Generated Code

# Size of variable arrays:
sizeAlgebraic = 4
sizeStates = 3
sizeConstants = 14
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 (min)"
    legend_states[0] = "Z in component Ca (uM)"
    legend_states[1] = "Y in component Ca (uM)"
    legend_constants[13] = "V_in in component V_in (uM_per_min)"
    legend_algebraic[0] = "V_2 in component V_2 (uM_per_min)"
    legend_algebraic[3] = "V_3 in component V_3 (uM_per_min)"
    legend_constants[0] = "K_f in component Ca (per_min)"
    legend_constants[1] = "K in component Ca (per_min)"
    legend_constants[2] = "beta in component Ca_flux (dimensionless)"
    legend_constants[3] = "v_0 in component V_in (uM_per_min)"
    legend_constants[4] = "v_1 in component V_in (uM_per_min)"
    legend_constants[5] = "V_M2 in component V_2 (uM_per_min)"
    legend_constants[6] = "K_2 in component V_2 (uM)"
    legend_constants[7] = "K_y in component V_3 (uM)"
    legend_constants[8] = "V_M3 in component V_3 (uM_per_min)"
    legend_algebraic[2] = "R_plus in component Ca_channels (dimensionless)"
    legend_states[2] = "rho in component Ca_channels (dimensionless)"
    legend_algebraic[1] = "gamma in component gamma (dimensionless)"
    legend_constants[9] = "k_d in component Ca_channels (per_min)"
    legend_constants[10] = "k_r in component Ca_channels (per_min)"
    legend_constants[11] = "a in component gamma (per_min)"
    legend_constants[12] = "d in component gamma (per_min)"
    legend_rates[0] = "d/dt Z in component Ca (uM)"
    legend_rates[1] = "d/dt Y in component Ca (uM)"
    legend_rates[2] = "d/dt rho in component Ca_channels (dimensionless)"
    return (legend_states, legend_algebraic, legend_voi, legend_constants)

def initConsts():
    constants = [0.0] * sizeConstants; states = [0.0] * sizeStates;
    states[0] = 0.3
    states[1] = 2.7
    constants[0] = 1
    constants[1] = 10
    constants[2] = 1
    constants[3] = 1
    constants[4] = 1
    constants[5] = 6.5
    constants[6] = 0.1
    constants[7] = 0.2
    constants[8] = 50
    states[2] = 0.2
    constants[9] = 5000.0
    constants[10] = 5.0
    constants[11] = 10000.0
    constants[12] = 100.0
    constants[13] = constants[3]+constants[4]*constants[2]
    return (states, constants)

def computeRates(voi, states, constants):
    rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic
    rates[2] = -(constants[9]*(power(states[0], 4.00000))*states[2]*1.00000)+constants[10]*(1.00000-states[2])
    algebraic[0] = constants[5]*((power(states[0], 2.00000))/(power(constants[6], 2.00000)+power(states[0], 2.00000)))
    algebraic[1] = (constants[11]/constants[12])*(power(states[0], 4.00000))*1.00000
    algebraic[2] = algebraic[1]*(states[2]/(1.00000+algebraic[1]))
    algebraic[3] = constants[2]*algebraic[2]*constants[8]*((power(states[1], 2.00000))/(power(constants[7], 2.00000)+power(states[1], 2.00000)))
    rates[0] = (constants[13]-algebraic[0])+algebraic[3]+(constants[0]*states[1]-constants[1]*states[0])
    rates[1] = (algebraic[0]-algebraic[3])-constants[0]*states[1]
    return(rates)

def computeAlgebraic(constants, states, voi):
    algebraic = array([[0.0] * len(voi)] * sizeAlgebraic)
    states = array(states)
    voi = array(voi)
    algebraic[0] = constants[5]*((power(states[0], 2.00000))/(power(constants[6], 2.00000)+power(states[0], 2.00000)))
    algebraic[1] = (constants[11]/constants[12])*(power(states[0], 4.00000))*1.00000
    algebraic[2] = algebraic[1]*(states[2]/(1.00000+algebraic[1]))
    algebraic[3] = constants[2]*algebraic[2]*constants[8]*((power(states[1], 2.00000))/(power(constants[7], 2.00000)+power(states[1], 2.00000)))
    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)