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)