM-1*s-1 AC5_Ca_ATP_kon,0.075,uM-1*s-1
AC5_Ca_ATP_koff,1,s-1 AC5_Ca_ATP_koff,1,s-1
AC5_Ca_ATP_to_cAMP,0.5,s-1 AC5_Ca_ATP_to_cAMP,0.5,s-1
AC5_Ca_ATP_to_cAMP_reverse,0.00015,s-1 AC5_Ca_ATP_to_cAMP_reverse,0.00015,s-1
AC5_ATP_Ca_kon,1.0,nM-1*s-1 AC5_ATP_Ca_kon,1.0,uM-1*s-1
AC5_ATP_Ca_koff,0.9, AC5_ATP_Ca_koff,0.9,
AC5_GaolfGTP_kon,200.0,nM-1*s-1 AC5_GaolfGTP_kon,200.0,uM-1*s-1
AC5_GaolfGTP_koff,0.1, AC5_GaolfGTP_koff,0.1,
AC5_GaolfGTP_ATP_i_kon,1.05,nM-1*s-1 AC5_GaolfGTP_ATP_i_kon,1.05,uM-1*s-1
AC5_GaolfGTP_ATP_i_koff,1, AC5_GaolfGTP_ATP_i_koff,1,
cAMP_formation,20,s-1 cAMP_formation,20,s-1
cAMP_reverse,0.084,s-1 cAMP_reverse,0.084,s-1
AC5_GaolfGTP_ATP_a_kon,200.0,nM-1*s-1 AC5_GaolfGTP_ATP_a_kon,200.0,uM-1*s-1
AC5_GaolfGTP_ATP_a_koff,0.1, AC5_GaolfGTP_ATP_a_koff,0.1,
AC5_GaolfGTP_decay,0.2,s-1 AC5_GaolfGTP_decay,0.2,s-1
AC5_GaolfGTP_ATP_decay,0.2,s-1 AC5_GaolfGTP_ATP_decay,0.2,s-1
AC5_Ca_GaolfGTP_kon,200.0,nM-1*s-1 AC5_Ca_GaolfGTP_kon,200.0,uM-1*s-1
AC5_Ca_GaolfGTP_koff,0.1,s-1 AC5_Ca_GaolfGTP_koff,0.1,s-1
AC5_Ca_GaolfGTP_ATP_kon,0.55,nM-1*s-1 AC5_Ca_GaolfGTP_ATP_kon,0.55,uM-1*s-1
AC5_Ca_GaolfGTP_ATP_koff,1,s-1 AC5_Ca_GaolfGTP_ATP_koff,1,s-1
AC5_CA_ATP_GaolfGTP_kon,200.0,nM-1*s-1 AC5_CA_ATP_GaolfGTP_kon,200.0,uM-1*s-1
AC5_CA_ATP_GaolfGTP_koff,0.1,s-1 AC5_CA_ATP_GaolfGTP_koff,0.1,s-1
AC5_Ca_GaolfGTP_ATP_to_cAMP,10,s-1 AC5_Ca_GaolfGTP_ATP_to_cAMP,10,s-1
AC5_Ca_GaolfGTP_ATP_to_cAMP_reverse,0.022,s-1 AC5_Ca_GaolfGTP_ATP_to_cAMP_reverse,0.022,s-1
AC5_Ca_GaolfGTP_decay,0.2,s-1 AC5_Ca_GaolfGTP_decay,0.2,s-1
AC5_Ca_GaolfGTP_ATP_decay,0.2,s-1 AC5_Ca_GaolfGTP_ATP_decay,0.2,s-1
PDE4_cAMP_kon,10.0,nM-1*s-1 PDE4_cAMP_kon,10.0,uM-1*s-1
PDE4_cAMP_koff,1,s-1 PDE4_cAMP_koff,1,s-1
PDE4_cAMP_to_AMP,2,s-1 PDE4_cAMP_to_AMP,2,s-1
PDE10_2cAMP_kon,0.001,nM-1*s-1 PDE10_2cAMP_kon,0.001,uM-1*s-1
PDE10_2cAMP_koff,9,s-1 PDE10_2cAMP_koff,9,s-1
PDE10_cAMP_kon,100.0,nM-1*s-1 PDE10_cAMP_kon,100.0,uM-1*s-1
PDE10_cAMP_koff,2,s-1 PDE10_cAMP_koff,2,s-1
PDE10_2cAMP_cAMP_kon,130.0,nM-1*s-1 PDE10_2cAMP_cAMP_kon,130.0,uM-1*s-1
PDE10_2cAMP_cAMP_koff,2,s-1 PDE10_2cAMP_cAMP_koff,2,s-1
PDE10_cAMP_decay,3,s-1 PDE10_cAMP_decay,3,s-1
PDE10_2cAMP_cAMP_decay,10,s-1 PDE10_2cAMP_cAMP_decay,10,s-1
PKA_cAMP2_kon,0.25999999999999995,nM-1*s-1 PKA_cAMP2_kon,0.25999999999999995,uM-1*s-1
PKA_cAMP2_koff,1,s-1 PKA_cAMP2_koff,1,s-1
PKA_cAMP4_kon,0.34600000000000003,nM-1*s-1 PKA_cAMP4_kon,0.34600000000000003,uM-1*s-1
PKA_cAMP4_koff,1,s-1 PKA_cAMP4_koff,1,s-1
PKA_activation,10000.0,nM-1*s-1 PKA_activation,10000.0,uM-1*s-1
PKA_activation_reverse,0.01,s-1 PKA_activation_reverse,0.01,s-1
src/lib/pathways/Gs_reactions.csv
+ 21
− 21
View file @ 566e6046
Reaction number,Reaction,Forward parameters names,Reverse parameter names,Forward default (1/(nM*s)),Reverse default (1/s) Reaction number,Reaction,Forward parameters names,Reverse parameter names,Forward default (1/(uM*s)),Reverse default (1/s)
1,D1R + DA <-> D1RDA,RL_kon,RL_koff,0.005,5 1,R + L <-> RL,RL_kon,RL_koff,5.0,5
3,D1RDA + Golf <-> D1RDAGolf,RL_Golf_kon,RL_Golf_koff,0.003,5 3,RL + Golf <-> RLGolf,RL_Golf_kon,RL_Golf_koff,3.0,5
9,D1RDAGolf -> Gbgolf + D1RDA + GaolfGTP,,RL_Golf_decay,,15 9,RLGolf -> Gbgolf + RL + GaolfGTP,,RL_Golf_decay,,15
10,GaolfGTP -> GaolfGDP,,GaolfGTP_decay,,30 10,GaolfGTP -> GaolfGDP,,GaolfGTP_decay,,30
11,GaolfGDP + Gbgolf -> Golf,,Golf_formation,,100 11,GaolfGDP + Gbgolf -> Golf,,Golf_formation,,100
15,AC5 + GaolfGTP <-> AC5GaolfGTP,AC5_GaolfGTP_kon,AC5_GaolfGTP_koff,0.2,0.1 15,AC5 + GaolfGTP <-> AC5GaolfGTP,AC5_GaolfGTP_kon,AC5_GaolfGTP_koff,200.0,0.1
16,AC5 + Ca <-> AC5Ca,AC5_Ca_kon,AC5_GaolfGTP_koff,0.001,0.9 16,AC5 + Ca <-> AC5Ca,AC5_Ca_kon,AC5_GaolfGTP_koff,1.0,0.9
17,AC5Ca + GaolfGTP <-> AC5CaGaolfGTP,AC5_Ca_GaolfGTP_kon,AC5_Ca_GaolfGTP_koff,0.2,0.1 17,AC5Ca + GaolfGTP <-> AC5CaGaolfGTP,AC5_Ca_GaolfGTP_kon,AC5_Ca_GaolfGTP_koff,200.0,0.1
18,AC5GaolfGTP + ATP <-> [AC5GaolfGTP*ATP],AC5_GaolfGTP_ATP_i_koff,AC5_GaolfGTP_ATP_i_koff,0.00105,1 18,AC5GaolfGTP + ATP <-> [AC5GaolfGTP*ATP],AC5_GaolfGTP_ATP_i_koff,AC5_GaolfGTP_ATP_i_koff,1.05,1
19,[AC5GaolfGTP*ATP] -> cAMP + AC5GaolfGTP,,cAMP_formation,,20 19,[AC5GaolfGTP*ATP] -> cAMP + AC5GaolfGTP,,cAMP_formation,,20
20,cAMP + AC5GaolfGTP -> [AC5GaolfGTP*ATP],,cAMP_reverse,,0.084 20,cAMP + AC5GaolfGTP -> [AC5GaolfGTP*ATP],,cAMP_reverse,,0.084
21,AC5 + ATP <-> [AC5*ATP],AC5_ATP_kon,AC5_ATP_koff,0.0001,1 21,AC5 + ATP <-> [AC5*ATP],AC5_ATP_kon,AC5_ATP_koff,0.1,1
22,[AC5*ATP] -> cAMP + AC5,,AC5_basal,,1 22,[AC5*ATP] -> cAMP + AC5,,AC5_basal,,1
23,cAMP + AC5 -> [AC5*ATP],,AC5_reverse_basal,,0.0004 23,cAMP + AC5 -> [AC5*ATP],,AC5_reverse_basal,,0.0004
24,AC5Ca + ATP <-> [AC5Ca*ATP],AC5_Ca_ATP_kon,AC5_Ca_ATP_koff,7.50E-05,1 24,AC5Ca + ATP <-> [AC5Ca*ATP],AC5_Ca_ATP_kon,AC5_Ca_ATP_koff,0.075,1
25,[AC5Ca*ATP] -> cAMP + AC5Ca,,AC5_Ca_ATP_to_cAMP,,0.5 25,[AC5Ca*ATP] -> cAMP + AC5Ca,,AC5_Ca_ATP_to_cAMP,,0.5
26,cAMP + AC5Ca -> [AC5Ca*ATP],,AC5_Ca_ATP_to_cAMP_reverse,,0.00015 26,cAMP + AC5Ca -> [AC5Ca*ATP],,AC5_Ca_ATP_to_cAMP_reverse,,0.00015
27,GaolfGTP + [AC5*ATP] <-> [AC5GaolfGTP*ATP],AC5_GaolfGTP_ATP_a_koff,AC5_GaolfGTP_ATP_a_koff,0.2,0.1 27,GaolfGTP + [AC5*ATP] <-> [AC5GaolfGTP*ATP],AC5_GaolfGTP_ATP_a_kon,AC5_GaolfGTP_ATP_a_koff,200.0,0.1
28,AC5GaolfGTP -> AC5 + GaolfGDP,,AC5_GaolfGTP_decay,,0.2 28,AC5GaolfGTP -> AC5 + GaolfGDP,,AC5_GaolfGTP_decay,,0.2
29,[AC5GaolfGTP*ATP] -> [AC5*ATP] + GaolfGDP,,AC5_GaolfGTP_ATP_decay,,0.2 29,[AC5GaolfGTP*ATP] -> [AC5*ATP] + GaolfGDP,,AC5_GaolfGTP_ATP_decay,,0.2
30,Ca + [AC5*ATP] <-> [AC5Ca*ATP],AC5_ATP_Ca_kon,AC5_ATP_Ca_koff,0.001,0.9 30,Ca + [AC5*ATP] <-> [AC5Ca*ATP],AC5_ATP_Ca_kon,AC5_ATP_Ca_koff,1.0,0.9
31,AC5CaGaolfGTP + ATP <-> [AC5CaGaolfGTP*ATP],AC5_Ca_GaolfGTP_ATP_kon,AC5_Ca_GaolfGTP_ATP_koff,0.00055,1 31,AC5CaGaolfGTP + ATP <-> [AC5CaGaolfGTP*ATP],AC5_Ca_GaolfGTP_ATP_kon,AC5_Ca_GaolfGTP_ATP_koff,0.55,1
32,GaolfGTP + [AC5Ca*ATP] <-> [AC5CaGaolfGTP*ATP],AC5_CA_ATP_GaolfGTP_kon,AC5_CA_ATP_GaolfGTP_koff,0.2,0.1 32,GaolfGTP + [AC5Ca*ATP] <-> [AC5CaGaolfGTP*ATP],AC5_CA_ATP_GaolfGTP_kon,AC5_CA_ATP_GaolfGTP_koff,200.0,0.1
33,[AC5CaGaolfGTP*ATP] -> cAMP + AC5CaGaolfGTP,,AC5_Ca_GaolfGTP_ATP_to_cAMP,,10 33,[AC5CaGaolfGTP*ATP] -> cAMP + AC5CaGaolfGTP,,AC5_Ca_GaolfGTP_ATP_to_cAMP,,10
34,cAMP + AC5CaGaolfGTP -> [AC5CaGaolfGTP*ATP],,AC5_Ca_GaolfGTP_ATP_to_cAMP_reverse,,0.022 34,cAMP + AC5CaGaolfGTP -> [AC5CaGaolfGTP*ATP],,AC5_Ca_GaolfGTP_ATP_to_cAMP_reverse,,0.022
35,AC5CaGaolfGTP -> AC5Ca + GaolfGDP,,AC5_Ca_GaolfGTP_decay,,0.2 35,AC5CaGaolfGTP -> AC5Ca + GaolfGDP,,AC5_Ca_GaolfGTP_decay,,0.2
36,[AC5CaGaolfGTP*ATP] -> [AC5Ca*ATP] + GaolfGDP,,AC5_Ca_GaolfGTP_ATP_decay,,0.2 36,[AC5CaGaolfGTP*ATP] -> [AC5Ca*ATP] + GaolfGDP,,AC5_Ca_GaolfGTP_ATP_decay,,0.2
73,cAMP + PDE4 <-> [PDE4*cAMP],PDE4_cAMP_kon,PDE4_cAMP_koff,0.01,1 73,cAMP + PDE4 <-> [PDE4*cAMP],PDE4_cAMP_kon,PDE4_cAMP_koff,10.0,1
74,[PDE4*cAMP] -> PDE4 + AMP,,PDE4_cAMP_to_AMP,,2 74,[PDE4*cAMP] -> PDE4 + AMP,,PDE4_cAMP_to_AMP,,2
75,PDE10 + 2 cAMP <-> PDE10c,PDE10_2cAMP_kon,PDE10_2cAMP_koff,1.00E-06,9 75,PDE10 + 2 cAMP <-> PDE10c,PDE10_2cAMP_kon,PDE10_2cAMP_koff,0.001,9
76,cAMP + PDE10 <-> [PDE10*cAMP],PDE10_cAMP_kon,PDE10_cAMP_koff,0.1,2 76,cAMP + PDE10 <-> [PDE10*cAMP],PDE10_cAMP_kon,PDE10_cAMP_koff,100.0,2
77,cAMP + PDE10c <-> [PDE10c*cAMP],PDE10_2cAMP_cAMP_kon,PDE10_2cAMP_cAMP_koff,0.13,2 77,cAMP + PDE10c <-> [PDE10c*cAMP],PDE10_2cAMP_cAMP_kon,PDE10_2cAMP_cAMP_koff,130.0,2
78,[PDE10*cAMP] -> PDE10 + AMP,,PDE10_cAMP_decay,,3 78,[PDE10*cAMP] -> PDE10 + AMP,,PDE10_cAMP_decay,,3
79,[PDE10c*cAMP] -> PDE10c + AMP,,PDE10_2cAMP_cAMP_decay,,10 79,[PDE10c*cAMP] -> PDE10c + AMP,,PDE10_2cAMP_cAMP_decay,,10
80,cAMP + PKA <-> PKAcAMP2,PKA_cAMP2_kon,PKA_cAMP2_koff,0.00026,1 80,cAMP + PKA <-> PKAcAMP2,PKA_cAMP2_kon,PKA_cAMP2_koff,0.26,1
81,cAMP + PKAcAMP2 <-> PKAcAMP4,PKA_cAMP4_kon,PKA_cAMP4_koff,0.000346,1 81,cAMP + PKAcAMP2 <-> PKAcAMP4,PKA_cAMP4_kon,PKA_cAMP4_koff,0.346,1
82,PKAcAMP4 <-> PKAc + PKAreg,PKA_activation,PKA_activation_reverse,10,0.01 82,PKAcAMP4 <-> PKAc + PKAreg,PKA_activation,PKA_activation_reverse,10000.0,0.01
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