Generated Code
The following is python code generated by the CellML API from this CellML file. (Back to language selection)
The raw code is available.
# Size of variable arrays:
sizeAlgebraic = 0
sizeStates = 33
sizeConstants = 80
from math import *
from numpy import *
def createLegends():
legend_states = [""] * sizeStates
legend_rates = [""] * sizeStates
legend_algebraic = [""] * sizeAlgebraic
legend_voi = ""
legend_constants = [""] * sizeConstants
legend_voi = "time in component environment (s)"
legend_constants[0] = "kf1 in component PI3K (second_order_rate_constant)"
legend_constants[1] = "kb1 in component PI3K (first_order_rate_constant)"
legend_constants[2] = "kf2 in component PI3K (second_order_rate_constant)"
legend_constants[3] = "kb2 in component PI3K (first_order_rate_constant)"
legend_constants[4] = "kf3 in component PI3K (first_order_rate_constant)"
legend_constants[5] = "kb3 in component PI3K (first_order_rate_constant)"
legend_constants[6] = "kf34 in component PI3K (first_order_rate_constant)"
legend_constants[7] = "kb34 in component PI3K (first_order_rate_constant)"
legend_constants[8] = "V4 in component PI3K (flux)"
legend_constants[9] = "k4 in component PI3K (nm)"
legend_constants[10] = "kf5 in component PI3K (second_order_rate_constant)"
legend_constants[11] = "kb5 in component PI3K (first_order_rate_constant)"
legend_constants[12] = "kf6 in component PI3K (first_order_rate_constant)"
legend_constants[13] = "kb6 in component PI3K (first_order_rate_constant)"
legend_constants[14] = "kf7 in component PI3K (first_order_rate_constant)"
legend_constants[15] = "kb7 in component PI3K (first_order_rate_constant)"
legend_constants[16] = "kf8 in component PI3K (first_order_rate_constant)"
legend_constants[17] = "kb8 in component PI3K (second_order_rate_constant)"
legend_constants[18] = "kf9 in component PI3K (first_order_rate_constant)"
legend_constants[19] = "kb9 in component PI3K (second_order_rate_constant)"
legend_constants[20] = "V10 in component PI3K (flux)"
legend_constants[21] = "k10 in component PI3K (nm)"
legend_constants[22] = "kf23 in component PI3K (second_order_rate_constant)"
legend_constants[23] = "kb23 in component PI3K (first_order_rate_constant)"
legend_constants[24] = "kf24 in component PI3K (first_order_rate_constant)"
legend_constants[25] = "kb24 in component PI3K (first_order_rate_constant)"
legend_constants[26] = "kf25 in component PI3K (first_order_rate_constant)"
legend_constants[27] = "kb25 in component PI3K (second_order_rate_constant)"
legend_constants[28] = "V26 in component PI3K (flux)"
legend_constants[29] = "k26 in component PI3K (nm)"
legend_states[0] = "R in component PI3K (nm)"
legend_states[1] = "Shc in component PI3K (nm)"
legend_states[2] = "PI3K in component PI3K (nm)"
legend_states[3] = "HRG in component PI3K (nm)"
legend_states[4] = "R_HRG in component PI3K (nm)"
legend_states[5] = "R_HRG2 in component PI3K (nm)"
legend_states[6] = "Internalisation in component PI3K (nm)"
legend_states[7] = "RP in component PI3K (nm)"
legend_states[8] = "R_Shc in component PI3K (nm)"
legend_states[9] = "R_ShP in component PI3K (nm)"
legend_states[10] = "ShP in component PI3K (nm)"
legend_states[11] = "R_ShGS in component PI3K (nm)"
legend_states[12] = "ShGS in component PI3K (nm)"
legend_states[13] = "GS in component PI3K (nm)"
legend_states[14] = "R_PI3K in component PI3K (nm)"
legend_states[15] = "R_PI3Kstar in component PI3K (nm)"
legend_states[16] = "PI3Kstar in component PI3K (nm)"
legend_constants[30] = "two in component PI3K (dimensionless)"
legend_states[17] = "RasGTP in component RasGDPtoRasGTP (nm)"
legend_constants[31] = "kf11 in component RasGDPtoRasGTP (first_order_rate_constant)"
legend_constants[32] = "k11 in component RasGDPtoRasGTP (nm)"
legend_constants[33] = "V12 in component RasGDPtoRasGTP (flux)"
legend_constants[34] = "k12 in component RasGDPtoRasGTP (nm)"
legend_states[18] = "RasGDP in component RasGDPtoRasGTP (nm)"
legend_states[19] = "Akt_PIPP in component Akt (nm)"
legend_states[20] = "RAF_star in component RAF (nm)"
legend_constants[35] = "kf13 in component RAF (first_order_rate_constant)"
legend_constants[36] = "k13 in component RAF (nm)"
legend_constants[37] = "kf14 in component RAF (first_order_rate_constant)"
legend_constants[38] = "k14 in component RAF (nm)"
legend_constants[39] = "E in component RAF (nm)"
legend_states[21] = "RAF in component RAF (nm)"
legend_states[22] = "MEKP in component MEK (nm)"
legend_states[23] = "MEKPP in component MEK (nm)"
legend_constants[40] = "kf27 in component Akt (first_order_rate_constant)"
legend_constants[41] = "k27 in component Akt (nm)"
legend_constants[42] = "V28 in component Akt (flux)"
legend_constants[43] = "k28 in component Akt (nm)"
legend_constants[44] = "kf29 in component Akt (second_order_rate_constant)"
legend_constants[45] = "kb29 in component Akt (first_order_rate_constant)"
legend_constants[46] = "V30 in component Akt (flux)"
legend_constants[47] = "k30 in component Akt (nm)"
legend_constants[48] = "kf31 in component Akt (first_order_rate_constant)"
legend_constants[49] = "k31 in component Akt (nm)"
legend_constants[50] = "V32 in component Akt (flux)"
legend_constants[51] = "k32 in component Akt (nm)"
legend_constants[52] = "kf33 in component Akt (first_order_rate_constant)"
legend_constants[53] = "k33 in component Akt (nm)"
legend_constants[54] = "k16 in component Akt (nm)"
legend_constants[55] = "k18 in component Akt (nm)"
legend_states[24] = "P in component Akt (nm)"
legend_states[25] = "PIP3 in component Akt (nm)"
legend_states[26] = "Akt in component Akt (nm)"
legend_states[27] = "Akt_PIP3 in component Akt (nm)"
legend_states[28] = "Akt_PIP in component Akt (nm)"
legend_constants[56] = "PP2A in component Akt (nm)"
legend_constants[57] = "one in component Akt (dimensionless)"
legend_constants[58] = "PP2A in component MEK (nm)"
legend_states[29] = "MEK in component MEK (nm)"
legend_constants[59] = "kf15 in component MEK (first_order_rate_constant)"
legend_constants[60] = "k15 in component MEK (nm)"
legend_constants[61] = "kf16 in component MEK (first_order_rate_constant)"
legend_constants[62] = "k16 in component MEK (nm)"
legend_constants[63] = "kf17 in component MEK (first_order_rate_constant)"
legend_constants[64] = "k17 in component MEK (nm)"
legend_constants[65] = "kf18 in component MEK (first_order_rate_constant)"
legend_constants[66] = "k18 in component MEK (nm)"
legend_constants[67] = "k31 in component MEK (nm)"
legend_constants[68] = "k33 in component MEK (nm)"
legend_constants[69] = "one in component MEK (dimensionless)"
legend_constants[70] = "MKP3 in component ERK (nm)"
legend_states[30] = "ERK in component ERK (nm)"
legend_states[31] = "ERKP in component ERK (nm)"
legend_states[32] = "ERKPP in component ERK (nm)"
legend_constants[71] = "kf19 in component ERK (first_order_rate_constant)"
legend_constants[72] = "k19 in component ERK (nm)"
legend_constants[73] = "kf20 in component ERK (first_order_rate_constant)"
legend_constants[74] = "k20 in component ERK (nm)"
legend_constants[75] = "kf21 in component ERK (first_order_rate_constant)"
legend_constants[76] = "k21 in component ERK (nm)"
legend_constants[77] = "kf22 in component ERK (first_order_rate_constant)"
legend_constants[78] = "k22 in component ERK (nm)"
legend_constants[79] = "one in component ERK (dimensionless)"
legend_rates[0] = "d/dt R in component PI3K (nm)"
legend_rates[3] = "d/dt HRG in component PI3K (nm)"
legend_rates[4] = "d/dt R_HRG in component PI3K (nm)"
legend_rates[5] = "d/dt R_HRG2 in component PI3K (nm)"
legend_rates[7] = "d/dt RP in component PI3K (nm)"
legend_rates[6] = "d/dt Internalisation in component PI3K (nm)"
legend_rates[8] = "d/dt R_Shc in component PI3K (nm)"
legend_rates[1] = "d/dt Shc in component PI3K (nm)"
legend_rates[9] = "d/dt R_ShP in component PI3K (nm)"
legend_rates[13] = "d/dt GS in component PI3K (nm)"
legend_rates[10] = "d/dt ShP in component PI3K (nm)"
legend_rates[11] = "d/dt R_ShGS in component PI3K (nm)"
legend_rates[12] = "d/dt ShGS in component PI3K (nm)"
legend_rates[14] = "d/dt R_PI3K in component PI3K (nm)"
legend_rates[2] = "d/dt PI3K in component PI3K (nm)"
legend_rates[15] = "d/dt R_PI3Kstar in component PI3K (nm)"
legend_rates[16] = "d/dt PI3Kstar in component PI3K (nm)"
legend_rates[18] = "d/dt RasGDP in component RasGDPtoRasGTP (nm)"
legend_rates[17] = "d/dt RasGTP in component RasGDPtoRasGTP (nm)"
legend_rates[21] = "d/dt RAF in component RAF (nm)"
legend_rates[20] = "d/dt RAF_star in component RAF (nm)"
legend_rates[24] = "d/dt P in component Akt (nm)"
legend_rates[25] = "d/dt PIP3 in component Akt (nm)"
legend_rates[26] = "d/dt Akt in component Akt (nm)"
legend_rates[27] = "d/dt Akt_PIP3 in component Akt (nm)"
legend_rates[28] = "d/dt Akt_PIP in component Akt (nm)"
legend_rates[19] = "d/dt Akt_PIPP in component Akt (nm)"
legend_rates[29] = "d/dt MEK in component MEK (nm)"
legend_rates[22] = "d/dt MEKP in component MEK (nm)"
legend_rates[23] = "d/dt MEKPP in component MEK (nm)"
legend_rates[30] = "d/dt ERK in component ERK (nm)"
legend_rates[32] = "d/dt ERKPP in component ERK (nm)"
legend_rates[31] = "d/dt ERKP in component ERK (nm)"
return (legend_states, legend_algebraic, legend_voi, legend_constants)
def initConsts():
constants = [0.0] * sizeConstants; states = [0.0] * sizeStates;
constants[0] = 0.0012
constants[1] = 0.00076
constants[2] = 0.01
constants[3] = 0.1
constants[4] = 1
constants[5] = 0.01
constants[6] = 0.001
constants[7] = 0
constants[8] = 62.5
constants[9] = 50
constants[10] = 0.1
constants[11] = 1
constants[12] = 20
constants[13] = 5
constants[14] = 60
constants[15] = 546
constants[16] = 2040
constants[17] = 15700
constants[18] = 40.8
constants[19] = 0
constants[20] = 0.0154
constants[21] = 340
constants[22] = 0.1
constants[23] = 2
constants[24] = 9.85
constants[25] = 0.0985
constants[26] = 45.8
constants[27] = 0.047
constants[28] = 2620
constants[29] = 3680
states[0] = 80
states[1] = 1000
states[2] = 10
states[3] = 10
states[4] = 0
states[5] = 0
states[6] = 0
states[7] = 0
states[8] = 0
states[9] = 0
states[10] = 0
states[11] = 0
states[12] = 0
states[13] = 10
states[14] = 0
states[15] = 0
states[16] = 0
constants[30] = 2
states[17] = 0
constants[31] = 0.222
constants[32] = 0.181
constants[33] = 0.289
constants[34] = 0.0571
states[18] = 120
states[19] = 0.0
states[20] = 100
constants[35] = 1.53
constants[36] = 11.7
constants[37] = 0.00673
constants[38] = 8.07
constants[39] = 7
states[21] = 0
states[22] = 0
states[23] = 0
constants[40] = 16.9
constants[41] = 39.1
constants[42] = 17000
constants[43] = 9.02
constants[44] = 507
constants[45] = 234
constants[46] = 20000
constants[47] = 80000
constants[48] = 0.107
constants[49] = 4.35
constants[50] = 20000
constants[51] = 80000
constants[52] = 0.211
constants[53] = 12
constants[54] = 2200
constants[55] = 60
states[24] = 800
states[25] = 0
states[26] = 10
states[27] = 0
states[28] = 0
constants[56] = 11.4
constants[57] = 1
constants[58] = 11.4
states[29] = 120
constants[59] = 3.5
constants[60] = 317
constants[61] = 0.058
constants[62] = 2200
constants[63] = 2.9
constants[64] = 317
constants[65] = 0.058
constants[66] = 60
constants[67] = 4.35
constants[68] = 12
constants[69] = 1
constants[70] = 2.4
states[30] = 1000
states[31] = 0
states[32] = 0
constants[71] = 9.5
constants[72] = 146000
constants[73] = 0.3
constants[74] = 160
constants[75] = 16
constants[76] = 146000
constants[77] = 0.27
constants[78] = 60
constants[79] = 1
return (states, constants)
def computeRates(voi, states, constants):
rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic
rates[0] = -constants[0]*states[0]*states[3]+constants[1]*states[4]
rates[3] = -constants[0]*states[0]*states[3]+constants[1]*states[4]
rates[4] = (constants[0]*states[0]*states[3]-constants[1]*states[4])-constants[30]*(constants[2]*states[4]*states[4]-constants[3]*states[5])
rates[5] = ((constants[2]*states[4]*states[4]-constants[3]*states[5])-(constants[4]*states[5]-constants[5]*states[7]))+(constants[8]*states[7])/(constants[9]+states[7])
rates[7] = ((((((constants[4]*states[5]-constants[5]*states[7])-(constants[8]*states[7])/(constants[9]+states[7]))-(constants[10]*states[7]*states[1]-constants[11]*states[8]))+(constants[16]*states[9]-constants[17]*states[12]*states[7]))-(constants[22]*states[7]*states[2]-constants[23]*states[14]))+(constants[26]*states[15]-constants[27]*states[7]*states[16]))-(constants[6]*states[7]-constants[7]*states[6])
rates[6] = constants[6]*states[7]-constants[7]*states[6]
rates[8] = (constants[10]*states[7]*states[1]-constants[11]*states[8])-(constants[12]*states[8]-constants[13]*states[9])
rates[1] = -(constants[10]*states[7]*states[1]-constants[11]*states[8])+(constants[20]*states[10])/(constants[21]+states[10])
rates[9] = (constants[12]*states[8]-constants[13]*states[9])-(constants[14]*states[9]-constants[15]*states[11])
rates[13] = -(constants[14]*states[9]-constants[15]*states[11])+(constants[18]*states[12]-constants[19]*states[13]*states[10])
rates[10] = (constants[18]*states[12]-constants[19]*states[13]*states[10])-(constants[20]*states[10])/(constants[21]+states[10])
rates[11] = (constants[14]*states[9]-constants[15]*states[11])-(constants[16]*states[9]-constants[17]*states[12]*states[7])
rates[12] = (constants[16]*states[9]-constants[17]*states[12]*states[7])-(constants[18]*states[12]-constants[19]*states[13]*states[10])
rates[14] = (constants[22]*states[7]*states[2]-constants[23]*states[14])-(constants[24]*states[14]-constants[25]*states[15])
rates[2] = -(constants[22]*states[7]*states[2]-constants[23]*states[14])+(constants[28]*states[16])/(constants[29]+states[16])
rates[15] = (constants[24]*states[14]-constants[25]*states[15])-(constants[26]*states[15]-constants[27]*states[7]*states[16])
rates[16] = (constants[26]*states[15]-constants[27]*states[7]*states[16])-(constants[28]*states[16])/(constants[29]+states[16])
rates[18] = -((constants[31]*states[12]*states[18])/(constants[32]+states[18]))+(constants[33]*states[17])/(constants[34]+states[17])
rates[17] = (constants[31]*states[12]*states[18])/(constants[32]+states[18])-(constants[33]*states[17])/(constants[34]+states[17])
rates[21] = (constants[37]*(states[19]+constants[39])*states[20])/(constants[38]+states[20])-(constants[35]*states[17]*states[21])/(constants[36]+states[21])
rates[20] = -((constants[37]*(states[19]+constants[39])*states[20])/(constants[38]+states[20]))+(constants[35]*states[17]*states[21])/(constants[36]+states[21])
rates[24] = (constants[42]*states[25])/(constants[43]+states[25])-(constants[40]*states[16]*states[24])/(constants[41]+states[24])
rates[25] = (-((constants[42]*states[25])/(constants[43]+states[25]))+(constants[40]*states[16]*states[24])/(constants[41]+states[24]))-(constants[44]*states[25]*states[26]-constants[45]*states[27])
rates[26] = -(constants[44]*states[25]*states[26]-constants[45]*states[27])
rates[27] = ((constants[44]*states[25]*states[26]-constants[45]*states[27])-(constants[46]*states[27])/(constants[47]*(constants[57]+states[28]/constants[51])+states[27]))+(constants[48]*constants[56]*states[28])/(constants[49]*(constants[57]+states[22]/constants[54]+states[23]/constants[55]+states[19]/constants[53])+states[28])
rates[28] = (((constants[46]*states[27])/(constants[47]*(constants[57]+states[28]/constants[51])+states[27])-(constants[48]*constants[56]*states[28])/(constants[49]*(constants[57]+states[22]/constants[54]+states[23]/constants[55]+states[19]/constants[53])+states[28]))-(constants[50]*states[28])/(constants[51]*(constants[57]+states[27]/constants[47])+states[28]))+(constants[52]*constants[56]*states[19])/(constants[53]*(constants[57]+states[22]/constants[54]+states[23]/constants[55]+states[28]/constants[49])+states[19])
rates[19] = (constants[50]*states[28])/(constants[51]*(constants[57]+states[27]/constants[47])+states[28])-(constants[52]*constants[56]*states[19])/(constants[53]*(constants[57]+states[22]/constants[54]+states[23]/constants[55]+states[28]/constants[49])+states[19])
rates[29] = -((constants[59]*states[20]*states[29])/(constants[60]*(constants[69]+states[22]/constants[64])+states[29]))+(constants[61]*constants[58]*states[22])/(constants[62]*(constants[69]+states[23]/constants[66]+states[28]/constants[67]+states[19]/constants[68])+states[22])
rates[22] = (((constants[59]*states[20]*states[29])/(constants[60]*(constants[69]+states[22]/constants[64])+states[29])-(constants[61]*constants[58]*states[22])/(constants[62]*(constants[69]+states[23]/constants[66]+states[28]/constants[67]+states[19]/constants[68])+states[22]))-(constants[63]*states[20]*states[22])/(constants[64]*(constants[69]+states[29]/constants[60])+states[22]))+(constants[65]*constants[58]*states[23])/(constants[66]*(constants[69]+states[22]/constants[62]+states[28]/constants[67]+states[19]/constants[68])+states[23])
rates[23] = (constants[63]*states[20]*states[22])/(constants[64]*(constants[69]+states[29]/constants[60])+states[22])-(constants[65]*constants[58]*states[23])/(constants[66]*(constants[69]+states[22]/constants[62]+states[28]/constants[67]+states[19]/constants[68])+states[23])
rates[30] = -((constants[71]*states[23]*states[30])/(constants[72]*(constants[79]+states[31]/constants[76])+states[30]))+(constants[73]*constants[70]*states[31])/(constants[74]*(constants[79]+states[32]/constants[78])+states[31])
rates[32] = (constants[75]*states[23]*states[31])/(constants[76]*(constants[79]+states[30]/constants[72])+states[31])-(constants[77]*constants[70]*states[32])/(constants[78]*(constants[79]+states[31]/constants[74])+states[32])
rates[31] = (((constants[71]*states[23]*states[30])/(constants[72]*(constants[79]+states[31]/constants[76])+states[30])-(constants[73]*constants[70]*states[31])/(constants[74]*(constants[79]+states[32]/constants[78])+states[31]))-(constants[75]*states[23]*states[31])/(constants[76]*(constants[79]+states[30]/constants[72])+states[31]))+(constants[77]*constants[70]*states[32])/(constants[78]*(constants[79]+states[31]/constants[74])+states[32])
return(rates)
def computeAlgebraic(constants, states, voi):
algebraic = array([[0.0] * len(voi)] * sizeAlgebraic)
states = array(states)
voi = array(voi)
return algebraic
def solve_model():
"""Solve model with ODE solver"""
from scipy.integrate import ode
# Initialise constants and state variables
(init_states, constants) = initConsts()
# Set timespan to solve over
voi = linspace(0, 10, 500)
# Construct ODE object to solve
r = ode(computeRates)
r.set_integrator('vode', method='bdf', atol=1e-06, rtol=1e-06, max_step=1)
r.set_initial_value(init_states, voi[0])
r.set_f_params(constants)
# Solve model
states = array([[0.0] * len(voi)] * sizeStates)
states[:,0] = init_states
for (i,t) in enumerate(voi[1:]):
if r.successful():
r.integrate(t)
states[:,i+1] = r.y
else:
break
# Compute algebraic variables
algebraic = computeAlgebraic(constants, states, voi)
return (voi, states, algebraic)
def plot_model(voi, states, algebraic):
"""Plot variables against variable of integration"""
import pylab
(legend_states, legend_algebraic, legend_voi, legend_constants) = createLegends()
pylab.figure(1)
pylab.plot(voi,vstack((states,algebraic)).T)
pylab.xlabel(legend_voi)
pylab.legend(legend_states + legend_algebraic, loc='best')
pylab.show()
if __name__ == "__main__":
(voi, states, algebraic) = solve_model()
plot_model(voi, states, algebraic)