# 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 = 1 sizeStates = 14 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 (second)" legend_states[0] = "Fe3 in component Fe3 (micromolar)" legend_constants[0] = "Arg in component model_constants (micromolar)" legend_states[1] = "Fe3_Arg in component Fe3_Arg (micromolar)" legend_states[2] = "Fe3_NO in component Fe3_NO (micromolar)" legend_states[3] = "Fe2_NO in component Fe2_NO (micromolar)" legend_constants[1] = "O2 in component model_constants (micromolar)" legend_constants[2] = "k1 in component model_constants (second_order_rate_constant)" legend_constants[3] = "k_1 in component model_constants (first_order_rate_constant)" legend_constants[4] = "k2 in component model_constants (first_order_rate_constant)" legend_constants[5] = "k13 in component model_constants (first_order_rate_constant)" legend_constants[6] = "k12 in component model_constants (second_order_rate_constant)" legend_constants[7] = "k3 in component model_constants (first_order_rate_constant)" legend_states[4] = "Fe2 in component Fe2 (micromolar)" legend_states[5] = "Fe2_Arg in component Fe2_Arg (micromolar)" legend_constants[8] = "k_4 in component model_constants (first_order_rate_constant)" legend_constants[9] = "k4 in component model_constants (second_order_rate_constant)" legend_states[6] = "Fe3_O2_Arg in component Fe3_O2_Arg (micromolar)" legend_constants[10] = "k5 in component model_constants (second_order_rate_constant)" legend_constants[11] = "k_5 in component model_constants (first_order_rate_constant)" legend_constants[12] = "k6 in component model_constants (first_order_rate_constant)" legend_states[7] = "Fe3_NOHA in component Fe3_NOHA (micromolar)" legend_constants[13] = "k7 in component model_constants (first_order_rate_constant)" legend_states[8] = "Fe2_NOHA in component Fe2_NOHA (micromolar)" legend_states[9] = "NOHA in component NOHA (micromolar)" legend_states[10] = "Fe3_O2_NOHA in component Fe3_O2_NOHA (micromolar)" legend_constants[14] = "k9 in component model_constants (second_order_rate_constant)" legend_constants[15] = "k_9 in component model_constants (first_order_rate_constant)" legend_constants[16] = "k_8 in component model_constants (first_order_rate_constant)" legend_constants[17] = "k8 in component model_constants (second_order_rate_constant)" legend_constants[18] = "k10 in component model_constants (first_order_rate_constant)" legend_constants[19] = "k11 in component model_constants (first_order_rate_constant)" legend_states[11] = "NO in component NO (micromolar)" legend_algebraic[0] = "dNOdt in component NO (flux)" legend_states[12] = "citrulline in component citrulline (micromolar)" legend_states[13] = "NO3 in component NO3 (micromolar)" legend_rates[0] = "d/dt Fe3 in component Fe3 (micromolar)" legend_rates[1] = "d/dt Fe3_Arg in component Fe3_Arg (micromolar)" legend_rates[4] = "d/dt Fe2 in component Fe2 (micromolar)" legend_rates[5] = "d/dt Fe2_Arg in component Fe2_Arg (micromolar)" legend_rates[6] = "d/dt Fe3_O2_Arg in component Fe3_O2_Arg (micromolar)" legend_rates[7] = "d/dt Fe3_NOHA in component Fe3_NOHA (micromolar)" legend_rates[8] = "d/dt Fe2_NOHA in component Fe2_NOHA (micromolar)" legend_rates[10] = "d/dt Fe3_O2_NOHA in component Fe3_O2_NOHA (micromolar)" legend_rates[2] = "d/dt Fe3_NO in component Fe3_NO (micromolar)" legend_rates[3] = "d/dt Fe2_NO in component Fe2_NO (micromolar)" legend_rates[11] = "d/dt NO in component NO (micromolar)" legend_rates[12] = "d/dt citrulline in component citrulline (micromolar)" legend_rates[13] = "d/dt NO3 in component NO3 (micromolar)" legend_rates[9] = "d/dt NOHA in component NOHA (micromolar)" return (legend_states, legend_algebraic, legend_voi, legend_constants) def initConsts(): constants = [0.0] * sizeConstants; states = [0.0] * sizeStates; states[0] = 0.9 constants[0] = 100.0 states[1] = 0.0 states[2] = 0.0 states[3] = 0.0 constants[1] = 100.0 constants[2] = 6.6 constants[3] = 6.6 constants[4] = 20.8 constants[5] = 39.9 constants[6] = 0.01 constants[7] = 20.8 states[4] = 0.0 states[5] = 0.0 constants[8] = 6.6 constants[9] = 6.6 states[6] = 0.0 constants[10] = 8.5 constants[11] = 215.6 constants[12] = 175.6 states[7] = 0.0 constants[13] = 20.8 states[8] = 0.0 states[9] = 0.0 states[10] = 0.0 constants[14] = 8.6 constants[15] = 399.2 constants[16] = 13.2 constants[17] = 13.2 constants[18] = 39.1 constants[19] = 20.8 states[11] = 0.0 states[12] = 0.0 states[13] = 0.0 return (states, constants) def computeRates(voi, states, constants): rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic rates[11] = constants[5]*states[2] rates[0] = (constants[3]*states[1]+constants[5]*states[2]+constants[6]*states[3]*constants[1])-(constants[2]*constants[0]*states[0]+constants[4]*states[0]) rates[1] = constants[2]*states[0]*constants[0]-(constants[3]*states[1]+constants[7]*states[1]) rates[4] = (constants[4]*states[0]+constants[8]*states[5])-constants[9]*states[4]*constants[0] rates[5] = (constants[7]*states[1]+constants[11]*states[6]+constants[9]*states[4]*constants[0])-(constants[10]*states[5]*constants[1]+constants[8]*states[5]) rates[6] = constants[10]*states[5]*constants[1]-(constants[12]*states[6]+constants[11]*states[6]) rates[7] = constants[12]*states[6]-constants[13]*states[7] rates[8] = (constants[13]*states[7]+constants[15]*states[10]+constants[17]*states[4]*states[9])-(constants[16]*states[8]+constants[14]*states[8]*constants[1]) rates[10] = constants[14]*states[8]*constants[1]-(constants[18]*states[10]+constants[15]*states[10]) rates[2] = constants[18]*states[10]-(constants[5]*states[2]+constants[19]*states[2]) rates[3] = constants[19]*states[2]-constants[6]*states[3]*constants[1] rates[12] = constants[18]*states[10] rates[13] = constants[6]*states[3]*constants[1] rates[9] = constants[16]*states[8]-constants[17]*states[4]*states[9] return(rates) def computeAlgebraic(constants, states, voi): algebraic = array([[0.0] * len(voi)] * sizeAlgebraic) states = array(states) voi = array(voi) algebraic[0] = rates[11] 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)