# 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 = 13 sizeStates = 9 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] = "S1 in component S1 (millimolar)" legend_constants[0] = "Jo in component glucose_influx_rate (flux)" legend_algebraic[3] = "v1 in component v1 (flux)" legend_states[1] = "S2 in component S2 (millimolar)" legend_algebraic[4] = "v2 in component v2 (flux)" legend_states[2] = "S3 in component S3 (millimolar)" legend_algebraic[5] = "v3 in component v3 (flux)" legend_algebraic[10] = "v8 in component v8 (flux)" legend_states[3] = "S4 in component S4 (millimolar)" legend_algebraic[6] = "v4 in component v4 (flux)" legend_states[4] = "S5 in component S5 (millimolar)" legend_algebraic[7] = "v5 in component v5 (flux)" legend_states[5] = "S6 in component S6 (millimolar)" legend_algebraic[9] = "v6 in component v6 (flux)" legend_algebraic[12] = "J in component S6_flux_rate_across_the_plasma_membrane (flux)" legend_states[6] = "S6_ex in component S6_ex (millimolar)" legend_constants[1] = "phi in component S6_ex (dimensionless)" legend_algebraic[11] = "v9 in component v9 (flux)" legend_states[7] = "A3 in component A3 (millimolar)" legend_algebraic[8] = "v7 in component v7 (flux)" legend_constants[2] = "A in component A (millimolar)" legend_algebraic[0] = "A2 in component A (millimolar)" legend_states[8] = "N2 in component N2 (millimolar)" legend_constants[3] = "N in component N (millimolar)" legend_algebraic[1] = "N1 in component N (millimolar)" legend_constants[4] = "K_i in component v1 (millimolar)" legend_constants[5] = "k_1 in component v1 (second_order_rate_constant)" legend_constants[6] = "n in component v1 (dimensionless)" legend_algebraic[2] = "f_A3 in component v1 (dimensionless)" legend_constants[7] = "k_2 in component v2 (first_order_rate_constant)" legend_constants[8] = "k_GAPDH_plus in component v3 (second_order_rate_constant)" legend_constants[9] = "k_GAPDH_minus in component v3 (second_order_rate_constant)" legend_constants[10] = "k_PGK_plus in component v3 (second_order_rate_constant)" legend_constants[11] = "k_PGK_minus in component v3 (second_order_rate_constant)" legend_constants[12] = "k_4 in component v4 (second_order_rate_constant)" legend_constants[13] = "k_5 in component v5 (first_order_rate_constant)" legend_constants[14] = "k_6 in component v6 (second_order_rate_constant)" legend_constants[15] = "k_7 in component v7 (first_order_rate_constant)" legend_constants[16] = "k_8 in component v8 (second_order_rate_constant)" legend_constants[17] = "k_9 in component v9 (first_order_rate_constant)" legend_constants[18] = "k in component S6_flux_rate_across_the_plasma_membrane (first_order_rate_constant)" legend_rates[0] = "d/dt S1 in component S1 (millimolar)" legend_rates[1] = "d/dt S2 in component S2 (millimolar)" legend_rates[2] = "d/dt S3 in component S3 (millimolar)" legend_rates[3] = "d/dt S4 in component S4 (millimolar)" legend_rates[4] = "d/dt S5 in component S5 (millimolar)" legend_rates[5] = "d/dt S6 in component S6 (millimolar)" legend_rates[6] = "d/dt S6_ex in component S6_ex (millimolar)" legend_rates[7] = "d/dt A3 in component A3 (millimolar)" legend_rates[8] = "d/dt N2 in component N2 (millimolar)" return (legend_states, legend_algebraic, legend_voi, legend_constants) def initConsts(): constants = [0.0] * sizeConstants; states = [0.0] * sizeStates; states[0] = 1.57981839 constants[0] = 50 states[1] = 4.8279999 states[2] = 0.468657507 states[3] = 0.589391932 states[4] = 8.210114438 states[5] = 0.078042624 states[6] = 0.025277594 constants[1] = 0.1 states[7] = 1.972814237 constants[2] = 4 states[8] = 0.384873894 constants[3] = 1 constants[4] = 1 constants[5] = 550 constants[6] = 4 constants[7] = 9.8 constants[8] = 323.8 constants[9] = 57823.1 constants[10] = 76411.1 constants[11] = 23.7 constants[12] = 80 constants[13] = 9.7 constants[14] = 2000 constants[15] = 28 constants[16] = 85.7 constants[17] = 80 constants[18] = 375 return (states, constants) def computeRates(voi, states, constants): rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic algebraic[2] = power(1.00000+power(states[7]/constants[4], constants[6]), -1.00000) algebraic[3] = constants[5]*states[0]*states[7]*algebraic[2] rates[0] = constants[0]-algebraic[3] algebraic[4] = constants[7]*states[1] rates[1] = algebraic[3]-algebraic[4] algebraic[0] = constants[2]-states[7] algebraic[1] = constants[3]-states[8] algebraic[5] = (constants[8]*constants[10]*states[2]*algebraic[1]*algebraic[0]-constants[9]*constants[11]*states[3]*states[7]*states[8])/(constants[9]*states[8]+constants[10]*algebraic[0]) algebraic[6] = constants[12]*states[3]*algebraic[0] rates[3] = algebraic[5]-algebraic[6] algebraic[7] = constants[13]*states[4] rates[4] = algebraic[6]-algebraic[7] algebraic[8] = constants[15]*states[7] rates[7] = (algebraic[5]+algebraic[6])-(2.00000*algebraic[3]+algebraic[8]) algebraic[10] = constants[16]*states[2]*states[8] rates[2] = 2.00000*algebraic[4]-(algebraic[5]+algebraic[10]) algebraic[9] = constants[14]*states[5]*states[8] rates[8] = algebraic[5]-(algebraic[9]+algebraic[10]) algebraic[12] = constants[18]*(states[5]-states[6]) rates[5] = algebraic[7]-(algebraic[9]+algebraic[12]) algebraic[11] = constants[17]*states[6] rates[6] = constants[1]*algebraic[12]-algebraic[11] return(rates) def computeAlgebraic(constants, states, voi): algebraic = array([[0.0] * len(voi)] * sizeAlgebraic) states = array(states) voi = array(voi) algebraic[2] = power(1.00000+power(states[7]/constants[4], constants[6]), -1.00000) algebraic[3] = constants[5]*states[0]*states[7]*algebraic[2] algebraic[4] = constants[7]*states[1] algebraic[0] = constants[2]-states[7] algebraic[1] = constants[3]-states[8] algebraic[5] = (constants[8]*constants[10]*states[2]*algebraic[1]*algebraic[0]-constants[9]*constants[11]*states[3]*states[7]*states[8])/(constants[9]*states[8]+constants[10]*algebraic[0]) algebraic[6] = constants[12]*states[3]*algebraic[0] algebraic[7] = constants[13]*states[4] algebraic[8] = constants[15]*states[7] algebraic[10] = constants[16]*states[2]*states[8] algebraic[9] = constants[14]*states[5]*states[8] algebraic[12] = constants[18]*(states[5]-states[6]) algebraic[11] = constants[17]*states[6] 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)