# 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 = 23 sizeStates = 13 sizeConstants = 28 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] = "S1 in component S1 (millimolar)" legend_algebraic[13] = "v8 in component v8 (flux)" legend_algebraic[15] = "v9 in component v9 (flux)" legend_constants[0] = "S in component S (millimolar)" legend_algebraic[0] = "S2 in component S (millimolar)" legend_states[1] = "sul in component sul (millimolar)" legend_algebraic[5] = "v1 in component v1 (flux)" legend_algebraic[6] = "v2 in component v2 (flux)" legend_states[2] = "aps in component aps (millimolar)" legend_algebraic[7] = "v3 in component v3 (flux)" legend_states[3] = "pap in component pap (millimolar)" legend_algebraic[8] = "v4 in component v4 (flux)" legend_states[4] = "hyd in component hyd (millimolar)" legend_algebraic[9] = "v5 in component v5 (flux)" legend_algebraic[11] = "v17 in component v17 (flux)" legend_states[5] = "cys in component cys (millimolar)" legend_algebraic[12] = "v6 in component v6 (flux)" legend_states[6] = "eth in component eth (millimolar)" legend_constants[1] = "v13 in component v13 (flux)" legend_algebraic[10] = "v7 in component v7 (flux)" legend_states[7] = "aco in component aco (millimolar)" legend_algebraic[14] = "v15 in component v15 (flux)" legend_states[8] = "oxy in component oxy (millimolar)" legend_constants[2] = "v10 in component v10 (flux)" legend_algebraic[18] = "v11A in component v11A (flux)" legend_algebraic[19] = "v14 in component v14 (flux)" legend_states[9] = "A3_c in component A3_c (millimolar)" legend_algebraic[21] = "v12 in component v12 (flux)" legend_algebraic[22] = "v16 in component v16 (flux)" legend_states[10] = "A3_m in component A3_m (millimolar)" legend_algebraic[20] = "v11B in component v11B (flux)" legend_constants[3] = "A_c in component A_c (millimolar)" legend_algebraic[1] = "A2_c in component A_c (millimolar)" legend_constants[4] = "A_m in component A_m (millimolar)" legend_algebraic[2] = "A2_m in component A_m (millimolar)" legend_states[11] = "N2 in component N2 (millimolar)" legend_constants[5] = "N in component N (millimolar)" legend_algebraic[3] = "N1 in component N (millimolar)" legend_states[12] = "oah in component oah (millimolar)" legend_algebraic[17] = "v18 in component v18 (flux)" legend_constants[6] = "v0 in component v1 (flux)" legend_algebraic[4] = "f1 in component v1 (dimensionless)" legend_constants[7] = "n in component v1 (dimensionless)" legend_constants[8] = "Kc in component v1 (millimolar)" legend_constants[9] = "k2 in component v2 (second_order_rate_constant)" legend_constants[10] = "k3 in component v3 (second_order_rate_constant)" legend_constants[11] = "k4 in component v4 (second_order_rate_constant)" legend_constants[12] = "k5 in component v5 (second_order_rate_constant)" legend_constants[13] = "k6 in component v6 (first_order_rate_constant)" legend_constants[14] = "k7 in component v7 (second_order_rate_constant)" legend_constants[15] = "k8 in component v8 (second_order_rate_constant)" legend_constants[16] = "k9 in component v9 (second_order_rate_constant)" legend_constants[17] = "alpha in component v11A (dimensionless)" legend_algebraic[16] = "f2 in component v11A (dimensionless)" legend_constants[18] = "m in component v11A (dimensionless)" legend_constants[19] = "KH in component v11A (millimolar)" legend_constants[20] = "k11 in component v11A (first_order_rate_constant)" legend_constants[21] = "KA in component v11B (millimolar)" legend_constants[22] = "k12 in component v12 (first_order_rate_constant)" legend_constants[23] = "k14 in component v14 (first_order_rate_constant)" legend_constants[24] = "k15 in component v15 (first_order_rate_constant)" legend_constants[25] = "k16 in component v16 (second_order_rate_constant)" legend_constants[26] = "k17 in component v17 (first_order_rate_constant)" legend_constants[27] = "k18 in component v18 (first_order_rate_constant)" legend_rates[0] = "d/dt S1 in component S1 (millimolar)" legend_rates[1] = "d/dt sul in component sul (millimolar)" legend_rates[2] = "d/dt aps in component aps (millimolar)" legend_rates[3] = "d/dt pap in component pap (millimolar)" legend_rates[4] = "d/dt hyd in component hyd (millimolar)" legend_rates[5] = "d/dt cys in component cys (millimolar)" legend_rates[6] = "d/dt eth in component eth (millimolar)" legend_rates[7] = "d/dt aco in component aco (millimolar)" legend_rates[8] = "d/dt oxy in component oxy (millimolar)" legend_rates[9] = "d/dt A3_c in component A3_c (millimolar)" legend_rates[10] = "d/dt A3_m in component A3_m (millimolar)" legend_rates[11] = "d/dt N2 in component N2 (millimolar)" legend_rates[12] = "d/dt oah in component oah (millimolar)" return (legend_states, legend_algebraic, legend_voi, legend_constants) def initConsts(): constants = [0.0] * sizeConstants; states = [0.0] * sizeStates; states[0] = 1.892468811 constants[0] = 2 states[1] = 0.012871557 states[2] = 0.053366179 states[3] = 0.082791522 states[4] = 0.159317029 states[5] = 0.805117739 states[6] = 10.25246999 constants[1] = 4 states[7] = 1.139360412 states[8] = 6.146549084 constants[2] = 80 states[9] = 1.570847601 states[10] = 1.835158493 constants[3] = 2 constants[4] = 2 states[11] = 1.933616149 constants[5] = 2 states[12] = 5.571685096 constants[6] = 1.6 constants[7] = 4 constants[8] = 0.1 constants[9] = 0.2 constants[10] = 0.2 constants[11] = 0.2 constants[12] = 0.1 constants[13] = 0.12 constants[14] = 10 constants[15] = 10 constants[16] = 10 constants[17] = 0.1 constants[18] = 4 constants[19] = 0.5 constants[20] = 10 constants[21] = 1 constants[22] = 5 constants[23] = 10 constants[24] = 5 constants[25] = 10 constants[26] = 0.02 constants[27] = 1 return (states, constants) def computeRates(voi, states, constants): rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic algebraic[4] = power(1.00000+power(states[5]/constants[8], constants[7]), -1.00000) algebraic[5] = constants[6]*algebraic[4] algebraic[6] = constants[9]*states[1]*states[9] rates[1] = algebraic[5]-algebraic[6] algebraic[7] = constants[10]*states[2]*states[9] rates[2] = algebraic[6]-algebraic[7] algebraic[8] = constants[11]*states[3]*states[11] rates[3] = algebraic[7]-algebraic[8] algebraic[9] = constants[12]*states[4]*states[12] algebraic[11] = constants[26]*states[4] rates[4] = algebraic[8]-(algebraic[9]+algebraic[11]) algebraic[12] = constants[13]*states[5] rates[5] = algebraic[9]-algebraic[12] algebraic[3] = constants[5]-states[11] algebraic[10] = constants[14]*states[6]*algebraic[3] rates[6] = constants[1]-algebraic[10] algebraic[0] = constants[0]-states[0] algebraic[13] = constants[15]*states[7]*algebraic[0] algebraic[15] = constants[16]*states[0]*algebraic[3] rates[0] = algebraic[13]-algebraic[15] algebraic[14] = constants[24]*states[7] rates[7] = algebraic[10]-(algebraic[13]+algebraic[14]) algebraic[17] = constants[27]*states[12] rates[12] = algebraic[14]-(algebraic[9]+algebraic[17]) algebraic[16] = power(1.00000+power(states[4]/constants[19], constants[18]), -1.00000) algebraic[18] = (constants[20]*states[11]*states[8]*algebraic[16])/(constants[17]*states[11]+states[8]) rates[11] = (2.00000*algebraic[10]+4.00000*algebraic[15])-(3.00000*algebraic[8]+algebraic[18]) algebraic[19] = constants[23]*states[8] rates[8] = constants[2]-(algebraic[18]+algebraic[19]) algebraic[21] = constants[22]*states[9] algebraic[1] = constants[3]-states[9] algebraic[22] = constants[25]*states[10]*algebraic[1] rates[9] = algebraic[22]-(algebraic[6]+algebraic[7]+algebraic[21]) algebraic[2] = constants[4]-states[10] algebraic[20] = (3.00000*algebraic[18]*algebraic[2])/(constants[21]+algebraic[2]) rates[10] = algebraic[20]-algebraic[22] return(rates) def computeAlgebraic(constants, states, voi): algebraic = array([[0.0] * len(voi)] * sizeAlgebraic) states = array(states) voi = array(voi) algebraic[4] = power(1.00000+power(states[5]/constants[8], constants[7]), -1.00000) algebraic[5] = constants[6]*algebraic[4] algebraic[6] = constants[9]*states[1]*states[9] algebraic[7] = constants[10]*states[2]*states[9] algebraic[8] = constants[11]*states[3]*states[11] algebraic[9] = constants[12]*states[4]*states[12] algebraic[11] = constants[26]*states[4] algebraic[12] = constants[13]*states[5] algebraic[3] = constants[5]-states[11] algebraic[10] = constants[14]*states[6]*algebraic[3] algebraic[0] = constants[0]-states[0] algebraic[13] = constants[15]*states[7]*algebraic[0] algebraic[15] = constants[16]*states[0]*algebraic[3] algebraic[14] = constants[24]*states[7] algebraic[17] = constants[27]*states[12] algebraic[16] = power(1.00000+power(states[4]/constants[19], constants[18]), -1.00000) algebraic[18] = (constants[20]*states[11]*states[8]*algebraic[16])/(constants[17]*states[11]+states[8]) algebraic[19] = constants[23]*states[8] algebraic[21] = constants[22]*states[9] algebraic[1] = constants[3]-states[9] algebraic[22] = constants[25]*states[10]*algebraic[1] algebraic[2] = constants[4]-states[10] algebraic[20] = (3.00000*algebraic[18]*algebraic[2])/(constants[21]+algebraic[2]) 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)