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 = 35
sizeStates = 29
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 (minute)"
legend_states[0] = "BMK1 in component BMK1 (micromolar)"
legend_algebraic[9] = "v10a in component v10 (flux)"
legend_algebraic[10] = "v10b in component v10 (flux)"
legend_states[1] = "MRNA in component MRNA (micromolar)"
legend_algebraic[28] = "v18 in component v18 (flux)"
legend_algebraic[30] = "v19 in component v19 (flux)"
legend_states[2] = "NFATc in component NFATc (micromolar)"
legend_algebraic[0] = "v1 in component v1 (flux)"
legend_algebraic[31] = "v14 in component v14 (flux)"
legend_algebraic[34] = "v15 in component v15 (flux)"
legend_states[3] = "NFATn in component NFATn (micromolar)"
legend_algebraic[19] = "v16 in component v16 (flux)"
legend_algebraic[25] = "v17 in component v17 (flux)"
legend_states[4] = "NFATpc in component NFATpc (micromolar)"
legend_algebraic[1] = "v2 in component v2 (flux)"
legend_algebraic[8] = "v9 in component v9 (flux)"
legend_states[5] = "NFATpn in component NFATpn (micromolar)"
legend_states[6] = "GSK3betac in component GSK3betac (micromolar)"
legend_algebraic[2] = "v3 in component v3 (flux)"
legend_algebraic[16] = "v12a in component v12 (flux)"
legend_algebraic[18] = "v12b in component v12 (flux)"
legend_algebraic[32] = "v15a in component v15 (flux)"
legend_algebraic[33] = "v15b in component v15 (flux)"
legend_states[7] = "GSK3betan in component GSK3betan (micromolar)"
legend_algebraic[21] = "v17a in component v17 (flux)"
legend_algebraic[23] = "v17b in component v17 (flux)"
legend_states[8] = "CaNc in component CaNc (micromolar)"
legend_algebraic[5] = "v6 in component v6 (flux)"
legend_states[9] = "CaNc_star in component CaNc_star (micromolar)"
legend_algebraic[3] = "v4 in component v4 (flux)"
legend_algebraic[6] = "v7 in component v7 (flux)"
legend_algebraic[12] = "v11a in component v11 (flux)"
legend_algebraic[13] = "v11b in component v11 (flux)"
legend_algebraic[22] = "v13a in component v13 (flux)"
legend_algebraic[24] = "v13b in component v13 (flux)"
legend_algebraic[26] = "v14a in component v14 (flux)"
legend_algebraic[29] = "v14b in component v14 (flux)"
legend_states[10] = "CaNn_star in component CaNn_star (micromolar)"
legend_algebraic[15] = "v16a in component v16 (flux)"
legend_algebraic[17] = "v16b in component v16 (flux)"
legend_states[11] = "CaNn in component CaNn (micromolar)"
legend_states[12] = "CaM in component CaM (micromolar)"
legend_algebraic[4] = "v5 in component v5 (flux)"
legend_states[13] = "CaMCa in component CaMCa (micromolar)"
legend_states[14] = "MCIP in component MCIP (micromolar)"
legend_algebraic[11] = "v10 in component v10 (flux)"
legend_algebraic[14] = "v11 in component v11 (flux)"
legend_states[15] = "MCIPp in component MCIPp (micromolar)"
legend_algebraic[20] = "v12 in component v12 (flux)"
legend_algebraic[27] = "v13 in component v13 (flux)"
legend_states[16] = "MCIPpp in component MCIPpp (micromolar)"
legend_algebraic[7] = "v8 in component v8 (flux)"
legend_states[17] = "Comp1 in component Comp1 (micromolar)"
legend_states[18] = "Comp2 in component Comp2 (micromolar)"
legend_states[19] = "Comp3 in component Comp3 (micromolar)"
legend_states[20] = "P1433 in component P1433 (micromolar)"
legend_states[21] = "MCIP_BMK1 in component MCIP_BMK1 (micromolar)"
legend_states[22] = "MCIPp_CaNc_star in component MCIPp_CaNc_star (micromolar)"
legend_states[23] = "MCIPp_GSK3betac in component MCIPp_GSK3betac (micromolar)"
legend_states[24] = "MCIPpp_CaNc_star in component MCIPpp_CaNc_star (micromolar)"
legend_states[25] = "NFATpc_CaNc_star in component NFATpc_CaNc_star (micromolar)"
legend_states[26] = "NFATc_GSK3betac in component NFATc_GSK3betac (micromolar)"
legend_states[27] = "NFATpn_CaNn_star in component NFATpn_CaNn_star (micromolar)"
legend_states[28] = "NFATn_GSK3betan in component NFATn_GSK3betan (micromolar)"
legend_constants[0] = "k29 in component model_parameters (first_order_rate_constant)"
legend_constants[1] = "k30 in component model_parameters (first_order_rate_constant)"
legend_constants[2] = "k31 in component model_parameters (first_order_rate_constant)"
legend_constants[3] = "k32 in component model_parameters (first_order_rate_constant)"
legend_constants[4] = "k33 in component model_parameters (first_order_rate_constant)"
legend_constants[5] = "k34 in component model_parameters (first_order_rate_constant)"
legend_constants[6] = "Ca in component model_parameters (micromolar)"
legend_constants[7] = "k1 in component model_parameters (fifth_order_rate_constant)"
legend_constants[8] = "k2 in component model_parameters (first_order_rate_constant)"
legend_constants[9] = "k3 in component model_parameters (second_order_rate_constant)"
legend_constants[10] = "k4 in component model_parameters (first_order_rate_constant)"
legend_constants[11] = "k5 in component model_parameters (second_order_rate_constant)"
legend_constants[12] = "k6 in component model_parameters (first_order_rate_constant)"
legend_constants[13] = "k19 in component model_parameters (second_order_rate_constant)"
legend_constants[14] = "k20 in component model_parameters (first_order_rate_constant)"
legend_constants[15] = "k27 in component model_parameters (second_order_rate_constant)"
legend_constants[16] = "k28 in component model_parameters (first_order_rate_constant)"
legend_constants[17] = "k7 in component model_parameters (second_order_rate_constant)"
legend_constants[18] = "k8 in component model_parameters (first_order_rate_constant)"
legend_constants[19] = "k9 in component model_parameters (first_order_rate_constant)"
legend_constants[20] = "k10 in component model_parameters (second_order_rate_constant)"
legend_constants[21] = "k11 in component model_parameters (first_order_rate_constant)"
legend_constants[22] = "k12 in component model_parameters (first_order_rate_constant)"
legend_constants[23] = "k13 in component model_parameters (second_order_rate_constant)"
legend_constants[24] = "k14 in component model_parameters (first_order_rate_constant)"
legend_constants[25] = "k15 in component model_parameters (first_order_rate_constant)"
legend_constants[26] = "k16 in component model_parameters (second_order_rate_constant)"
legend_constants[27] = "k17 in component model_parameters (first_order_rate_constant)"
legend_constants[28] = "k18 in component model_parameters (first_order_rate_constant)"
legend_constants[29] = "k21 in component model_parameters (second_order_rate_constant)"
legend_constants[30] = "k22 in component model_parameters (first_order_rate_constant)"
legend_constants[31] = "k23 in component model_parameters (first_order_rate_constant)"
legend_constants[32] = "k24 in component model_parameters (second_order_rate_constant)"
legend_constants[33] = "k25 in component model_parameters (first_order_rate_constant)"
legend_constants[34] = "k26 in component model_parameters (first_order_rate_constant)"
legend_constants[35] = "k35 in component model_parameters (second_order_rate_constant)"
legend_constants[36] = "k36 in component model_parameters (first_order_rate_constant)"
legend_constants[37] = "k37 in component model_parameters (first_order_rate_constant)"
legend_constants[38] = "k38 in component model_parameters (second_order_rate_constant)"
legend_constants[39] = "k39 in component model_parameters (first_order_rate_constant)"
legend_constants[40] = "k40 in component model_parameters (first_order_rate_constant)"
legend_constants[41] = "k41 in component model_parameters (first_order_rate_constant)"
legend_constants[42] = "k42 in component model_parameters (first_order_rate_constant)"
legend_constants[43] = "t_half in component model_parameters (minute)"
legend_constants[44] = "k43 in component model_parameters (first_order_rate_constant)"
legend_rates[0] = "d/dt BMK1 in component BMK1 (micromolar)"
legend_rates[1] = "d/dt MRNA in component MRNA (micromolar)"
legend_rates[2] = "d/dt NFATc in component NFATc (micromolar)"
legend_rates[3] = "d/dt NFATn in component NFATn (micromolar)"
legend_rates[4] = "d/dt NFATpc in component NFATpc (micromolar)"
legend_rates[5] = "d/dt NFATpn in component NFATpn (micromolar)"
legend_rates[6] = "d/dt GSK3betac in component GSK3betac (micromolar)"
legend_rates[7] = "d/dt GSK3betan in component GSK3betan (micromolar)"
legend_rates[8] = "d/dt CaNc in component CaNc (micromolar)"
legend_rates[9] = "d/dt CaNc_star in component CaNc_star (micromolar)"
legend_rates[10] = "d/dt CaNn_star in component CaNn_star (micromolar)"
legend_rates[11] = "d/dt CaNn in component CaNn (micromolar)"
legend_rates[12] = "d/dt CaM in component CaM (micromolar)"
legend_rates[13] = "d/dt CaMCa in component CaMCa (micromolar)"
legend_rates[14] = "d/dt MCIP in component MCIP (micromolar)"
legend_rates[15] = "d/dt MCIPp in component MCIPp (micromolar)"
legend_rates[16] = "d/dt MCIPpp in component MCIPpp (micromolar)"
legend_rates[17] = "d/dt Comp1 in component Comp1 (micromolar)"
legend_rates[18] = "d/dt Comp2 in component Comp2 (micromolar)"
legend_rates[19] = "d/dt Comp3 in component Comp3 (micromolar)"
legend_rates[20] = "d/dt P1433 in component P1433 (micromolar)"
legend_rates[21] = "d/dt MCIP_BMK1 in component MCIP_BMK1 (micromolar)"
legend_rates[22] = "d/dt MCIPp_CaNc_star in component MCIPp_CaNc_star (micromolar)"
legend_rates[23] = "d/dt MCIPp_GSK3betac in component MCIPp_GSK3betac (micromolar)"
legend_rates[24] = "d/dt MCIPpp_CaNc_star in component MCIPpp_CaNc_star (micromolar)"
legend_rates[25] = "d/dt NFATpc_CaNc_star in component NFATpc_CaNc_star (micromolar)"
legend_rates[26] = "d/dt NFATc_GSK3betac in component NFATc_GSK3betac (micromolar)"
legend_rates[27] = "d/dt NFATpn_CaNn_star in component NFATpn_CaNn_star (micromolar)"
legend_rates[28] = "d/dt NFATn_GSK3betan in component NFATn_GSK3betan (micromolar)"
return (legend_states, legend_algebraic, legend_voi, legend_constants)
def initConsts():
constants = [0.0] * sizeConstants; states = [0.0] * sizeStates;
states[0] = 0.012
states[1] = 3.33E-4
states[2] = 2E-5
states[3] = 4.99E-4
states[4] = 4.94E-3
states[5] = 8.01E-5
states[6] = 0.17
states[7] = 0.339
states[8] = 0.91
states[9] = 0.0275
states[10] = 0.0568
states[11] = 0.0057
states[12] = 25.2
states[13] = 7.88E-7
states[14] = 2.15E-4
states[15] = 7.76E-3
states[16] = 0.0798
states[17] = 5.21E-3
states[18] = 0.283
states[19] = 0.014
states[20] = 0.708
states[21] = 2.14E-5
states[22] = 1.07E-4
states[23] = 1.1E-3
states[24] = 1.1E-3
states[25] = 8.15E-5
states[26] = 1.36E-6
states[27] = 2.27E-6
states[28] = 8.46E-5
constants[0] = 0.4
constants[1] = 0.1
constants[2] = 0.1
constants[3] = 0.05
constants[4] = 0.114
constants[5] = 0.0552
constants[6] = 0.2
constants[7] = 5
constants[8] = 100
constants[9] = 2760
constants[10] = 0.072
constants[11] = 50
constants[12] = 0.0567
constants[13] = 0.5
constants[14] = 0.1
constants[15] = 0.4
constants[16] = 0.1
constants[17] = 5
constants[18] = 0.1
constants[19] = 0.5
constants[20] = 0.1
constants[21] = 0.1
constants[22] = 0.1
constants[23] = 0.5
constants[24] = 0.5
constants[25] = 0.1
constants[26] = 0.1
constants[27] = 0.1
constants[28] = 0.1
constants[29] = 0.15
constants[30] = 0.15
constants[31] = 0.15
constants[32] = 0.1
constants[33] = 0.15
constants[34] = 0.1
constants[35] = 0.15
constants[36] = 0.1
constants[37] = 0.2
constants[38] = 0.1
constants[39] = 0.1
constants[40] = 0.1
constants[41] = 0.02
constants[42] = 0.03
constants[43] = 15
constants[44] = 0.03
return (states, constants)
def computeRates(voi, states, constants):
rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic
algebraic[4] = constants[7]*states[12]*(power(constants[6], 4.00000))-constants[8]*states[13]
rates[12] = -algebraic[4]
algebraic[5] = constants[9]*states[13]*states[8]-constants[10]*states[9]
rates[8] = -algebraic[5]
rates[11] = -algebraic[5]
rates[13] = algebraic[4]-algebraic[5]
algebraic[6] = constants[11]*states[9]*states[14]-constants[12]*states[17]
rates[17] = algebraic[6]
algebraic[7] = constants[13]*states[20]*states[16]-constants[14]*states[18]
rates[18] = algebraic[7]
algebraic[8] = constants[15]*states[4]*states[20]-constants[16]*states[19]
rates[19] = algebraic[8]
rates[20] = -(algebraic[7]+algebraic[8])
algebraic[9] = constants[17]*states[14]*states[0]-constants[18]*states[21]
algebraic[10] = constants[19]*states[21]
rates[0] = algebraic[10]-algebraic[9]
rates[21] = algebraic[9]-algebraic[10]
algebraic[12] = constants[20]*states[15]*states[9]-constants[21]*states[22]
algebraic[13] = constants[22]*states[22]
rates[22] = algebraic[12]-algebraic[13]
algebraic[3] = constants[4]*states[9]-constants[5]*states[10]
algebraic[15] = constants[35]*states[5]*states[10]-constants[36]*states[27]
algebraic[17] = constants[37]*states[27]
rates[10] = (algebraic[3]+algebraic[17])-algebraic[15]
algebraic[16] = constants[23]*states[15]*states[6]-constants[24]*states[23]
algebraic[18] = constants[25]*states[23]
rates[23] = algebraic[16]-algebraic[18]
rates[27] = algebraic[15]-algebraic[17]
algebraic[2] = constants[2]*states[6]-constants[3]*states[7]
algebraic[21] = constants[38]*states[3]*states[7]-constants[39]*states[28]
algebraic[23] = constants[40]*states[28]
rates[7] = (algebraic[2]+algebraic[23])-algebraic[21]
algebraic[22] = constants[26]*states[16]*states[9]-constants[27]*states[24]
algebraic[24] = constants[28]*states[24]
rates[24] = algebraic[22]-algebraic[24]
rates[28] = algebraic[21]-algebraic[23]
algebraic[19] = algebraic[15]+algebraic[17]
algebraic[25] = algebraic[21]+algebraic[23]
algebraic[1] = constants[1]*states[5]
rates[5] = algebraic[25]-(algebraic[1]+algebraic[19])
algebraic[11] = algebraic[9]+algebraic[10]
algebraic[14] = algebraic[12]+algebraic[13]
algebraic[20] = algebraic[16]+algebraic[18]
algebraic[27] = algebraic[22]+algebraic[24]
rates[15] = (algebraic[11]+algebraic[27])-(algebraic[14]+algebraic[20])
rates[16] = algebraic[20]-(algebraic[7]+algebraic[27])
algebraic[28] = constants[41]*states[3]-constants[42]*states[1]
algebraic[0] = constants[0]*states[2]
rates[3] = (algebraic[0]+algebraic[19])-(algebraic[25]+algebraic[28])
algebraic[26] = constants[29]*states[4]*states[9]-constants[30]*states[25]
algebraic[29] = constants[31]*states[25]
rates[9] = (algebraic[5]+algebraic[13]+algebraic[24]+algebraic[29])-(algebraic[3]+algebraic[6]+algebraic[12]+algebraic[22]+algebraic[26])
rates[25] = algebraic[26]-algebraic[29]
algebraic[30] = constants[44]*states[1]-(log(2.00000)/constants[43])*states[14]
rates[1] = algebraic[30]-algebraic[28]
rates[14] = algebraic[14]-(algebraic[6]+algebraic[11]+algebraic[30])
algebraic[32] = constants[32]*states[2]*states[6]-constants[33]*states[26]
algebraic[33] = constants[34]*states[26]
rates[6] = (algebraic[18]+algebraic[33])-(algebraic[2]+algebraic[16]+algebraic[32])
rates[26] = algebraic[32]-algebraic[33]
algebraic[31] = algebraic[26]+algebraic[29]
algebraic[34] = algebraic[32]+algebraic[33]
rates[2] = algebraic[31]-(algebraic[0]+algebraic[34])
rates[4] = (algebraic[1]+algebraic[34])-(algebraic[8]+algebraic[31])
return(rates)
def computeAlgebraic(constants, states, voi):
algebraic = array([[0.0] * len(voi)] * sizeAlgebraic)
states = array(states)
voi = array(voi)
algebraic[4] = constants[7]*states[12]*(power(constants[6], 4.00000))-constants[8]*states[13]
algebraic[5] = constants[9]*states[13]*states[8]-constants[10]*states[9]
algebraic[6] = constants[11]*states[9]*states[14]-constants[12]*states[17]
algebraic[7] = constants[13]*states[20]*states[16]-constants[14]*states[18]
algebraic[8] = constants[15]*states[4]*states[20]-constants[16]*states[19]
algebraic[9] = constants[17]*states[14]*states[0]-constants[18]*states[21]
algebraic[10] = constants[19]*states[21]
algebraic[12] = constants[20]*states[15]*states[9]-constants[21]*states[22]
algebraic[13] = constants[22]*states[22]
algebraic[3] = constants[4]*states[9]-constants[5]*states[10]
algebraic[15] = constants[35]*states[5]*states[10]-constants[36]*states[27]
algebraic[17] = constants[37]*states[27]
algebraic[16] = constants[23]*states[15]*states[6]-constants[24]*states[23]
algebraic[18] = constants[25]*states[23]
algebraic[2] = constants[2]*states[6]-constants[3]*states[7]
algebraic[21] = constants[38]*states[3]*states[7]-constants[39]*states[28]
algebraic[23] = constants[40]*states[28]
algebraic[22] = constants[26]*states[16]*states[9]-constants[27]*states[24]
algebraic[24] = constants[28]*states[24]
algebraic[19] = algebraic[15]+algebraic[17]
algebraic[25] = algebraic[21]+algebraic[23]
algebraic[1] = constants[1]*states[5]
algebraic[11] = algebraic[9]+algebraic[10]
algebraic[14] = algebraic[12]+algebraic[13]
algebraic[20] = algebraic[16]+algebraic[18]
algebraic[27] = algebraic[22]+algebraic[24]
algebraic[28] = constants[41]*states[3]-constants[42]*states[1]
algebraic[0] = constants[0]*states[2]
algebraic[26] = constants[29]*states[4]*states[9]-constants[30]*states[25]
algebraic[29] = constants[31]*states[25]
algebraic[30] = constants[44]*states[1]-(log(2.00000)/constants[43])*states[14]
algebraic[32] = constants[32]*states[2]*states[6]-constants[33]*states[26]
algebraic[33] = constants[34]*states[26]
algebraic[31] = algebraic[26]+algebraic[29]
algebraic[34] = algebraic[32]+algebraic[33]
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)