# 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 = 19 sizeStates = 9 sizeConstants = 29 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 (hour)" legend_algebraic[1] = "v_1 in component main (pmol_per_ug_DNA_per_hour)" legend_constants[25] = "v_2 in component main (pmol_per_ug_DNA_per_hour)" legend_constants[26] = "v_3 in component main (pmol_per_ug_DNA_per_hour)" legend_algebraic[2] = "v_4 in component main (pmol_per_ug_DNA_per_hour)" legend_constants[27] = "v_5 in component main (pmol_per_ug_DNA_per_hour)" legend_algebraic[3] = "v_6 in component main (pmol_per_ug_DNA_per_hour)" legend_constants[28] = "v_7 in component main (pmol_per_ug_DNA_per_hour)" legend_algebraic[4] = "v_8 in component main (pmol_per_ug_DNA_per_hour)" legend_algebraic[5] = "v_9 in component main (pmol_per_ug_DNA_per_hour)" legend_algebraic[6] = "v_10 in component main (pmol_per_ug_DNA_per_hour)" legend_algebraic[7] = "v_11 in component main (pmol_per_ug_DNA_per_hour)" legend_algebraic[8] = "v_12 in component main (pmol_per_ug_DNA_per_hour)" legend_algebraic[9] = "v_13 in component main (pmol_per_ug_DNA_per_hour)" legend_algebraic[10] = "v_14 in component main (pmol_per_ug_DNA_per_hour)" legend_algebraic[11] = "v_15 in component main (pmol_per_ug_DNA_per_hour)" legend_algebraic[12] = "v_16 in component main (pmol_per_ug_DNA_per_hour)" legend_algebraic[13] = "v_17 in component main (pmol_per_ug_DNA_per_hour)" legend_algebraic[14] = "v_18 in component main (pmol_per_ug_DNA_per_hour)" legend_algebraic[15] = "v_19 in component main (pmol_per_ug_DNA_per_hour)" legend_algebraic[17] = "v_20 in component main (pmol_per_ug_DNA_per_hour)" legend_algebraic[16] = "v_21 in component main (pmol_per_ug_DNA_per_hour)" legend_algebraic[18] = "v_22 in component main (pmol_per_ug_DNA_per_hour)" legend_constants[0] = "k_1 in component main (pmol_per_ug_DNA_per_hour)" legend_constants[1] = "k_2 in component main (pmol_per_ug_DNA_per_hour)" legend_constants[2] = "k_3 in component main (per_hour)" legend_constants[3] = "k_4 in component main (per_hour)" legend_constants[4] = "k_5 in component main (ug_DNA_per_pmol_per_hour)" legend_constants[5] = "k_6 in component main (per_hour)" legend_constants[6] = "k_7 in component main (per_hour)" legend_constants[7] = "k_8 in component main (per_hour)" legend_constants[8] = "k_9 in component main (per_hour)" legend_constants[9] = "k_10 in component main (ug_DNA_per_pmol_per_hour)" legend_constants[10] = "k_11 in component main (per_hour)" legend_constants[11] = "k_12 in component main (per_hour)" legend_constants[12] = "k_13 in component main (per_hour)" legend_constants[13] = "k_14 in component main (per_hour)" legend_constants[14] = "k_15 in component main (per_hour)" legend_constants[15] = "k_16 in component main (per_hour)" legend_constants[16] = "k_17 in component main (per_hour)" legend_constants[17] = "k_18 in component main (per_hour)" legend_constants[18] = "k_19 in component main (per_hour)" legend_constants[19] = "k_20 in component main (per_hour)" legend_constants[20] = "k_21 in component main (per_hour)" legend_constants[21] = "k_22 in component main (per_hour)" legend_algebraic[0] = "LPS in component main (dimensionless)" legend_constants[22] = "PIP_2 in component main (dimensionless)" legend_constants[23] = "DG in component main (pmol_per_ug_DNA)" legend_constants[24] = "GPCho in component main (pmol_per_ug_DNA)" legend_states[0] = "AA in component main (pmol_per_ug_DNA)" legend_states[1] = "HETE in component main (pmol_per_ug_DNA)" legend_states[2] = "PGH_2 in component main (pmol_per_ug_DNA)" legend_states[3] = "PGE_2 in component main (pmol_per_ug_DNA)" legend_states[4] = "PGF_2a in component main (pmol_per_ug_DNA)" legend_states[5] = "PGD_2 in component main (pmol_per_ug_DNA)" legend_states[6] = "PGJ_2 in component main (pmol_per_ug_DNA)" legend_states[7] = "dPGD_2 in component main (pmol_per_ug_DNA)" legend_states[8] = "dPGJ_2 in component main (pmol_per_ug_DNA)" legend_rates[0] = "d/dt AA in component main (pmol_per_ug_DNA)" legend_rates[1] = "d/dt HETE in component main (pmol_per_ug_DNA)" legend_rates[2] = "d/dt PGH_2 in component main (pmol_per_ug_DNA)" legend_rates[3] = "d/dt PGE_2 in component main (pmol_per_ug_DNA)" legend_rates[4] = "d/dt PGF_2a in component main (pmol_per_ug_DNA)" legend_rates[5] = "d/dt PGD_2 in component main (pmol_per_ug_DNA)" legend_rates[6] = "d/dt PGJ_2 in component main (pmol_per_ug_DNA)" legend_rates[7] = "d/dt dPGD_2 in component main (pmol_per_ug_DNA)" legend_rates[8] = "d/dt dPGJ_2 in component main (pmol_per_ug_DNA)" return (legend_states, legend_algebraic, legend_voi, legend_constants) def initConsts(): constants = [0.0] * sizeConstants; states = [0.0] * sizeStates; constants[0] = 355.637 constants[1] = 1e-15 constants[2] = 1e-15 constants[3] = 1e-15 constants[4] = 1e-15 constants[5] = 0.33 constants[6] = 1e-15 constants[7] = 0.007 constants[8] = 0.187 constants[9] = 0.024 constants[10] = 0.111 constants[11] = 0.098 constants[12] = 0.204 constants[13] = 1e-15 constants[14] = 0.061 constants[15] = 1e-15 constants[16] = 3.116 constants[17] = 0.054 constants[18] = 0.029 constants[19] = 0.014 constants[20] = 0.034 constants[21] = 0.116 constants[22] = 1 constants[23] = 0 constants[24] = 1 states[0] = 25 states[1] = 0 states[2] = 0 states[3] = 0 states[4] = 0 states[5] = 0 states[6] = 0 states[7] = 0 states[8] = 0 constants[25] = constants[22]*constants[1] constants[26] = constants[23]*constants[2] constants[27] = constants[23]*constants[24]*constants[4] constants[28] = constants[24]*constants[6] return (states, constants) def computeRates(voi, states, constants): rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic algebraic[4] = states[0]*constants[7] algebraic[5] = states[1]*constants[8] rates[1] = algebraic[4]-algebraic[5] algebraic[0] = custom_piecewise([less_equal(voi , 0.500000), voi*2.00000 , greater(voi , 0.500000) & less(voi , 2.00000), 1.00000-(voi-0.500000)/1.50000 , True, 0.00000]) algebraic[1] = algebraic[0]*constants[22]*constants[0] algebraic[2] = states[0]*constants[3] algebraic[3] = algebraic[0]*constants[24]*constants[5] algebraic[6] = constants[23]*states[0]*constants[9] algebraic[7] = algebraic[0]*states[0]*constants[10] algebraic[8] = states[0]*constants[11] rates[0] = ((((((algebraic[1]+constants[25]+constants[26])-algebraic[2])+constants[27]+algebraic[3]+constants[28])-algebraic[4])-algebraic[6])-algebraic[7])-algebraic[8] algebraic[9] = states[2]*constants[12] algebraic[10] = states[3]*constants[13] rates[3] = algebraic[9]-algebraic[10] algebraic[11] = states[2]*constants[14] algebraic[13] = states[2]*constants[16] rates[2] = (((algebraic[6]+algebraic[7]+algebraic[8])-algebraic[9])-algebraic[11])-algebraic[13] algebraic[12] = states[4]*constants[15] rates[4] = algebraic[11]-algebraic[12] algebraic[14] = states[5]*constants[17] algebraic[15] = states[5]*constants[18] rates[5] = (algebraic[13]-algebraic[14])-algebraic[15] algebraic[16] = states[6]*constants[20] rates[6] = algebraic[14]-algebraic[16] algebraic[17] = states[7]*constants[19] rates[7] = algebraic[15]-algebraic[17] algebraic[18] = states[8]*constants[21] rates[8] = algebraic[16]-algebraic[18] return(rates) def computeAlgebraic(constants, states, voi): algebraic = array([[0.0] * len(voi)] * sizeAlgebraic) states = array(states) voi = array(voi) algebraic[4] = states[0]*constants[7] algebraic[5] = states[1]*constants[8] algebraic[0] = custom_piecewise([less_equal(voi , 0.500000), voi*2.00000 , greater(voi , 0.500000) & less(voi , 2.00000), 1.00000-(voi-0.500000)/1.50000 , True, 0.00000]) algebraic[1] = algebraic[0]*constants[22]*constants[0] algebraic[2] = states[0]*constants[3] algebraic[3] = algebraic[0]*constants[24]*constants[5] algebraic[6] = constants[23]*states[0]*constants[9] algebraic[7] = algebraic[0]*states[0]*constants[10] algebraic[8] = states[0]*constants[11] algebraic[9] = states[2]*constants[12] algebraic[10] = states[3]*constants[13] algebraic[11] = states[2]*constants[14] algebraic[13] = states[2]*constants[16] algebraic[12] = states[4]*constants[15] algebraic[14] = states[5]*constants[17] algebraic[15] = states[5]*constants[18] algebraic[16] = states[6]*constants[20] algebraic[17] = states[7]*constants[19] algebraic[18] = states[8]*constants[21] 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)