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 = 32
sizeStates = 23
sizeConstants = 50
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 (second)"
legend_states[0] = "EGF in component EGF (nanomolar)"
legend_algebraic[0] = "v1 in component v1 (flux)"
legend_states[1] = "R in component R (nanomolar)"
legend_states[2] = "Ra in component Ra (nanomolar)"
legend_algebraic[8] = "v2 in component v2 (flux)"
legend_states[3] = "R2 in component R2 (nanomolar)"
legend_algebraic[9] = "v3 in component v3 (flux)"
legend_algebraic[10] = "v4 in component v4 (flux)"
legend_states[4] = "RP in component RP (nanomolar)"
legend_algebraic[13] = "v7 in component v7 (flux)"
legend_algebraic[18] = "v11 in component v11 (flux)"
legend_algebraic[22] = "v15 in component v15 (flux)"
legend_algebraic[25] = "v18 in component v18 (flux)"
legend_algebraic[27] = "v20 in component v20 (flux)"
legend_algebraic[11] = "v5 in component v5 (flux)"
legend_algebraic[14] = "v9 in component v9 (flux)"
legend_algebraic[20] = "v13 in component v13 (flux)"
legend_states[5] = "R_PL in component R_PL (nanomolar)"
legend_algebraic[12] = "v6 in component v6 (flux)"
legend_states[6] = "R_PLP in component R_PLP (nanomolar)"
legend_states[7] = "R_G in component R_G (nanomolar)"
legend_algebraic[16] = "v10 in component v10 (flux)"
legend_states[8] = "R_G_S in component R_G_S (nanomolar)"
legend_states[9] = "R_Sh in component R_Sh (nanomolar)"
legend_algebraic[21] = "v14 in component v14 (flux)"
legend_states[10] = "R_ShP in component R_ShP (nanomolar)"
legend_algebraic[31] = "v24 in component v24 (flux)"
legend_algebraic[24] = "v17 in component v17 (flux)"
legend_states[11] = "R_Sh_G in component R_Sh_G (nanomolar)"
legend_algebraic[26] = "v19 in component v19 (flux)"
legend_states[12] = "R_Sh_G_S in component R_Sh_G_S (nanomolar)"
legend_states[13] = "G_S in component G_S (nanomolar)"
legend_algebraic[30] = "v23 in component v23 (flux)"
legend_algebraic[19] = "v12 in component v12 (flux)"
legend_states[14] = "ShP in component ShP (nanomolar)"
legend_algebraic[28] = "v21 in component v21 (flux)"
legend_algebraic[23] = "v16 in component v16 (flux)"
legend_states[15] = "Sh_G in component Sh_G (nanomolar)"
legend_algebraic[29] = "v22 in component v22 (flux)"
legend_states[16] = "Sh_G_S in component Sh_G_S (nanomolar)"
legend_states[17] = "PLC_gamma in component PLC_gamma (nanomolar)"
legend_algebraic[15] = "v8 in component v8 (flux)"
legend_states[18] = "PLC_gamma_P in component PLC_gamma_P (nanomolar)"
legend_algebraic[17] = "v25 in component v25 (flux)"
legend_states[19] = "PLC_gamma_P_I in component PLC_gamma_P_I (nanomolar)"
legend_states[20] = "Grb in component Grb (nanomolar)"
legend_states[21] = "Shc in component Shc (nanomolar)"
legend_states[22] = "SOS in component SOS (nanomolar)"
legend_constants[0] = "k1 in component v1 (second_order_rate_constant)"
legend_constants[1] = "k1_ in component v1 (first_order_rate_constant)"
legend_constants[2] = "k2 in component v2 (second_order_rate_constant)"
legend_constants[3] = "k2_ in component v2 (first_order_rate_constant)"
legend_constants[4] = "k3 in component v3 (first_order_rate_constant)"
legend_constants[5] = "k3_ in component v3 (first_order_rate_constant)"
legend_constants[6] = "K4 in component v4 (nanomolar)"
legend_constants[7] = "V4 in component v4 (flux)"
legend_constants[8] = "k5 in component v5 (second_order_rate_constant)"
legend_constants[9] = "k5_ in component v5 (first_order_rate_constant)"
legend_constants[10] = "k6 in component v6 (first_order_rate_constant)"
legend_constants[11] = "k6_ in component v6 (first_order_rate_constant)"
legend_constants[12] = "k7 in component v7 (first_order_rate_constant)"
legend_constants[13] = "k7_ in component v7 (second_order_rate_constant)"
legend_constants[14] = "K8 in component v8 (nanomolar)"
legend_constants[15] = "V8 in component v8 (flux)"
legend_constants[16] = "k9 in component v9 (second_order_rate_constant)"
legend_constants[17] = "k9_ in component v9 (first_order_rate_constant)"
legend_constants[18] = "k10 in component v10 (second_order_rate_constant)"
legend_constants[19] = "k10_ in component v10 (first_order_rate_constant)"
legend_constants[20] = "k11 in component v11 (first_order_rate_constant)"
legend_constants[21] = "k11_ in component v11 (second_order_rate_constant)"
legend_constants[22] = "k12 in component v12 (first_order_rate_constant)"
legend_constants[23] = "k12_ in component v12 (second_order_rate_constant)"
legend_constants[24] = "k13 in component v13 (second_order_rate_constant)"
legend_constants[25] = "k13_ in component v13 (first_order_rate_constant)"
legend_constants[26] = "k14 in component v14 (first_order_rate_constant)"
legend_constants[27] = "k14_ in component v14 (first_order_rate_constant)"
legend_constants[28] = "k15 in component v15 (first_order_rate_constant)"
legend_constants[29] = "k15_ in component v15 (second_order_rate_constant)"
legend_constants[30] = "K16 in component v16 (nanomolar)"
legend_constants[31] = "V16 in component v16 (flux)"
legend_constants[32] = "k17 in component v17 (second_order_rate_constant)"
legend_constants[33] = "k17_ in component v17 (first_order_rate_constant)"
legend_constants[34] = "k18 in component v18 (first_order_rate_constant)"
legend_constants[35] = "k18_ in component v18 (second_order_rate_constant)"
legend_constants[36] = "k19 in component v19 (second_order_rate_constant)"
legend_constants[37] = "k19_ in component v19 (first_order_rate_constant)"
legend_constants[38] = "k20 in component v20 (first_order_rate_constant)"
legend_constants[39] = "k20_ in component v20 (second_order_rate_constant)"
legend_constants[40] = "k21 in component v21 (second_order_rate_constant)"
legend_constants[41] = "k21_ in component v21 (first_order_rate_constant)"
legend_constants[42] = "k22 in component v22 (second_order_rate_constant)"
legend_constants[43] = "k22_ in component v22 (first_order_rate_constant)"
legend_constants[44] = "k23 in component v23 (first_order_rate_constant)"
legend_constants[45] = "k23_ in component v23 (second_order_rate_constant)"
legend_constants[46] = "k24 in component v24 (second_order_rate_constant)"
legend_constants[47] = "k24_ in component v24 (first_order_rate_constant)"
legend_constants[48] = "k25 in component v25 (first_order_rate_constant)"
legend_constants[49] = "k25_ in component v25 (first_order_rate_constant)"
legend_algebraic[1] = "totEGFRphos in component combined_concs (nanomolar)"
legend_algebraic[2] = "totPLCgammaphos in component combined_concs (nanomolar)"
legend_algebraic[3] = "totGrb_EGFR in component combined_concs (nanomolar)"
legend_algebraic[4] = "totGrb_Shc in component combined_concs (nanomolar)"
legend_algebraic[5] = "totShcphos in component combined_concs (nanomolar)"
legend_algebraic[6] = "totShc_EGFR in component combined_concs (nanomolar)"
legend_algebraic[7] = "totSOS_EGFR in component combined_concs (nanomolar)"
legend_rates[0] = "d/dt EGF in component EGF (nanomolar)"
legend_rates[1] = "d/dt R in component R (nanomolar)"
legend_rates[2] = "d/dt Ra in component Ra (nanomolar)"
legend_rates[3] = "d/dt R2 in component R2 (nanomolar)"
legend_rates[4] = "d/dt RP in component RP (nanomolar)"
legend_rates[5] = "d/dt R_PL in component R_PL (nanomolar)"
legend_rates[6] = "d/dt R_PLP in component R_PLP (nanomolar)"
legend_rates[7] = "d/dt R_G in component R_G (nanomolar)"
legend_rates[8] = "d/dt R_G_S in component R_G_S (nanomolar)"
legend_rates[9] = "d/dt R_Sh in component R_Sh (nanomolar)"
legend_rates[10] = "d/dt R_ShP in component R_ShP (nanomolar)"
legend_rates[11] = "d/dt R_Sh_G in component R_Sh_G (nanomolar)"
legend_rates[12] = "d/dt R_Sh_G_S in component R_Sh_G_S (nanomolar)"
legend_rates[13] = "d/dt G_S in component G_S (nanomolar)"
legend_rates[14] = "d/dt ShP in component ShP (nanomolar)"
legend_rates[15] = "d/dt Sh_G in component Sh_G (nanomolar)"
legend_rates[16] = "d/dt Sh_G_S in component Sh_G_S (nanomolar)"
legend_rates[17] = "d/dt PLC_gamma in component PLC_gamma (nanomolar)"
legend_rates[18] = "d/dt PLC_gamma_P in component PLC_gamma_P (nanomolar)"
legend_rates[19] = "d/dt PLC_gamma_P_I in component PLC_gamma_P_I (nanomolar)"
legend_rates[20] = "d/dt Grb in component Grb (nanomolar)"
legend_rates[21] = "d/dt Shc in component Shc (nanomolar)"
legend_rates[22] = "d/dt SOS in component SOS (nanomolar)"
return (legend_states, legend_algebraic, legend_voi, legend_constants)
def initConsts():
constants = [0.0] * sizeConstants; states = [0.0] * sizeStates;
states[0] = 680
states[1] = 100
states[2] = 0
states[3] = 0
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] = 0
states[14] = 0
states[15] = 0
states[16] = 0
states[17] = 105
states[18] = 0
states[19] = 0
states[20] = 85
states[21] = 150
states[22] = 34
constants[0] = 0.003
constants[1] = 0.06
constants[2] = 0.01
constants[3] = 0.1
constants[4] = 1
constants[5] = 0.01
constants[6] = 50
constants[7] = 450
constants[8] = 0.06
constants[9] = 0.2
constants[10] = 1
constants[11] = 0.05
constants[12] = 0.3
constants[13] = 0.006
constants[14] = 100
constants[15] = 1
constants[16] = 0.003
constants[17] = 0.05
constants[18] = 0.01
constants[19] = 0.06
constants[20] = 0.03
constants[21] = 4.5e-3
constants[22] = 1.5e-3
constants[23] = 1e-4
constants[24] = 0.09
constants[25] = 0.6
constants[26] = 6
constants[27] = 0.06
constants[28] = 0.3
constants[29] = 9e-4
constants[30] = 340
constants[31] = 1.7
constants[32] = 0.003
constants[33] = 0.1
constants[34] = 0.3
constants[35] = 9e-4
constants[36] = 0.01
constants[37] = 2.14e-2
constants[38] = 0.12
constants[39] = 2.4e-4
constants[40] = 0.003
constants[41] = 0.1
constants[42] = 0.03
constants[43] = 0.064
constants[44] = 0.1
constants[45] = 0.021
constants[46] = 0.009
constants[47] = 4.29e-2
constants[48] = 1
constants[49] = 0.03
return (states, constants)
def computeRates(voi, states, constants):
rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic
algebraic[0] = constants[0]*states[1]*states[0]-constants[1]*states[2]
rates[0] = -algebraic[0]
rates[1] = -algebraic[0]
algebraic[8] = constants[2]*states[2]*states[2]-constants[3]*states[3]
rates[2] = algebraic[0]-2.00000*algebraic[8]
algebraic[9] = constants[4]*states[3]-constants[5]*states[4]
algebraic[10] = (constants[7]*states[4])/(constants[6]+states[4])
rates[3] = (algebraic[8]+algebraic[10])-algebraic[9]
algebraic[11] = constants[8]*states[4]*states[17]-constants[9]*states[5]
algebraic[12] = constants[10]*states[5]-constants[11]*states[6]
rates[5] = algebraic[11]-algebraic[12]
algebraic[13] = constants[12]*states[6]-constants[13]*states[4]*states[18]
rates[6] = algebraic[12]-algebraic[13]
algebraic[15] = (constants[15]*states[18])/(constants[14]+states[18])
rates[17] = algebraic[15]-algebraic[11]
algebraic[14] = constants[16]*states[4]*states[20]-constants[17]*states[7]
algebraic[16] = constants[18]*states[7]*states[22]-constants[19]*states[8]
rates[7] = algebraic[14]-algebraic[16]
algebraic[17] = constants[48]*states[18]-constants[49]*states[19]
rates[18] = algebraic[13]-(algebraic[15]+algebraic[17])
rates[19] = algebraic[17]
algebraic[18] = constants[20]*states[8]-constants[21]*states[4]*states[13]
rates[8] = algebraic[16]-algebraic[18]
algebraic[20] = constants[24]*states[4]*states[21]-constants[25]*states[9]
algebraic[21] = constants[26]*states[9]-constants[27]*states[10]
rates[9] = algebraic[20]-algebraic[21]
algebraic[23] = (constants[31]*states[14])/(constants[30]+states[14])
rates[21] = algebraic[23]-algebraic[20]
algebraic[25] = constants[34]*states[11]-constants[35]*states[4]*states[15]
algebraic[24] = constants[32]*states[10]*states[20]-constants[33]*states[11]
algebraic[26] = constants[36]*states[11]*states[22]-constants[37]*states[12]
rates[11] = algebraic[24]-(algebraic[25]+algebraic[26])
algebraic[22] = constants[28]*states[10]-constants[29]*states[14]*states[4]
algebraic[27] = constants[38]*states[12]-constants[39]*states[16]*states[4]
rates[4] = (algebraic[9]+algebraic[13]+algebraic[18]+algebraic[22]+algebraic[25]+algebraic[27])-(algebraic[10]+algebraic[11]+algebraic[14]+algebraic[20])
algebraic[19] = constants[22]*states[13]-constants[23]*states[20]*states[22]
algebraic[28] = constants[40]*states[14]*states[20]-constants[41]*states[15]
rates[20] = algebraic[19]-(algebraic[14]+algebraic[24]+algebraic[28])
algebraic[29] = constants[42]*states[15]*states[22]-constants[43]*states[16]
rates[15] = (algebraic[25]+algebraic[28])-algebraic[29]
rates[22] = algebraic[19]-(algebraic[16]+algebraic[26]+algebraic[29])
algebraic[30] = constants[44]*states[16]-constants[45]*states[14]*states[13]
rates[14] = (algebraic[22]+algebraic[30])-(algebraic[28]+algebraic[23])
rates[16] = (algebraic[27]+algebraic[29])-algebraic[30]
algebraic[31] = constants[46]*states[10]*states[13]-constants[47]*states[12]
rates[10] = algebraic[21]-(algebraic[31]+algebraic[22]+algebraic[24])
rates[12] = (algebraic[26]+algebraic[31])-algebraic[27]
rates[13] = (algebraic[18]+algebraic[30])-(algebraic[19]+algebraic[31])
return(rates)
def computeAlgebraic(constants, states, voi):
algebraic = array([[0.0] * len(voi)] * sizeAlgebraic)
states = array(states)
voi = array(voi)
algebraic[0] = constants[0]*states[1]*states[0]-constants[1]*states[2]
algebraic[8] = constants[2]*states[2]*states[2]-constants[3]*states[3]
algebraic[9] = constants[4]*states[3]-constants[5]*states[4]
algebraic[10] = (constants[7]*states[4])/(constants[6]+states[4])
algebraic[11] = constants[8]*states[4]*states[17]-constants[9]*states[5]
algebraic[12] = constants[10]*states[5]-constants[11]*states[6]
algebraic[13] = constants[12]*states[6]-constants[13]*states[4]*states[18]
algebraic[15] = (constants[15]*states[18])/(constants[14]+states[18])
algebraic[14] = constants[16]*states[4]*states[20]-constants[17]*states[7]
algebraic[16] = constants[18]*states[7]*states[22]-constants[19]*states[8]
algebraic[17] = constants[48]*states[18]-constants[49]*states[19]
algebraic[18] = constants[20]*states[8]-constants[21]*states[4]*states[13]
algebraic[20] = constants[24]*states[4]*states[21]-constants[25]*states[9]
algebraic[21] = constants[26]*states[9]-constants[27]*states[10]
algebraic[23] = (constants[31]*states[14])/(constants[30]+states[14])
algebraic[25] = constants[34]*states[11]-constants[35]*states[4]*states[15]
algebraic[24] = constants[32]*states[10]*states[20]-constants[33]*states[11]
algebraic[26] = constants[36]*states[11]*states[22]-constants[37]*states[12]
algebraic[22] = constants[28]*states[10]-constants[29]*states[14]*states[4]
algebraic[27] = constants[38]*states[12]-constants[39]*states[16]*states[4]
algebraic[19] = constants[22]*states[13]-constants[23]*states[20]*states[22]
algebraic[28] = constants[40]*states[14]*states[20]-constants[41]*states[15]
algebraic[29] = constants[42]*states[15]*states[22]-constants[43]*states[16]
algebraic[30] = constants[44]*states[16]-constants[45]*states[14]*states[13]
algebraic[31] = constants[46]*states[10]*states[13]-constants[47]*states[12]
algebraic[1] = 2.00000*(states[4]+states[5]+states[6]+states[7]+states[8]+states[9]+states[10]+states[11]+states[12])
algebraic[2] = states[6]+states[18]
algebraic[3] = states[7]+states[8]+states[11]+states[12]
algebraic[4] = states[11]+states[15]+states[12]+states[16]
algebraic[5] = states[10]+states[11]+states[12]+states[14]+states[15]+states[16]
algebraic[6] = states[10]+states[11]+states[12]
algebraic[7] = states[8]+states[12]
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)