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 = 34
sizeStates = 16
sizeConstants = 47
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_algebraic[0] = "v1 in component v1 (flux)"
legend_constants[0] = "Vmax in component v1 (flux)"
legend_constants[1] = "Km in component v1 (umol_per_g)"
legend_states[0] = "GL in component GL (umol_per_g)"
legend_algebraic[1] = "v2 in component v2 (flux)"
legend_constants[2] = "Vmax in component v2 (flux)"
legend_constants[3] = "Km in component v2 (umol_per_g)"
legend_states[1] = "O2 in component O2 (umol_per_g)"
legend_algebraic[15] = "v3 in component v3 (flux)"
legend_constants[4] = "Vmax in component v3 (first_order_rate_constant)"
legend_algebraic[14] = "k3 in component v3 (first_order_rate_constant)"
legend_states[2] = "FA in component FA (umol_per_g)"
legend_algebraic[13] = "PS in component PS (dimensionless)"
legend_constants[5] = "PS0 in component PS0 (dimensionless)"
legend_algebraic[30] = "v4 in component v4 (flux)"
legend_constants[6] = "Vmax in component v4 (first_order_rate_constant)"
legend_algebraic[29] = "k4 in component v4 (first_order_rate_constant)"
legend_constants[7] = "epsilon in component v4 (dimensionless)"
legend_algebraic[4] = "RS in component RS (dimensionless)"
legend_constants[8] = "RS0 in component RS0 (dimensionless)"
legend_algebraic[28] = "AF in component AF (dimensionless)"
legend_constants[9] = "AF0 in component AF0 (dimensionless)"
legend_algebraic[17] = "v5 in component v5 (flux)"
legend_constants[10] = "Vmax in component v5 (first_order_rate_constant)"
legend_algebraic[16] = "k5 in component v5 (first_order_rate_constant)"
legend_constants[11] = "epsilon in component v5 (dimensionless)"
legend_states[3] = "GP in component GP (umol_per_g)"
legend_algebraic[19] = "v6 in component v6 (flux)"
legend_constants[12] = "Vmax in component v6 (first_order_rate_constant)"
legend_algebraic[18] = "k6 in component v6 (first_order_rate_constant)"
legend_constants[13] = "epsilon in component v6 (dimensionless)"
legend_algebraic[3] = "CS in component CS (dimensionless)"
legend_constants[14] = "CS0 in component CS0 (dimensionless)"
legend_algebraic[23] = "v7 in component v7 (flux)"
legend_constants[15] = "Vmax in component v7 (first_order_rate_constant)"
legend_algebraic[21] = "k7 in component v7 (first_order_rate_constant)"
legend_constants[16] = "epsilon in component v7 (dimensionless)"
legend_states[4] = "GY in component GY (umol_per_g)"
legend_algebraic[2] = "v8 in component v8 (flux)"
legend_constants[17] = "Vmax in component v8 (first_order_rate_constant)"
legend_constants[45] = "k8 in component v8 (first_order_rate_constant)"
legend_states[5] = "TG in component TG (umol_per_g)"
legend_algebraic[6] = "v9 in component v9 (flux)"
legend_constants[18] = "Vmax in component v9 (first_order_rate_constant)"
legend_algebraic[5] = "k9 in component v9 (first_order_rate_constant)"
legend_states[6] = "PY in component PY (umol_per_g)"
legend_algebraic[32] = "v10 in component v10 (flux)"
legend_constants[19] = "Vmax in component v10 (first_order_rate_constant)"
legend_algebraic[31] = "k10 in component v10 (first_order_rate_constant)"
legend_constants[20] = "epsilon in component v10 (dimensionless)"
legend_algebraic[8] = "v11 in component v11 (flux)"
legend_constants[21] = "Vmax in component v11 (first_order_rate_constant)"
legend_algebraic[7] = "k11 in component v11 (first_order_rate_constant)"
legend_states[7] = "LA in component LA (umol_per_g)"
legend_algebraic[22] = "v12 in component v12 (flux)"
legend_constants[22] = "Vmax in component v12 (first_order_rate_constant)"
legend_algebraic[20] = "k12 in component v12 (first_order_rate_constant)"
legend_constants[23] = "epsilon in component v12 (dimensionless)"
legend_states[8] = "AC in component AC (umol_per_g)"
legend_algebraic[25] = "v13 in component v13 (flux)"
legend_constants[24] = "Vmax in component v13 (first_order_rate_constant)"
legend_algebraic[24] = "k13 in component v13 (first_order_rate_constant)"
legend_states[9] = "CR in component CR (umol_per_g)"
legend_algebraic[27] = "v14 in component v14 (flux)"
legend_constants[25] = "Vmax in component v14 (first_order_rate_constant)"
legend_algebraic[26] = "k14 in component v14 (first_order_rate_constant)"
legend_states[10] = "PC in component PC (umol_per_g)"
legend_algebraic[10] = "v15 in component v15 (flux)"
legend_constants[26] = "Vmax in component v15 (first_order_rate_constant)"
legend_algebraic[9] = "k15 in component v15 (first_order_rate_constant)"
legend_constants[27] = "epsilon in component v15 (dimensionless)"
legend_states[11] = "CoA_pool in component CoA_pool (umol_per_g)"
legend_states[12] = "FC in component FC (umol_per_g)"
legend_constants[28] = "FC0 in component FC0 (umol_per_g)"
legend_algebraic[12] = "v16 in component v16 (flux)"
legend_constants[29] = "Vmax in component v16 (first_order_rate_constant)"
legend_algebraic[11] = "k16 in component v16 (first_order_rate_constant)"
legend_constants[30] = "epsilon in component v16 (dimensionless)"
legend_constants[46] = "v17 in component v17 (flux)"
legend_constants[31] = "Vmax in component v17 (first_order_rate_constant)"
legend_constants[44] = "k17 in component v17 (first_order_rate_constant)"
legend_constants[32] = "ATP in component ATP (umol_per_g)"
legend_constants[33] = "aGL in component GL (umol_per_ml)"
legend_constants[34] = "sigmaGL in component GL (g_per_ml)"
legend_algebraic[33] = "F in component model_parameters (ml_per_g_min)"
legend_constants[35] = "aFA in component FA (umol_per_ml)"
legend_constants[36] = "sigmaFA in component FA (g_per_ml)"
legend_constants[37] = "aLA in component LA (umol_per_ml)"
legend_constants[38] = "sigmaLA in component LA (g_per_ml)"
legend_constants[39] = "aO2 in component O2 (umol_per_ml)"
legend_constants[40] = "sigmaO2 in component O2 (g_per_ml)"
legend_states[13] = "CO2 in component CO2 (umol_per_g)"
legend_constants[41] = "aCO2 in component CO2 (umol_per_ml)"
legend_constants[42] = "sigmaCO2 in component CO2 (g_per_ml)"
legend_states[14] = "NAD in component NAD (umol_per_g)"
legend_states[15] = "ADP in component ADP (umol_per_g)"
legend_constants[43] = "NADH in component NADH (umol_per_g)"
legend_rates[0] = "d/dt GL in component GL (umol_per_g)"
legend_rates[2] = "d/dt FA in component FA (umol_per_g)"
legend_rates[3] = "d/dt GP in component GP (umol_per_g)"
legend_rates[4] = "d/dt GY in component GY (umol_per_g)"
legend_rates[5] = "d/dt TG in component TG (umol_per_g)"
legend_rates[6] = "d/dt PY in component PY (umol_per_g)"
legend_rates[7] = "d/dt LA in component LA (umol_per_g)"
legend_rates[8] = "d/dt AC in component AC (umol_per_g)"
legend_rates[12] = "d/dt FC in component FC (umol_per_g)"
legend_rates[11] = "d/dt CoA_pool in component CoA_pool (umol_per_g)"
legend_rates[1] = "d/dt O2 in component O2 (umol_per_g)"
legend_rates[13] = "d/dt CO2 in component CO2 (umol_per_g)"
legend_rates[14] = "d/dt NAD in component NAD (umol_per_g)"
legend_rates[15] = "d/dt ADP in component ADP (umol_per_g)"
legend_rates[10] = "d/dt PC in component PC (umol_per_g)"
legend_rates[9] = "d/dt CR in component CR (umol_per_g)"
return (legend_states, legend_algebraic, legend_voi, legend_constants)
def initConsts():
constants = [0.0] * sizeConstants; states = [0.0] * sizeStates;
constants[0] = 5.90
constants[1] = 0.05
states[0] = 0.998
constants[2] = 67.6
constants[3] = 0.01
states[1] = 0.963
constants[4] = 4.90
states[2] = 0.021
constants[5] = 0.2
constants[6] = 21.3
constants[7] = 0.6
constants[8] = 0.111
constants[9] = 0.523
constants[10] = 2.82
constants[11] = 0.254
states[3] = 0.171
constants[12] = 3.14
constants[13] = 0.5
constants[14] = 1.0
constants[15] = 0.0162
constants[16] = 0.5
states[4] = 33.0
constants[17] = 0.005
states[5] = 3.96
constants[18] = 1.8
states[6] = 0.20
constants[19] = 12.6
constants[20] = 0.98
constants[21] = 0.96
states[7] = 1.98
constants[22] = 695.7
constants[23] = 0.75
states[8] = 0.0046
constants[24] = 0.455
states[9] = 3.5
constants[25] = 0.455
states[10] = 8.80
constants[26] = 626.1
constants[27] = 0.669
states[11] = 0.043
states[12] = 0.0088
constants[28] = 0.0088
constants[29] = 67.0
constants[30] = 0.775
constants[31] = 7.76
constants[32] = 4.5
constants[33] = 4.0
constants[34] = 3.76
constants[35] = 0.5
constants[36] = 13.2
constants[37] = 1.8
constants[38] = 0.51
constants[39] = 6.53
constants[40] = 1.0
states[13] = 20.0
constants[41] = 15.5
constants[42] = 1.0
states[14] = 1.81
states[15] = 0.90
constants[43] = 0.19
constants[44] = constants[31]
constants[45] = constants[17]
constants[46] = constants[44]*constants[32]
return (states, constants)
def computeRates(voi, states, constants):
rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic
algebraic[4] = constants[43]/states[14]
algebraic[9] = constants[26]*(constants[27]*((power(algebraic[4], -1.00000))/(power(constants[8], -1.00000)+power(algebraic[4], -1.00000)))+(1.00000-constants[27])*((power(states[12], -1.00000))/(power(constants[28], -1.00000)+power(states[12], -1.00000))))
algebraic[10] = algebraic[9]*states[11]
algebraic[11] = constants[29]*(constants[30]*((power(algebraic[4], -1.00000))/(power(constants[8], -1.00000)+power(algebraic[4], -1.00000)))+(1.00000-constants[30])*((power(states[12], -1.00000))/(power(constants[28], -1.00000)+power(states[12], -1.00000))))
algebraic[12] = algebraic[11]*states[8]
rates[11] = algebraic[12]-algebraic[10]
algebraic[13] = states[15]/constants[32]
algebraic[14] = constants[4]*((power(algebraic[13], -1.00000))/(power(constants[5], -1.00000)+power(algebraic[13], -1.00000)))
algebraic[15] = algebraic[14]*states[2]
algebraic[2] = constants[45]*states[5]
rates[5] = (1.00000/3.00000)*algebraic[15]-algebraic[2]
algebraic[0] = constants[0]*(states[0]/(constants[1]+states[0]))
algebraic[16] = constants[10]*(constants[11]*(algebraic[13]/(constants[5]+algebraic[13]))+(1.00000-constants[11])*((power(algebraic[4], -1.00000))/(power(constants[8], -1.00000)+power(algebraic[4], -1.00000))))
algebraic[17] = algebraic[16]*states[3]
algebraic[3] = states[9]/states[10]
algebraic[18] = constants[12]*(constants[13]*((power(algebraic[13], -1.00000))/(power(constants[5], -1.00000)+power(algebraic[13], -1.00000)))+(1.00000-constants[13])*(power((power(algebraic[3], -1.00000))/(power(constants[14], -1.00000)+power(algebraic[3], -1.00000)), 2.00000)))
algebraic[19] = algebraic[18]*states[3]
algebraic[21] = constants[15]*(constants[16]*(algebraic[13]/(constants[5]+algebraic[13]))+(1.00000-constants[16])*(power(algebraic[3]/(constants[14]+algebraic[3]), 2.00000)))
algebraic[23] = algebraic[21]*states[4]
rates[3] = (algebraic[0]+algebraic[23])-(algebraic[17]+algebraic[19])
rates[4] = algebraic[19]-algebraic[23]
algebraic[24] = constants[24]*((power(algebraic[13], -1.00000))/(power(constants[5], -1.00000)+power(algebraic[13], -1.00000)))
algebraic[25] = algebraic[24]*states[9]
algebraic[26] = constants[25]*(algebraic[13]/(constants[5]+algebraic[13]))
algebraic[27] = algebraic[26]*states[10]
rates[10] = algebraic[25]-algebraic[27]
rates[9] = algebraic[27]-algebraic[25]
algebraic[1] = constants[2]*(states[1]/(constants[3]+states[1]))
algebraic[28] = states[8]/states[12]
algebraic[29] = constants[6]*(constants[7]*((power(algebraic[28], -1.00000))/(power(constants[9], -1.00000)+power(algebraic[28], -1.00000)))+(1.00000-constants[7])*((power(algebraic[4], -1.00000))/(power(constants[8], -1.00000)+power(algebraic[4], -1.00000))))
algebraic[30] = algebraic[29]*states[2]
algebraic[20] = constants[22]*(constants[23]*((power(algebraic[4], -1.00000))/(power(constants[8], -1.00000)+power(algebraic[4], -1.00000)))+(1.00000-constants[23])*(algebraic[13]/(constants[5]+algebraic[13])))
algebraic[22] = algebraic[20]*states[8]
rates[15] = (algebraic[0]+algebraic[19]+2.00000*algebraic[30]+2.00000*algebraic[15]+algebraic[25]+constants[46])-(3.00000*algebraic[17]+algebraic[22]+6.00000*algebraic[1]+algebraic[27])
algebraic[5] = constants[18]*(algebraic[4]/(constants[8]+algebraic[4]))
algebraic[6] = algebraic[5]*states[6]
algebraic[31] = constants[19]*(constants[20]*((power(algebraic[4], -1.00000))/(power(constants[8], -1.00000)+power(algebraic[4], -1.00000)))+(1.00000-constants[20])*((power(algebraic[28], -1.00000))/(power(constants[9], -1.00000)+power(algebraic[28], -1.00000))))
algebraic[32] = algebraic[31]*states[6]
algebraic[7] = constants[21]*((power(algebraic[4], -1.00000))/(power(constants[8], -1.00000)+power(algebraic[4], -1.00000)))
algebraic[8] = algebraic[7]*states[7]
rates[6] = (2.00000*algebraic[17]+algebraic[8])-(algebraic[6]+algebraic[32])
rates[8] = (algebraic[32]+algebraic[30])-(algebraic[22]+algebraic[12])
rates[12] = (algebraic[22]+algebraic[10]+algebraic[12])-(algebraic[32]+algebraic[30])
rates[14] = (algebraic[6]+2.00000*algebraic[1])-(2.00000*algebraic[17]+algebraic[32]+algebraic[8]+(11.0000/3.00000)*algebraic[22]+(35.0000/3.00000)*algebraic[30])
algebraic[33] = custom_piecewise([greater(voi , 0.00000) & less(voi , 5.00000), 1.00000 , True, 0.400000])
rates[0] = algebraic[33]*(constants[33]-constants[34]*states[0])-algebraic[0]
rates[2] = (3.00000*algebraic[2]+algebraic[33]*(constants[35]-constants[36]*states[2]))-(algebraic[15]+algebraic[30])
rates[7] = (algebraic[6]+algebraic[33]*(constants[37]-constants[38]*states[7]))-algebraic[8]
rates[1] = algebraic[33]*(constants[39]-constants[40]*states[1])-algebraic[1]
rates[13] = algebraic[32]+2.00000*algebraic[22]+algebraic[33]*(constants[41]-constants[42]*states[13])
return(rates)
def computeAlgebraic(constants, states, voi):
algebraic = array([[0.0] * len(voi)] * sizeAlgebraic)
states = array(states)
voi = array(voi)
algebraic[4] = constants[43]/states[14]
algebraic[9] = constants[26]*(constants[27]*((power(algebraic[4], -1.00000))/(power(constants[8], -1.00000)+power(algebraic[4], -1.00000)))+(1.00000-constants[27])*((power(states[12], -1.00000))/(power(constants[28], -1.00000)+power(states[12], -1.00000))))
algebraic[10] = algebraic[9]*states[11]
algebraic[11] = constants[29]*(constants[30]*((power(algebraic[4], -1.00000))/(power(constants[8], -1.00000)+power(algebraic[4], -1.00000)))+(1.00000-constants[30])*((power(states[12], -1.00000))/(power(constants[28], -1.00000)+power(states[12], -1.00000))))
algebraic[12] = algebraic[11]*states[8]
algebraic[13] = states[15]/constants[32]
algebraic[14] = constants[4]*((power(algebraic[13], -1.00000))/(power(constants[5], -1.00000)+power(algebraic[13], -1.00000)))
algebraic[15] = algebraic[14]*states[2]
algebraic[2] = constants[45]*states[5]
algebraic[0] = constants[0]*(states[0]/(constants[1]+states[0]))
algebraic[16] = constants[10]*(constants[11]*(algebraic[13]/(constants[5]+algebraic[13]))+(1.00000-constants[11])*((power(algebraic[4], -1.00000))/(power(constants[8], -1.00000)+power(algebraic[4], -1.00000))))
algebraic[17] = algebraic[16]*states[3]
algebraic[3] = states[9]/states[10]
algebraic[18] = constants[12]*(constants[13]*((power(algebraic[13], -1.00000))/(power(constants[5], -1.00000)+power(algebraic[13], -1.00000)))+(1.00000-constants[13])*(power((power(algebraic[3], -1.00000))/(power(constants[14], -1.00000)+power(algebraic[3], -1.00000)), 2.00000)))
algebraic[19] = algebraic[18]*states[3]
algebraic[21] = constants[15]*(constants[16]*(algebraic[13]/(constants[5]+algebraic[13]))+(1.00000-constants[16])*(power(algebraic[3]/(constants[14]+algebraic[3]), 2.00000)))
algebraic[23] = algebraic[21]*states[4]
algebraic[24] = constants[24]*((power(algebraic[13], -1.00000))/(power(constants[5], -1.00000)+power(algebraic[13], -1.00000)))
algebraic[25] = algebraic[24]*states[9]
algebraic[26] = constants[25]*(algebraic[13]/(constants[5]+algebraic[13]))
algebraic[27] = algebraic[26]*states[10]
algebraic[1] = constants[2]*(states[1]/(constants[3]+states[1]))
algebraic[28] = states[8]/states[12]
algebraic[29] = constants[6]*(constants[7]*((power(algebraic[28], -1.00000))/(power(constants[9], -1.00000)+power(algebraic[28], -1.00000)))+(1.00000-constants[7])*((power(algebraic[4], -1.00000))/(power(constants[8], -1.00000)+power(algebraic[4], -1.00000))))
algebraic[30] = algebraic[29]*states[2]
algebraic[20] = constants[22]*(constants[23]*((power(algebraic[4], -1.00000))/(power(constants[8], -1.00000)+power(algebraic[4], -1.00000)))+(1.00000-constants[23])*(algebraic[13]/(constants[5]+algebraic[13])))
algebraic[22] = algebraic[20]*states[8]
algebraic[5] = constants[18]*(algebraic[4]/(constants[8]+algebraic[4]))
algebraic[6] = algebraic[5]*states[6]
algebraic[31] = constants[19]*(constants[20]*((power(algebraic[4], -1.00000))/(power(constants[8], -1.00000)+power(algebraic[4], -1.00000)))+(1.00000-constants[20])*((power(algebraic[28], -1.00000))/(power(constants[9], -1.00000)+power(algebraic[28], -1.00000))))
algebraic[32] = algebraic[31]*states[6]
algebraic[7] = constants[21]*((power(algebraic[4], -1.00000))/(power(constants[8], -1.00000)+power(algebraic[4], -1.00000)))
algebraic[8] = algebraic[7]*states[7]
algebraic[33] = custom_piecewise([greater(voi , 0.00000) & less(voi , 5.00000), 1.00000 , True, 0.400000])
return algebraic
def custom_piecewise(cases):
"""Compute result of a piecewise function"""
return select(cases[0::2],cases[1::2])
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)