# 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 = 3 sizeStates = 5 sizeConstants = 18 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 (day)" legend_states[0] = "T in component T (per_ml)" legend_constants[0] = "lamda in component T (second_order_rate_constant)" legend_constants[1] = "d in component T (first_order_rate_constant)" legend_constants[2] = "k in component kinetic_parameters (flux)" legend_states[1] = "VI in component VI (per_ml)" legend_states[2] = "T_ in component T_ (per_ml)" legend_constants[3] = "tau in component T_ (first_order_rate_constant)" legend_constants[4] = "m in component T_ (first_order_rate_constant)" legend_constants[5] = "delta in component kinetic_parameters (first_order_rate_constant)" legend_constants[6] = "N in component kinetic_parameters (dimensionless)" legend_constants[7] = "c in component kinetic_parameters (first_order_rate_constant)" legend_algebraic[0] = "epsilon_PI in component epsilon_PI (dimensionless)" legend_states[3] = "VNI in component VNI (per_ml)" legend_constants[8] = "IC50 in component epsilon_PI (mg_per_ml)" legend_states[4] = "Cc in component Cc (mg_per_ml)" legend_algebraic[1] = "Cb in component Cb (mg_per_ml)" legend_constants[9] = "Vd in component Cb (ml)" legend_constants[10] = "F in component Cb (dimensionless)" legend_constants[11] = "D in component Cb (mg)" legend_constants[12] = "ka in component kinetic_parameters (first_order_rate_constant)" legend_constants[13] = "ke in component kinetic_parameters (first_order_rate_constant)" legend_constants[14] = "kacell in component Cc (first_order_rate_constant)" legend_constants[15] = "kecell in component Cc (first_order_rate_constant)" legend_algebraic[2] = "Cx in component Cx (mg_per_ml)" legend_constants[16] = "H in component Cx (dimensionless)" legend_constants[17] = "fb in component Cx (dimensionless)" legend_rates[0] = "d/dt T in component T (per_ml)" legend_rates[2] = "d/dt T_ in component T_ (per_ml)" legend_rates[1] = "d/dt VI in component VI (per_ml)" legend_rates[3] = "d/dt VNI in component VNI (per_ml)" legend_rates[4] = "d/dt Cc in component Cc (mg_per_ml)" return (legend_states, legend_algebraic, legend_voi, legend_constants) def initConsts(): constants = [0.0] * sizeConstants; states = [0.0] * sizeStates; states[0] = 1e6 constants[0] = 1e4 constants[1] = 0.01 constants[2] = 2.4e-8 states[1] = 1 states[2] = 1 constants[3] = 1.5 constants[4] = 0.01 constants[5] = 0.01 constants[6] = 2500 constants[7] = 23 states[3] = 2 constants[8] = 9e-7 states[4] = 0 constants[9] = 28000 constants[10] = 1 constants[11] = 600 constants[12] = 14.64 constants[13] = 6.86 constants[14] = 24000 constants[15] = 1.1 constants[16] = 0.052 constants[17] = 0.99 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]) rates[2] = constants[2]*states[0]*(voi-constants[3])*states[1]*(voi-constants[3])*exp(-constants[4]*constants[3])-constants[5]*states[2] algebraic[0] = states[4]/(constants[8]+states[4]) rates[1] = constants[6]*constants[5]*states[2]*(1.00000-algebraic[0])-constants[7]*states[1] rates[3] = constants[6]*constants[5]*states[2]*algebraic[0]-constants[7]*states[3] algebraic[1] = ((constants[10]*constants[11])/constants[9])*(constants[12]/(constants[13]-constants[12]))*(exp(-constants[12]*voi)-exp(-constants[13]*voi)) algebraic[2] = custom_piecewise([greater((1.00000-constants[17])*constants[16]*algebraic[1]-states[4] , 0.00000), (1.00000-constants[17])*constants[16]*algebraic[1]-states[4] , True, 0.00000]) rates[4] = constants[14]*algebraic[2]-constants[15]*states[4] return(rates) def computeAlgebraic(constants, states, voi): algebraic = array([[0.0] * len(voi)] * sizeAlgebraic) states = array(states) voi = array(voi) algebraic[0] = states[4]/(constants[8]+states[4]) algebraic[1] = ((constants[10]*constants[11])/constants[9])*(constants[12]/(constants[13]-constants[12]))*(exp(-constants[12]*voi)-exp(-constants[13]*voi)) algebraic[2] = custom_piecewise([greater((1.00000-constants[17])*constants[16]*algebraic[1]-states[4] , 0.00000), (1.00000-constants[17])*constants[16]*algebraic[1]-states[4] , True, 0.00000]) 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)