Generated Code
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The raw code is available.
# Size of variable arrays:
sizeAlgebraic = 0
sizeStates = 7
sizeConstants = 27
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] = "G_a in component G_a (micromolar)"
legend_constants[0] = "k1 in component model_parameters (dimensionless)"
legend_constants[1] = "k2 in component model_parameters (dimensionless)"
legend_constants[2] = "k3 in component model_parameters (dimensionless)"
legend_states[1] = "PLC in component PLC (micromolar)"
legend_states[2] = "Ca_cyt in component Ca_cyt (micromolar)"
legend_constants[3] = "K4 in component model_parameters (dimensionless)"
legend_constants[4] = "k5 in component model_parameters (dimensionless)"
legend_constants[5] = "K6 in component model_parameters (dimensionless)"
legend_constants[6] = "k7 in component model_parameters (dimensionless)"
legend_constants[7] = "k8 in component model_parameters (dimensionless)"
legend_constants[8] = "K9 in component model_parameters (dimensionless)"
legend_states[3] = "Ca_ER in component Ca_ER (micromolar)"
legend_constants[9] = "k10 in component model_parameters (dimensionless)"
legend_constants[10] = "K11 in component model_parameters (dimensionless)"
legend_constants[11] = "k16 in component model_parameters (dimensionless)"
legend_constants[12] = "K17 in component model_parameters (dimensionless)"
legend_states[4] = "Ca_mit in component Ca_mit (micromolar)"
legend_constants[13] = "k18 in component model_parameters (dimensionless)"
legend_constants[14] = "K19 in component model_parameters (dimensionless)"
legend_constants[15] = "k20 in component model_parameters (dimensionless)"
legend_constants[16] = "K21 in component model_parameters (dimensionless)"
legend_constants[17] = "k12 in component model_parameters (dimensionless)"
legend_constants[18] = "k13 in component model_parameters (dimensionless)"
legend_constants[19] = "k14 in component model_parameters (dimensionless)"
legend_constants[20] = "K15 in component model_parameters (dimensionless)"
legend_states[5] = "Enz in component Enz (micromolar)"
legend_constants[21] = "k_act in component Enz (dimensionless)"
legend_constants[22] = "K_M in component Enz (dimensionless)"
legend_constants[23] = "k_inact in component Enz (dimensionless)"
legend_constants[24] = "p in component Enz (dimensionless)"
legend_states[6] = "Pro in component Pro (micromolar)"
legend_constants[25] = "k_enz in component Pro (dimensionless)"
legend_constants[26] = "k_rem in component Pro (dimensionless)"
legend_rates[0] = "d/dt G_a in component G_a (micromolar)"
legend_rates[1] = "d/dt PLC in component PLC (micromolar)"
legend_rates[3] = "d/dt Ca_ER in component Ca_ER (micromolar)"
legend_rates[4] = "d/dt Ca_mit in component Ca_mit (micromolar)"
legend_rates[2] = "d/dt Ca_cyt in component Ca_cyt (micromolar)"
legend_rates[5] = "d/dt Enz in component Enz (micromolar)"
legend_rates[6] = "d/dt Pro in component Pro (micromolar)"
return (legend_states, legend_algebraic, legend_voi, legend_constants)
def initConsts():
constants = [0.0] * sizeConstants; states = [0.0] * sizeStates;
states[0] = 0.01
constants[0] = 0.55
constants[1] = 0
constants[2] = 0.0001
states[1] = 0.01
states[2] = 0.01
constants[3] = 0.783
constants[4] = 1.24
constants[5] = 0.7
constants[6] = 5.82
constants[7] = 32.24
constants[8] = 29.09
states[3] = 10
constants[9] = 0.93
constants[10] = 2.667
constants[11] = 20.9
constants[12] = 0.05
states[4] = 0.001
constants[13] = 79
constants[14] = 2
constants[15] = 1.5
constants[16] = 1.5
constants[17] = 0.76
constants[18] = 0
constants[19] = 149
constants[20] = 0.16
states[5] = 0
constants[21] = 0.1
constants[22] = 0.02
constants[23] = 0.043
constants[24] = 4
states[6] = 0
constants[25] = 3
constants[26] = 3
return (states, constants)
def computeRates(voi, states, constants):
rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic
rates[0] = ((constants[0]+constants[1]*states[0])-(constants[2]*states[0]*states[1])/(states[0]+constants[3]))-(constants[4]*states[2]*states[0])/(states[0]+constants[5])
rates[1] = constants[6]*states[0]-(constants[7]*states[1])/(states[1]+constants[8])
rates[3] = -(states[3]-states[2])*((constants[9]*states[2]*(power(states[1], 4.00000)))/(power(states[1], 4.00000)+power(constants[10], 4.00000)))+(constants[11]*states[2])/(states[2]+constants[12])
rates[4] = (constants[13]*(power(states[2], 8.00000)))/(power(constants[14], 8.00000)+power(states[2], 8.00000))-(states[4]-states[2])*((constants[15]*states[2])/(states[2]+constants[16]))
rates[2] = (((((states[3]-states[2])*((constants[9]*states[2]*(power(states[1], 4.00000)))/(power(states[1], 4.00000)+power(constants[10], 4.00000)))+constants[17]*states[1]+constants[18]*states[0])-(constants[19]*states[2])/(constants[20]+states[2]))-(constants[11]*states[2])/(constants[12]+states[2]))-(constants[13]*(power(states[2], 8.00000)))/(power(constants[14], 8.00000)+power(states[2], 8.00000)))+(states[4]-states[2])*((constants[15]*states[2])/(states[2]+constants[16]))
rates[5] = (constants[21]*(power(states[2], constants[24])))/(power(constants[22], constants[24])+power(states[2], constants[24]))-constants[23]*states[5]
rates[6] = constants[25]*states[5]-constants[26]*states[6]
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)