# 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 = 5 sizeConstants = 35 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_states[0] = "GH in component GH (ng_ml)" legend_constants[0] = "GHS in component GH (dimensionless)" legend_constants[1] = "k1 in component GH (first_order_rate_constant)" legend_constants[2] = "kr1 in component GH (ng_ml_hr)" legend_constants[3] = "t1 in component GH (pg_ml)" legend_constants[4] = "n1 in component GH (dimensionless)" legend_constants[5] = "n2 in component GH (dimensionless)" legend_constants[6] = "g0 in component GH (dimensionless)" legend_constants[7] = "ng0 in component GH (dimensionless)" legend_constants[8] = "tg0 in component GH (dimensionless)" legend_constants[9] = "t2 in component GH (pg_ml)" legend_states[1] = "SRIF_PeV in component SRIF_PeV (pg_ml)" legend_constants[33] = "F1_GHS in component F (dimensionless)" legend_states[2] = "GHRH in component GHRH (pg_ml)" legend_states[3] = "ghr_GHRH in component ghr_GHRH (pg_ml)" legend_constants[10] = "k4 in component SRIF_PeV (first_order_rate_constant)" legend_constants[11] = "kr4 in component SRIF_PeV (pg_ml_hr)" legend_constants[12] = "t5 in component SRIF_PeV (ng_ml)" legend_constants[13] = "n5 in component SRIF_PeV (dimensionless)" legend_constants[14] = "S_basal in component SRIF_PeV (pg_ml_hr)" legend_states[4] = "SRIF_ArC in component SRIF_ArC (pg_ml)" legend_constants[15] = "k2 in component SRIF_ArC (first_order_rate_constant)" legend_constants[16] = "kr2 in component SRIF_ArC (pg_ml_hr)" legend_constants[17] = "t3 in component SRIF_ArC (pg_ml)" legend_constants[18] = "n3 in component SRIF_ArC (dimensionless)" legend_constants[19] = "k3 in component GHRH (first_order_rate_constant)" legend_constants[20] = "kr3 in component GHRH (pg_ml_hr)" legend_constants[21] = "t4 in component GHRH (pg_ml)" legend_constants[22] = "n4 in component GHRH (dimensionless)" legend_constants[34] = "F2_GHS in component F (dimensionless)" legend_constants[23] = "g1 in component F (dimensionless)" legend_constants[24] = "g2 in component F (dimensionless)" legend_constants[25] = "tg1 in component F (dimensionless)" legend_constants[26] = "tg2 in component F (dimensionless)" legend_constants[27] = "ng1 in component F (dimensionless)" legend_constants[28] = "ng2 in component F (dimensionless)" legend_algebraic[1] = "dghr_GHRH_dt in component ghr_GHRH (pg_ml_hr)" legend_algebraic[0] = "inject in component ghr_GHRH (pg_ml_hr)" legend_constants[29] = "kghr in component ghr_GHRH (first_order_rate_constant)" legend_constants[30] = "C in component ghr_GHRH (pg_ml_hr)" legend_constants[31] = "onset in component ghr_GHRH (hour)" legend_constants[32] = "duration in component ghr_GHRH (hour)" legend_rates[0] = "d/dt GH in component GH (ng_ml)" legend_rates[1] = "d/dt SRIF_PeV in component SRIF_PeV (pg_ml)" legend_rates[4] = "d/dt SRIF_ArC in component SRIF_ArC (pg_ml)" legend_rates[2] = "d/dt GHRH in component GHRH (pg_ml)" legend_rates[3] = "d/dt ghr_GHRH in component ghr_GHRH (pg_ml)" 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] = 20.0 constants[1] = 3.0 constants[2] = 600.0 constants[3] = 357.0 constants[4] = 5.0 constants[5] = 2.0 constants[6] = 2.0 constants[7] = 2.9 constants[8] = 200.0 constants[9] = 10.0 states[1] = 0.0 states[2] = 0.0 states[3] = 0.0 constants[10] = 25.0 constants[11] = 20400.0 constants[12] = 10.0 constants[13] = 2.0 constants[14] = 900.0 states[4] = 0.0 constants[15] = 25.0 constants[16] = 2200.0 constants[17] = 400.0 constants[18] = 2.0 constants[19] = 40.0 constants[20] = 63000.0 constants[21] = 28.0 constants[22] = 5.0 constants[23] = 90000.0 constants[24] = 100.0 constants[25] = 390.0 constants[26] = 10000.0 constants[27] = 3.0 constants[28] = 2.0 constants[29] = 15.0 constants[30] = 10000.0 constants[31] = 2.0 constants[32] = 0.2 constants[33] = constants[23]*((power(constants[0]/constants[25], constants[27]))/(1.00000+power(constants[0]/constants[25], constants[27]))) constants[34] = constants[24]*((power(constants[0]/constants[26], constants[28]))/(1.00000+power(constants[0]/constants[26], constants[28]))) return (states, constants) def computeRates(voi, states, constants): rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic rates[0] = constants[2]*((power((states[2]+states[3])/constants[3], constants[4]))/(power((states[2]+states[3])/constants[3], constants[4])+1.00000)+constants[6]*((power(constants[0]/constants[8], constants[7]))/(1.00000+power(constants[0]/constants[8], constants[7])))+(1.00000+constants[33])/(1.00000+power(states[1]/constants[9], constants[5])+constants[33]))-constants[1]*states[0] rates[1] = -(constants[10]*states[1])+constants[11]*((power(states[0]/constants[12], constants[13]))/(power(states[0]/constants[12], constants[13])+1.00000))+constants[14] rates[4] = constants[16]*((power((states[2]+states[3])/constants[17], constants[18]))/(1.00000+power((states[2]+states[3])/constants[17], constants[18])))-constants[15]*states[4] rates[2] = (constants[20]*((1.00000+constants[34])/(1.00000+power((states[1]+states[4])/constants[21], constants[22])+constants[34]))+states[3]*1.00000)-constants[19]*states[2] algebraic[0] = custom_piecewise([less(voi , constants[31]), 0.00000 , greater_equal(voi , constants[31]) & less_equal(voi , constants[31]+constants[32]), constants[30] , greater(voi , constants[31]+constants[32]), 0.00000 , True, float('nan')]) rates[3] = algebraic[0]-constants[29]*states[3] return(rates) def computeAlgebraic(constants, states, voi): algebraic = array([[0.0] * len(voi)] * sizeAlgebraic) states = array(states) voi = array(voi) algebraic[0] = custom_piecewise([less(voi , constants[31]), 0.00000 , greater_equal(voi , constants[31]) & less_equal(voi , constants[31]+constants[32]), constants[30] , greater(voi , constants[31]+constants[32]), 0.00000 , True, float('nan')]) algebraic[1] = algebraic[0]-constants[29]*states[3] 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)