-
Notifications
You must be signed in to change notification settings - Fork 1
/
HSM_ODEsSystem10or9eqs.py
144 lines (119 loc) · 5.62 KB
/
HSM_ODEsSystem10or9eqs.py
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
from HSM_Reactions import *
########## RIGHT MEMBERS OF ODEs, rewritten with only 10 equations to isolate those that are independent ##############
def f10eqs(t, y, ksetDict, TparamSet, REACparamSet, DirectControlnuPp, IC_PplusPp, IC_SplusSs):
#P = y[0]
Ph = y[0]
#S = y[2]
Ss = y[1]
F = y[2]
Fs = y[3]
G = y[4]
FsG = y[5]
FG = y[6]
RF = y[7]
RHP = y[8]
HP = y[9]
kP0 = ksetDict["kP0"]
kP0p = ksetDict["kP0p"]
kS = ksetDict["kS"]
kSp0 = ksetDict["kSp0"]
kFp0 = ksetDict["kFp0"]
kF0 = ksetDict["kF0"]
kFpi0 = ksetDict["kFpi0"]
kFGp = ksetDict["kFGp"]
kFG = ksetDict["kFG"]
ketaF = ksetDict["ketaF"]
kFsG = ksetDict["kFsG"]
kFsGp = ksetDict["kFsGp"]
kFsp = ksetDict["kFsp"]
kFs = ksetDict["kFs"]
kpiRF = ksetDict["kpiRF"]
kpiRH = ksetDict["kpiRH"]
kpiHP = ksetDict["kpiHP"]
ketaHP = ksetDict["ketaHP"]
ketaRF = ksetDict["ketaRF"]
ketaRHP = ksetDict["ketaRHP"]
n1 = REACparamSet["n1"]
n2 = REACparamSet["n2"]
P0const = REACparamSet["P0const"]
I = REACparamSet["I"]
T0const = REACparamSet["T0const"]
piRFconst = REACparamSet["piRFconst"]
piRHPconst = REACparamSet["piRHPconst"]
PplusPpCONST = IC_PplusPp # (microM) Initial Condition protein P
SplusSsCONST = IC_SplusSs # (microM) Initial Condition stresskinease S
system = [
#nuP(Ph, HP, kP0) - nuPp(P, t, kP0p, n1, T0const, TparamSet, DirectControlnuPp), # P
- nuP(Ph, HP, kP0) + nuPp(PplusPpCONST - Ph, t, kP0p, n1, T0const, TparamSet, DirectControlnuPp), # Ph
#nuS(Ss, kS) - nuSp(S, Ph, kSp0, n2, P0const), # S
- nuS(Ss, kS) + nuSp(SplusSsCONST - Ss, Ph, kSp0, n2, P0const), # Ss
nuF(I, Fs, kF0) + piF(RF, kFpi0) + nuFGp(FG, kFGp) - nuFG(G, F, kFG) - nuFp(F, Ss, kFp0) - etaF(F, ketaF), # F
- nuF(I, Fs, kF0) + nuFp(F, Ss, kFp0) + nuFsGp(FsG, kFsGp) - nuFsG(G, Fs, kFsG), # Fs
nuFsGp(FsG, kFsGp) + nuFGp(FG, kFGp) - nuFG(G, F, kFG) - nuFsG(G, Fs, kFsG), # G
nuFsG(G, Fs, kFsG) + nuFs(FG, kFs) - nuFsp(FsG, I, kFsp) - nuFsGp(FsG, kFsGp), # FsG
nuFsp(FsG, I, kFsp) + nuFG(G, F, kFG) - nuFGp(FG, kFGp) - nuFs(FG, kFs), # FG
piRF(FsG, kpiRF) + piRFAddConst(piRFconst) - etaRF(RF, ketaRF), # RF Added const to Alex model
piRHP(FsG, kpiRH) + piRHPAddConst(piRHPconst) - etaRHP(RHP, ketaRHP), # RHP Aded const to Alex model
piHP(RHP, kpiHP) - etaHP(HP, ketaHP)] # HP
# Notice presence of nuFG() in line of F, presence of nuFsG() in that of Fs, absence of pi in that of FsG.
return system
########## RIGHT MEMBERS OF ODEs, rewritten with only 9 equations to isolate those that are independent ##############
def f9eqs(t, y, ksetDict, TparamSet, REACparamSet, DirectControlnuPp, IC_PplusPp, IC_SplusSs, IC_GplusFsGplusFG):
#P = y[0]
Ph = y[0]
#S = y[2]
Ss = y[1]
F = y[2]
Fs = y[3]
#G = y[4]
FsG = y[4]
FG = y[5]
RF = y[6]
RHP = y[7]
HP = y[8]
kP0 = ksetDict["kP0"]
kP0p = ksetDict["kP0p"]
kS = ksetDict["kS"]
kSp0 = ksetDict["kSp0"]
kFp0 = ksetDict["kFp0"]
kF0 = ksetDict["kF0"]
kFpi0 = ksetDict["kFpi0"]
kFGp = ksetDict["kFGp"]
kFG = ksetDict["kFG"]
ketaF = ksetDict["ketaF"]
kFsG = ksetDict["kFsG"]
kFsGp = ksetDict["kFsGp"]
kFsp = ksetDict["kFsp"]
kFs = ksetDict["kFs"]
kpiRF = ksetDict["kpiRF"]
kpiRH = ksetDict["kpiRH"]
kpiHP = ksetDict["kpiHP"]
ketaHP = ksetDict["ketaHP"]
ketaRF = ksetDict["ketaRF"]
ketaRHP = ksetDict["ketaRHP"]
n1 = REACparamSet["n1"]
n2 = REACparamSet["n2"]
P0const = REACparamSet["P0const"]
I = REACparamSet["I"]
T0const = REACparamSet["T0const"]
piRFconst = REACparamSet["piRFconst"]
piRHPconst = REACparamSet["piRHPconst"]
PplusPpCONST = IC_PplusPp # (microM) Initial Condition protein P
SplusSsCONST = IC_SplusSs # (microM) Initial Condition stresskinease S
GplusFsGplusFG = IC_GplusFsGplusFG # (microM) Initial Condition gene G
G = GplusFsGplusFG - FsG - FG
system = [
#nuP(Ph, HP, kP0) - nuPp(P, t, kP0p, n1, T0const, TparamSet, DirectControlnuPp), # P
- nuP(Ph, HP, kP0) + nuPp(PplusPpCONST - Ph, t, kP0p, n1, T0const, TparamSet, DirectControlnuPp), # Ph
#nuS(Ss, kS) - nuSp(S, Ph, kSp0, n2, P0const), # S
- nuS(Ss, kS) + nuSp(SplusSsCONST - Ss, Ph, kSp0, n2, P0const), # Ss
nuF(I, Fs, kF0) + piF(RF, kFpi0) + nuFGp(FG, kFGp) - nuFG(G, F, kFG) - nuFp(F, Ss, kFp0) - etaF(F, ketaF), # F
- nuF(I, Fs, kF0) + nuFp(F, Ss, kFp0) + nuFsGp(FsG, kFsGp) - nuFsG(G, Fs, kFsG), # Fs
#nuFsGp(FsG, kFsGp) + nuFGp(FG, kFGp) - nuFG(G, F, kFG) - nuFsG(G, Fs, kFsG), # G
nuFsG(G, Fs, kFsG) + nuFs(FG, kFs) - nuFsp(FsG, I, kFsp) - nuFsGp(FsG, kFsGp), # FsG
nuFsp(FsG, I, kFsp) + nuFG(G, F, kFG) - nuFGp(FG, kFGp) - nuFs(FG, kFs), # FG
piRF(FsG, kpiRF) + piRFAddConst(piRFconst) - etaRF(RF, ketaRF), # RF Added const to Alex model
piRHP(FsG, kpiRH) + piRHPAddConst(piRHPconst) - etaRHP(RHP, ketaRHP), # RHP Aded const to Alex model
piHP(RHP, kpiHP) - etaHP(HP, ketaHP)] # HP
# Notice presence of nuFG() in line of F, presence of nuFsG() in that of Fs, absence of pi in that of FsG.
return system