-
Notifications
You must be signed in to change notification settings - Fork 1
/
input.bngl
118 lines (118 loc) · 2.08 KB
/
input.bngl
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
begin model
begin parameters
a0 1000.000000
d0 1000.000000
h0 1000.000000
i0 100000.000000
k0 3000000.000000
l0 1000.000000
p0 30000.000000
k1 0.000010
k2 0.000010
k2b 0.100000
k3 0.000010
k4 0.000010
k4b 0.100000
k5 0.000010
k6 0.000010
k7 0.000010
k8 0.000010
Prey 0.000000
Predator 0.000000
ED7 0.000000
AE7 0.000000
Group_Prey 0.000000
Group_Predator 0.000000
Group_ED7 0.000000
Group_AE7 0.000000
end parameters
begin molecules
S1()
S2()
S3()
S4()
S5()
S6()
S7()
S8()
S9()
S10()
S11()
S12()
S13()
S14()
S15()
S16()
S17()
S18()
S19()
end molecules
begin seed species
S1 1000.000000
S2 1000.000000
S3 1000.000000
S4 100000.000000
S5 3000000.000000
S6 1000.000000
S7 30000.000000
S8 0.000000
S9 0.000000
S10 0.000000
S11 0.000000
S12 0.000000
S13 0.000000
S14 0.000000
S15 0.000000
S16 0.000000
S17 0.000000
S18 0.000000
S19 0.000000
end seed species
begin functions
functionRate0() = k1
functionRate1() = 2 * k2
functionRate2() = 2 * k4
functionRate3() = k5
functionRate4() = k2b
functionRate5() = 4 * k3
functionRate6() = k4b
functionRate7() = k6
functionRate8() = k7
functionRate9() = 4 * k8
end functions
begin observables
Species S1 S1()
Species S2 S2()
Species S3 S3()
Species S4 S4()
Species S5 S5()
Species S6 S6()
Species S7 S7()
Species S8 S8()
Species S9 S9()
Species S10 S10()
Species S11 S11()
Species S12 S12()
Species S13 S13()
Species S14 S14()
Species S15 S15()
Species S16 S16()
Species S17 S17()
Species S18 S18()
Species S19 S19()
end observables
begin rules
S1() + S3() -> S8() + S9() functionRate0()
S1() + S7() -> S10() functionRate1()
S2() + S7() -> S11() functionRate2()
S2() + S6() -> S12() + S13() functionRate3()
S10() -> S1() + S7() functionRate4()
S4() + S9() -> S1() + S1() + S14() + S15() functionRate5()
S11() -> S2() + S7() functionRate6()
S2() + S10() -> S16() + S17() functionRate7()
S1() + S11() -> S16() + S17() functionRate8()
S5() + S17() -> S2() + S2() + S18() + S19() functionRate9()
end rules
end model
generate_network();
simulate_ode({t_end=>400,n_steps=>50});