# 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 = 6 sizeStates = 5 sizeConstants = 20 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_states[0] = "C in component C (dimensionless)" legend_algebraic[0] = "Ctot in component C (dimensionless)" legend_constants[0] = "vi in component model_parameters (per_minute)" legend_constants[1] = "k1 in component model_parameters (per_minute)" legend_states[1] = "X in component X (dimensionless)" legend_constants[2] = "K5 in component model_parameters (dimensionless)" legend_constants[3] = "kd in component model_parameters (per_minute)" legend_states[2] = "Z in component Z (dimensionless)" legend_states[3] = "M in component M (dimensionless)" legend_constants[19] = "M_ in component M (dimensionless)" legend_algebraic[1] = "V1 in component model_parameters (per_minute)" legend_constants[4] = "K1 in component model_parameters (dimensionless)" legend_constants[5] = "V2 in component model_parameters (per_minute)" legend_constants[6] = "K2 in component model_parameters (dimensionless)" legend_algebraic[2] = "X_ in component X (dimensionless)" legend_algebraic[4] = "V3 in component model_parameters (per_minute)" legend_constants[7] = "K3 in component model_parameters (dimensionless)" legend_constants[8] = "V4 in component model_parameters (per_minute)" legend_constants[9] = "K4 in component model_parameters (dimensionless)" legend_states[4] = "Y in component Y (dimensionless)" legend_algebraic[3] = "Ytot in component Y (dimensionless)" legend_constants[10] = "vs in component model_parameters (per_minute)" legend_constants[11] = "d1 in component model_parameters (per_minute)" legend_constants[12] = "a1 in component model_parameters (per_minute)" legend_constants[13] = "a2 in component model_parameters (per_minute)" legend_constants[14] = "alpha in component model_parameters (dimensionless)" legend_algebraic[5] = "BP in component BP (dimensionless)" legend_constants[15] = "Kd in component model_parameters (dimensionless)" legend_constants[16] = "K6 in component model_parameters (dimensionless)" legend_constants[17] = "V1_dash in component model_parameters (per_minute)" legend_constants[18] = "V3_dash in component model_parameters (per_minute)" legend_rates[0] = "d/dt C in component C (dimensionless)" legend_rates[3] = "d/dt M in component M (dimensionless)" legend_rates[1] = "d/dt X in component X (dimensionless)" legend_rates[4] = "d/dt Y in component Y (dimensionless)" legend_rates[2] = "d/dt Z in component Z (dimensionless)" 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] = 0.1 constants[1] = 0.5 states[1] = 0.01 constants[2] = 0.02 constants[3] = 0.02 states[2] = 0.28 states[3] = 0.01 constants[4] = 0.02 constants[5] = 0.25 constants[6] = 0.02 constants[7] = 0.1 constants[8] = 0.1 constants[9] = 0.1 states[4] = 0.01 constants[10] = 0.1 constants[11] = 0.05 constants[12] = 1.5 constants[13] = 1.5 constants[14] = 0.1 constants[15] = 1 constants[16] = 0.3 constants[17] = 0.75 constants[18] = 0.3 constants[19] = -1.00000 return (states, constants) def computeRates(voi, states, constants): rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic rates[0] = (constants[0]-(constants[1]*states[1]*states[0])/(states[0]+constants[2]))-constants[3]*states[0] rates[4] = ((constants[10]-constants[11]*states[4])-constants[12]*states[0]*states[4])+(constants[13]+constants[14]*constants[3])*states[2] rates[2] = constants[12]*states[0]*states[4]-(constants[13]+constants[14]*constants[3]+constants[14]*constants[11])*states[2] algebraic[1] = (states[0]*constants[17])/(states[0]+constants[16]) rates[3] = (algebraic[1]*constants[19])/(constants[19]+constants[4])-(constants[5]*states[3])/(states[3]+constants[6]) algebraic[2] = 1.00000-states[1] algebraic[4] = states[3]*constants[18] rates[1] = (algebraic[4]*algebraic[2])/(algebraic[2]+constants[7])-(constants[8]*states[1])/(states[1]+constants[9]) return(rates) def computeAlgebraic(constants, states, voi): algebraic = array([[0.0] * len(voi)] * sizeAlgebraic) states = array(states) voi = array(voi) algebraic[1] = (states[0]*constants[17])/(states[0]+constants[16]) algebraic[2] = 1.00000-states[1] algebraic[4] = states[3]*constants[18] algebraic[0] = states[0]+states[2] algebraic[3] = states[4]+states[2] algebraic[5] = 1.00000+(constants[15]*algebraic[3])/(power(states[0]+constants[15], 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)