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 = 9
sizeStates = 22
sizeConstants = 45
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] = "T2 in component T2 (micromolar)"
legend_algebraic[0] = "Vmax in component T2 (flux)"
legend_constants[37] = "KR in component T2 (molar)"
legend_states[1] = "LT2 in component LT2 (micromolar)"
legend_states[2] = "T2R in component T2R (micromolar)"
legend_constants[0] = "R in component R (micromolar)"
legend_states[3] = "T3 in component T3 (micromolar)"
legend_constants[1] = "L in component L (micromolar)"
legend_states[4] = "Bp in component Bp (micromolar)"
legend_states[5] = "T2p in component T2p (micromolar)"
legend_constants[2] = "Y0 in component Y0 (micromolar)"
legend_states[6] = "Yp in component Yp (micromolar)"
legend_constants[3] = "B0 in component B0 (micromolar)"
legend_constants[4] = "k5 in component model_parameters (second_order_rate_constant)"
legend_constants[5] = "k_5 in component model_parameters (first_order_rate_constant)"
legend_constants[6] = "k8 in component model_parameters (first_order_rate_constant)"
legend_constants[7] = "k_1 in component model_parameters (second_order_rate_constant)"
legend_constants[8] = "ky in component model_parameters (second_order_rate_constant)"
legend_constants[9] = "kb in component model_parameters (second_order_rate_constant)"
legend_constants[10] = "k1a in component model_parameters (first_order_rate_constant)"
legend_constants[11] = "k1b in component model_parameters (second_order_rate_constant)"
legend_constants[12] = "k1c in component model_parameters (first_order_rate_constant)"
legend_algebraic[1] = "Vmax in component T3 (flux)"
legend_constants[38] = "KR in component T3 (molar)"
legend_states[7] = "LT3 in component LT3 (micromolar)"
legend_states[8] = "T3R in component T3R (micromolar)"
legend_states[9] = "T4 in component T4 (micromolar)"
legend_states[10] = "T3p in component T3p (micromolar)"
legend_constants[13] = "k6 in component model_parameters (second_order_rate_constant)"
legend_constants[14] = "k_6 in component model_parameters (first_order_rate_constant)"
legend_constants[15] = "k9 in component model_parameters (first_order_rate_constant)"
legend_constants[16] = "k_2 in component model_parameters (second_order_rate_constant)"
legend_constants[17] = "k2a in component model_parameters (first_order_rate_constant)"
legend_constants[18] = "k2b in component model_parameters (second_order_rate_constant)"
legend_constants[19] = "k2c in component model_parameters (first_order_rate_constant)"
legend_states[11] = "LT4 in component LT4 (micromolar)"
legend_states[12] = "T4p in component T4p (micromolar)"
legend_constants[20] = "k7 in component model_parameters (second_order_rate_constant)"
legend_constants[21] = "k_7 in component model_parameters (first_order_rate_constant)"
legend_constants[22] = "k10 in component model_parameters (first_order_rate_constant)"
legend_algebraic[2] = "Vmax in component T2p (flux)"
legend_constants[39] = "KR in component T2p (molar)"
legend_states[13] = "LT2p in component LT2p (micromolar)"
legend_states[14] = "T2pR in component T2pR (micromolar)"
legend_algebraic[3] = "Vmax in component T3p (flux)"
legend_constants[40] = "KR in component T3p (molar)"
legend_states[15] = "LT3p in component LT3p (micromolar)"
legend_states[16] = "T3pR in component T3pR (micromolar)"
legend_states[17] = "LT4p in component LT4p (micromolar)"
legend_algebraic[4] = "Vmax in component LT2 (flux)"
legend_constants[41] = "KR in component LT2 (molar)"
legend_states[18] = "LT2R in component LT2R (micromolar)"
legend_constants[23] = "k11 in component model_parameters (first_order_rate_constant)"
legend_constants[24] = "k_3 in component model_parameters (second_order_rate_constant)"
legend_constants[25] = "k3a in component model_parameters (first_order_rate_constant)"
legend_constants[26] = "k3b in component model_parameters (second_order_rate_constant)"
legend_constants[27] = "k3c in component model_parameters (first_order_rate_constant)"
legend_algebraic[5] = "Vmax in component LT3 (flux)"
legend_constants[42] = "KR in component LT3 (molar)"
legend_states[19] = "LT3R in component LT3R (micromolar)"
legend_constants[28] = "k12 in component model_parameters (first_order_rate_constant)"
legend_constants[29] = "k_4 in component model_parameters (second_order_rate_constant)"
legend_constants[30] = "k4a in component model_parameters (first_order_rate_constant)"
legend_constants[31] = "k4b in component model_parameters (second_order_rate_constant)"
legend_constants[32] = "k4c in component model_parameters (first_order_rate_constant)"
legend_constants[33] = "k13 in component model_parameters (first_order_rate_constant)"
legend_algebraic[6] = "Vmax in component LT2p (flux)"
legend_constants[43] = "KR in component LT2p (molar)"
legend_states[20] = "LT2pR in component LT2pR (micromolar)"
legend_algebraic[7] = "Vmax in component LT3p (flux)"
legend_constants[44] = "KR in component LT3p (molar)"
legend_states[21] = "LT3pR in component LT3pR (micromolar)"
legend_algebraic[8] = "P in component P (micromolar)"
legend_constants[34] = "Z in component Z (micromolar)"
legend_constants[35] = "k_y in component model_parameters (second_order_rate_constant)"
legend_constants[36] = "k_b in component model_parameters (first_order_rate_constant)"
legend_rates[0] = "d/dt T2 in component T2 (micromolar)"
legend_rates[3] = "d/dt T3 in component T3 (micromolar)"
legend_rates[9] = "d/dt T4 in component T4 (micromolar)"
legend_rates[5] = "d/dt T2p in component T2p (micromolar)"
legend_rates[10] = "d/dt T3p in component T3p (micromolar)"
legend_rates[12] = "d/dt T4p in component T4p (micromolar)"
legend_rates[1] = "d/dt LT2 in component LT2 (micromolar)"
legend_rates[7] = "d/dt LT3 in component LT3 (micromolar)"
legend_rates[11] = "d/dt LT4 in component LT4 (micromolar)"
legend_rates[13] = "d/dt LT2p in component LT2p (micromolar)"
legend_rates[15] = "d/dt LT3p in component LT3p (micromolar)"
legend_rates[17] = "d/dt LT4p in component LT4p (micromolar)"
legend_rates[6] = "d/dt Yp in component Yp (micromolar)"
legend_rates[4] = "d/dt Bp in component Bp (micromolar)"
legend_rates[2] = "d/dt T2R in component T2R (micromolar)"
legend_rates[8] = "d/dt T3R in component T3R (micromolar)"
legend_rates[14] = "d/dt T2pR in component T2pR (micromolar)"
legend_rates[16] = "d/dt T3pR in component T3pR (micromolar)"
legend_rates[18] = "d/dt LT2R in component LT2R (micromolar)"
legend_rates[19] = "d/dt LT3R in component LT3R (micromolar)"
legend_rates[20] = "d/dt LT2pR in component LT2pR (micromolar)"
legend_rates[21] = "d/dt LT3pR in component LT3pR (micromolar)"
return (legend_states, legend_algebraic, legend_voi, legend_constants)
def initConsts():
constants = [0.0] * sizeConstants; states = [0.0] * sizeStates;
states[0] = 0.01
states[1] = 0.01
states[2] = 0.01
constants[0] = 0.3
states[3] = 0.01
constants[1] = 3.0
states[4] = 0.01
states[5] = 0.01
constants[2] = 20.0
states[6] = 0.01
constants[3] = 1.7
constants[4] = 7E7
constants[5] = 70.0
constants[6] = 15.0
constants[7] = 4E5
constants[8] = 3E7
constants[9] = 8E5
constants[10] = 10
constants[11] = 17
constants[12] = 0.17
states[7] = 0.01
states[8] = 0.01
states[9] = 0.01
states[10] = 0.01
constants[13] = 7E7
constants[14] = 70.0
constants[15] = 45.0
constants[16] = 3E4
constants[17] = 10
constants[18] = 17
constants[19] = 0.017
states[11] = 0.01
states[12] = 0.01
constants[20] = 7E7
constants[21] = 70.0
constants[22] = 48.0
states[13] = 0.01
states[14] = 0.01
states[15] = 0.01
states[16] = 0.01
states[17] = 0.01
states[18] = 0.01
constants[23] = 0.0
constants[24] = 4E5
constants[25] = 10
constants[26] = 17
constants[27] = 5.1
states[19] = 0.01
constants[28] = 16.5
constants[29] = 3E4
constants[30] = 10
constants[31] = 17
constants[32] = 0.51
constants[33] = 34.56
states[20] = 0.01
states[21] = 0.01
constants[34] = 40.0
constants[35] = 5E5
constants[36] = 0.35
constants[37] = (constants[10]+constants[12])/constants[11]
constants[38] = (constants[17]+constants[19])/constants[18]
constants[39] = (constants[10]+constants[12])/constants[11]
constants[40] = (constants[17]+constants[19])/constants[18]
constants[41] = (constants[25]+constants[27])/constants[26]
constants[42] = (constants[30]+constants[32])/constants[31]
constants[43] = (constants[25]+constants[27])/constants[26]
constants[44] = (constants[30]+constants[32])/constants[31]
return (states, constants)
def computeRates(voi, states, constants):
rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic
rates[9] = (constants[21]*states[11]+constants[8]*states[12]*(constants[2]-states[6])+constants[9]*states[12]*(constants[3]-states[4]))-(constants[20]*constants[1]*states[9]+constants[22]*states[9])
rates[12] = (constants[21]*states[17]+constants[8]*states[9]*(constants[2]-states[6])+constants[9]*states[9]*(constants[3]-states[4]))-(constants[20]*constants[1]*states[12]+constants[22]*states[12])
rates[11] = (constants[21]*states[9]+constants[8]*states[17]*(constants[2]-states[6])+constants[9]*states[17]*(constants[3]-states[4]))-(constants[20]*constants[1]*states[11]+constants[33]*states[11])
rates[17] = (constants[21]*states[12]+constants[8]*states[17]*(constants[2]-states[6])+constants[9]*states[17]*(constants[3]-states[4]))-(constants[20]*constants[1]*states[17]+constants[33]*states[17])
rates[2] = constants[11]*states[0]*constants[0]-(constants[10]*states[2]+constants[12]*states[2])
rates[8] = constants[18]*states[3]*constants[0]-(constants[17]*states[8]+constants[19]*states[8])
rates[14] = constants[11]*states[5]*constants[0]-(constants[10]*states[14]+constants[12]*states[14])
rates[16] = constants[18]*states[10]*constants[0]-(constants[17]*states[16]+constants[19]*states[16])
rates[18] = constants[26]*states[1]*constants[0]-(constants[25]*states[18]+constants[27]*states[18])
rates[19] = constants[31]*states[7]*constants[0]-(constants[30]*states[19]+constants[32]*states[19])
rates[20] = constants[26]*states[13]*constants[0]-(constants[25]*states[20]+constants[27]*states[20])
rates[21] = constants[31]*states[15]*constants[0]-(constants[30]*states[21]+constants[32]*states[21])
algebraic[0] = constants[12]*(constants[0]+states[2])
rates[0] = (constants[5]*states[1]+constants[7]*states[4]*states[3]+constants[8]*states[5]*(constants[2]-states[6])+constants[9]*states[5]*(constants[3]-states[4]))-(constants[4]*constants[1]*states[0]+constants[6]*states[0]+algebraic[0]*(states[0]/(constants[37]+states[0])))
algebraic[1] = constants[19]*(constants[0]+states[8])
rates[3] = (constants[14]*states[7]+constants[16]*states[4]*states[9]+constants[8]*states[10]*(constants[2]-states[6])+constants[9]*states[10]*(constants[3]-states[4]))-(constants[13]*constants[1]*states[3]+constants[15]*states[3]+algebraic[1]*(states[3]/(constants[38]+states[3])))
algebraic[2] = constants[12]*(constants[0]+states[14])
rates[5] = (constants[5]*states[13]+constants[7]*states[4]*states[10]+constants[8]*states[0]*(constants[2]-states[6])+constants[9]*states[0]*(constants[3]-states[4]))-(constants[4]*constants[1]*states[5]+constants[6]*states[5]+algebraic[2]*(states[5]/(constants[39]+states[5])))
algebraic[3] = constants[19]*(constants[0]+states[16])
rates[10] = (constants[14]*states[15]+constants[16]*states[4]*states[12]+constants[8]*states[3]*(constants[2]-states[6])+constants[9]*states[3]*(constants[3]-states[4]))-(constants[13]*constants[1]*states[10]+constants[15]*states[10]+algebraic[3]*(states[10]/(constants[40]+states[10])))
algebraic[4] = constants[27]*(constants[0]+states[18])
rates[1] = (constants[5]*states[0]+constants[24]*states[4]*states[7]+constants[8]*states[13]*(constants[2]-states[6])+constants[9]*states[13]*(constants[3]-states[4]))-(constants[4]*constants[1]*states[1]+constants[23]*states[1]+algebraic[4]*(states[1]/(constants[41]+states[1])))
algebraic[5] = constants[32]*(constants[0]+states[19])
rates[7] = (constants[14]*states[3]+constants[29]*states[4]*states[11]+constants[8]*states[15]*(constants[2]-states[6])+constants[9]*states[15]*(constants[3]-states[4]))-(constants[13]*constants[1]*states[7]+constants[28]*states[7]+algebraic[5]*(states[7]/(constants[42]+states[7])))
algebraic[6] = constants[27]*(constants[0]+states[20])
rates[13] = (constants[5]*states[5]+constants[24]*states[4]*states[15]+constants[8]*states[1]*(constants[2]-states[6])+constants[9]*states[1]*(constants[3]-states[4]))-(constants[4]*constants[1]*states[13]+constants[23]*states[13]+algebraic[6]*(states[13]/(constants[43]+states[13])))
algebraic[7] = constants[32]*(constants[0]+states[21])
rates[15] = (constants[14]*states[10]+constants[29]*states[4]*states[17]+constants[8]*states[7]*(constants[2]-states[6])+constants[9]*states[7]*(constants[3]-states[4]))-(constants[13]*constants[1]*states[15]+constants[28]*states[15]+algebraic[7]*(states[15]/(constants[44]+states[15])))
algebraic[8] = states[5]+states[13]+states[10]+states[15]+states[12]+states[17]
rates[6] = constants[8]*algebraic[8]*(constants[2]-states[6])-constants[35]*constants[34]*states[6]
rates[4] = constants[9]*algebraic[8]*(constants[3]-states[4])-constants[36]*states[4]
return(rates)
def computeAlgebraic(constants, states, voi):
algebraic = array([[0.0] * len(voi)] * sizeAlgebraic)
states = array(states)
voi = array(voi)
algebraic[0] = constants[12]*(constants[0]+states[2])
algebraic[1] = constants[19]*(constants[0]+states[8])
algebraic[2] = constants[12]*(constants[0]+states[14])
algebraic[3] = constants[19]*(constants[0]+states[16])
algebraic[4] = constants[27]*(constants[0]+states[18])
algebraic[5] = constants[32]*(constants[0]+states[19])
algebraic[6] = constants[27]*(constants[0]+states[20])
algebraic[7] = constants[32]*(constants[0]+states[21])
algebraic[8] = states[5]+states[13]+states[10]+states[15]+states[12]+states[17]
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)