# 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 = 2 sizeStates = 6 sizeConstants = 19 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] = "y1 in component y1 (micromolar)" legend_constants[0] = "a1 in component y1 (flux)" legend_algebraic[0] = "g1 in component y1 (micromolar)" legend_constants[1] = "b1 in component y1 (micromolar)" legend_constants[2] = "d1 in component y1 (first_order_rate_constant)" legend_states[1] = "y2 in component y2 (micromolar)" legend_constants[3] = "a2 in component y2 (flux)" legend_algebraic[1] = "g2 in component y2 (micromolar)" legend_constants[4] = "b2 in component y2 (micromolar)" legend_constants[5] = "d2 in component y2 (first_order_rate_constant)" legend_states[2] = "y3 in component y3 (micromolar)" legend_constants[6] = "f53 in component y3 (second_order_rate_constant)" legend_constants[7] = "f13 in component y3 (second_order_rate_constant)" legend_constants[8] = "h36 in component y3 (second_order_rate_constant)" legend_constants[9] = "d3 in component y3 (first_order_rate_constant)" legend_constants[10] = "E in component y3 (micromolar)" legend_states[3] = "y5 in component y5 (micromolar)" legend_states[4] = "y6 in component y6 (micromolar)" legend_states[5] = "y4 in component y4 (micromolar)" legend_constants[11] = "f14 in component y4 (first_order_rate_constant)" legend_constants[12] = "f24 in component y4 (first_order_rate_constant)" legend_constants[13] = "d4 in component y4 (first_order_rate_constant)" legend_constants[14] = "f35 in component y5 (first_order_rate_constant)" legend_constants[15] = "f45 in component y5 (first_order_rate_constant)" legend_constants[16] = "d5 in component y5 (first_order_rate_constant)" legend_constants[17] = "h36 in component y6 (second_order_rate_constant)" legend_constants[18] = "d6 in component y6 (first_order_rate_constant)" legend_rates[0] = "d/dt y1 in component y1 (micromolar)" legend_rates[1] = "d/dt y2 in component y2 (micromolar)" legend_rates[2] = "d/dt y3 in component y3 (micromolar)" legend_rates[5] = "d/dt y4 in component y4 (micromolar)" legend_rates[3] = "d/dt y5 in component y5 (micromolar)" legend_rates[4] = "d/dt y6 in component y6 (micromolar)" return (legend_states, legend_algebraic, legend_voi, legend_constants) def initConsts(): constants = [0.0] * sizeConstants; states = [0.0] * sizeStates; states[0] = 0.0 constants[0] = 10.0 constants[1] = 10.0 constants[2] = 0.2 states[1] = 0.0 constants[3] = 10.0 constants[4] = 10.0 constants[5] = 0.1 states[2] = 0.0 constants[6] = 1.5 constants[7] = 0.6 constants[8] = 0.1 constants[9] = 1.0 constants[10] = 10.0 states[3] = 0.0 states[4] = 0.0 states[5] = 0.0 constants[11] = 0.1 constants[12] = 0.8 constants[13] = 1.1 constants[14] = 0.3 constants[15] = 0.1 constants[16] = 1.0 constants[17] = 0.1 constants[18] = 0.001 return (states, constants) def computeRates(voi, states, constants): rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic rates[2] = (constants[7]*(constants[10]-(states[2]+states[4]))*states[0]+constants[6]*(constants[10]-(states[2]+states[4]))*states[3])-(constants[8]*states[1]*states[2]+constants[9]*states[2]) rates[5] = (constants[11]*states[0]+constants[12]*states[1])-constants[13]*states[5] rates[3] = (constants[14]*states[2]+constants[15]*states[5])-constants[16]*states[3] rates[4] = constants[17]*states[1]*states[2]-constants[18]*states[4] algebraic[0] = custom_piecewise([greater_equal(voi , 0.00000) & less(voi , 5.00000), 0.00000 , greater_equal(voi , 5.00000) & less_equal(voi , 10.0000), 1.00000 , True, 0.00000]) rates[0] = constants[0]*(algebraic[0]/(constants[1]+algebraic[0]))-constants[2]*states[0] algebraic[1] = custom_piecewise([greater_equal(voi , 0.00000) & less_equal(voi , 5.00000), 1.00000 , True, 0.00000]) rates[1] = constants[3]*(algebraic[1]/(constants[4]+algebraic[1]))-constants[5]*states[1] return(rates) def computeAlgebraic(constants, states, voi): algebraic = array([[0.0] * len(voi)] * sizeAlgebraic) states = array(states) voi = array(voi) algebraic[0] = custom_piecewise([greater_equal(voi , 0.00000) & less(voi , 5.00000), 0.00000 , greater_equal(voi , 5.00000) & less_equal(voi , 10.0000), 1.00000 , True, 0.00000]) algebraic[1] = custom_piecewise([greater_equal(voi , 0.00000) & less_equal(voi , 5.00000), 1.00000 , 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)