Biomodel-Hegerat2014/simulation.py at master · h-munakata/Biomodel-Hegerat2014 · GitHub

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
import numpy as np
from scipy.integrate import odeint

from model.name2idx import parameters as C
from model.name2idx import variables as V
from model.param_const import f_params
from model.initial_condition import initial_values
from model.differential_equation import diffeq


class Simulation(object):
    tspan = [i/10 for i in range(120*10+1)]
    t = np.array(tspan)

    condition = 9

    Gwl = np.empty((len(t),condition))
    Cdc25 = np.empty((len(t),condition))
    ENSAP = np.empty((len(t),condition))
    Y15 = np.empty((len(t),condition))
    B55 = np.empty((len(t),condition))

    x = f_params()
    y0 = initial_values()

    for i in range(condition):
        #OA insensitive phosphatase
        if i in [0,3,6]:
            x[C.kigwl] = 0
            x[C.kigwl_d] = 2
            x[C.kigwl_dd] = 0
        #OA sensitive phosphatase
        if i in [1,4,7]:
            x[C.kigwl] = 0
            x[C.kigwl_d] = 0.02
            x[C.kigwl_dd] = 2
        #PP2A-B55
        if i in [2,5,8]:
            x[C.kigwl] = 2
            x[C.kigwl_d] = 0.02
            x[C.kigwl_dd] = 0

        #Cdk1 Inhibition +OA
        if i in [3,4,5]:
            x[C.OA] = 100
            x[C.RO] = 25

        #Mitotic block
        if i in [6,7,8]:
            y0[V.MPF] = 0.96
            y0[V.Cdc25] = 0.97
            y0[V.Wee1] = 0.03
            y0[V.Gwl] = 0.9
            y0[V.ENSAPt] = 0.75
            y0[V.PP2] = 0.027

            x[C.OA] = 0
            x[C.RO] = 100

        Y = odeint(diffeq,y0,tspan,args=tuple(x))
        Gwl[:,i] = Y[:,V.Gwl]
        Cdc25[:,i] = Y[:,V.Cdc25]
        ENSAP[:,i] = Y[:,V.ENSAPt]
        B55[:,i] = Y[:,V.PP2]
        Y15[:,i] = x[C.CycT] - Y[:,V.MPF]