# 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 = 35 sizeStates = 29 sizeConstants = 45 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] = "BMK1 in component BMK1 (micromolar)" legend_algebraic[9] = "v10a in component v10 (flux)" legend_algebraic[10] = "v10b in component v10 (flux)" legend_states[1] = "MRNA in component MRNA (micromolar)" legend_algebraic[28] = "v18 in component v18 (flux)" legend_algebraic[30] = "v19 in component v19 (flux)" legend_states[2] = "NFATc in component NFATc (micromolar)" legend_algebraic[0] = "v1 in component v1 (flux)" legend_algebraic[31] = "v14 in component v14 (flux)" legend_algebraic[34] = "v15 in component v15 (flux)" legend_states[3] = "NFATn in component NFATn (micromolar)" legend_algebraic[19] = "v16 in component v16 (flux)" legend_algebraic[25] = "v17 in component v17 (flux)" legend_states[4] = "NFATpc in component NFATpc (micromolar)" legend_algebraic[1] = "v2 in component v2 (flux)" legend_algebraic[8] = "v9 in component v9 (flux)" legend_states[5] = "NFATpn in component NFATpn (micromolar)" legend_states[6] = "GSK3betac in component GSK3betac (micromolar)" legend_algebraic[2] = "v3 in component v3 (flux)" legend_algebraic[16] = "v12a in component v12 (flux)" legend_algebraic[18] = "v12b in component v12 (flux)" legend_algebraic[32] = "v15a in component v15 (flux)" legend_algebraic[33] = "v15b in component v15 (flux)" legend_states[7] = "GSK3betan in component GSK3betan (micromolar)" legend_algebraic[21] = "v17a in component v17 (flux)" legend_algebraic[23] = "v17b in component v17 (flux)" legend_states[8] = "CaNc in component CaNc (micromolar)" legend_algebraic[5] = "v6 in component v6 (flux)" legend_states[9] = "CaNc_star in component CaNc_star (micromolar)" legend_algebraic[3] = "v4 in component v4 (flux)" legend_algebraic[6] = "v7 in component v7 (flux)" legend_algebraic[12] = "v11a in component v11 (flux)" legend_algebraic[13] = "v11b in component v11 (flux)" legend_algebraic[22] = "v13a in component v13 (flux)" legend_algebraic[24] = "v13b in component v13 (flux)" legend_algebraic[26] = "v14a in component v14 (flux)" legend_algebraic[29] = "v14b in component v14 (flux)" legend_states[10] = "CaNn_star in component CaNn_star (micromolar)" legend_algebraic[15] = "v16a in component v16 (flux)" legend_algebraic[17] = "v16b in component v16 (flux)" legend_states[11] = "CaNn in component CaNn (micromolar)" legend_states[12] = "CaM in component CaM (micromolar)" legend_algebraic[4] = "v5 in component v5 (flux)" legend_states[13] = "CaMCa in component CaMCa (micromolar)" legend_states[14] = "MCIP in component MCIP (micromolar)" legend_algebraic[11] = "v10 in component v10 (flux)" legend_algebraic[14] = "v11 in component v11 (flux)" legend_states[15] = "MCIPp in component MCIPp (micromolar)" legend_algebraic[20] = "v12 in component v12 (flux)" legend_algebraic[27] = "v13 in component v13 (flux)" legend_states[16] = "MCIPpp in component MCIPpp (micromolar)" legend_algebraic[7] = "v8 in component v8 (flux)" legend_states[17] = "Comp1 in component Comp1 (micromolar)" legend_states[18] = "Comp2 in component Comp2 (micromolar)" legend_states[19] = "Comp3 in component Comp3 (micromolar)" legend_states[20] = "P1433 in component P1433 (micromolar)" legend_states[21] = "MCIP_BMK1 in component MCIP_BMK1 (micromolar)" legend_states[22] = "MCIPp_CaNc_star in component MCIPp_CaNc_star (micromolar)" legend_states[23] = "MCIPp_GSK3betac in component MCIPp_GSK3betac (micromolar)" legend_states[24] = "MCIPpp_CaNc_star in component MCIPpp_CaNc_star (micromolar)" legend_states[25] = "NFATpc_CaNc_star in component NFATpc_CaNc_star (micromolar)" legend_states[26] = "NFATc_GSK3betac in component NFATc_GSK3betac (micromolar)" legend_states[27] = "NFATpn_CaNn_star in component NFATpn_CaNn_star (micromolar)" legend_states[28] = "NFATn_GSK3betan in component NFATn_GSK3betan (micromolar)" legend_constants[0] = "k29 in component model_parameters (first_order_rate_constant)" legend_constants[1] = "k30 in component model_parameters (first_order_rate_constant)" legend_constants[2] = "k31 in component model_parameters (first_order_rate_constant)" legend_constants[3] = "k32 in component model_parameters (first_order_rate_constant)" legend_constants[4] = "k33 in component model_parameters (first_order_rate_constant)" legend_constants[5] = "k34 in component model_parameters (first_order_rate_constant)" legend_constants[6] = "Ca in component model_parameters (micromolar)" legend_constants[7] = "k1 in component model_parameters (fifth_order_rate_constant)" legend_constants[8] = "k2 in component model_parameters (first_order_rate_constant)" legend_constants[9] = "k3 in component model_parameters (second_order_rate_constant)" legend_constants[10] = "k4 in component model_parameters (first_order_rate_constant)" legend_constants[11] = "k5 in component model_parameters (second_order_rate_constant)" legend_constants[12] = "k6 in component model_parameters (first_order_rate_constant)" legend_constants[13] = "k19 in component model_parameters (second_order_rate_constant)" legend_constants[14] = "k20 in component model_parameters (first_order_rate_constant)" legend_constants[15] = "k27 in component model_parameters (second_order_rate_constant)" legend_constants[16] = "k28 in component model_parameters (first_order_rate_constant)" legend_constants[17] = "k7 in component model_parameters (second_order_rate_constant)" legend_constants[18] = "k8 in component model_parameters (first_order_rate_constant)" legend_constants[19] = "k9 in component model_parameters (first_order_rate_constant)" legend_constants[20] = "k10 in component model_parameters (second_order_rate_constant)" legend_constants[21] = "k11 in component model_parameters (first_order_rate_constant)" legend_constants[22] = "k12 in component model_parameters (first_order_rate_constant)" legend_constants[23] = "k13 in component model_parameters (second_order_rate_constant)" legend_constants[24] = "k14 in component model_parameters (first_order_rate_constant)" legend_constants[25] = "k15 in component model_parameters (first_order_rate_constant)" legend_constants[26] = "k16 in component model_parameters (second_order_rate_constant)" legend_constants[27] = "k17 in component model_parameters (first_order_rate_constant)" legend_constants[28] = "k18 in component model_parameters (first_order_rate_constant)" legend_constants[29] = "k21 in component model_parameters (second_order_rate_constant)" legend_constants[30] = "k22 in component model_parameters (first_order_rate_constant)" legend_constants[31] = "k23 in component model_parameters (first_order_rate_constant)" legend_constants[32] = "k24 in component model_parameters (second_order_rate_constant)" legend_constants[33] = "k25 in component model_parameters (first_order_rate_constant)" legend_constants[34] = "k26 in component model_parameters (first_order_rate_constant)" legend_constants[35] = "k35 in component model_parameters (second_order_rate_constant)" legend_constants[36] = "k36 in component model_parameters (first_order_rate_constant)" legend_constants[37] = "k37 in component model_parameters (first_order_rate_constant)" legend_constants[38] = "k38 in component model_parameters (second_order_rate_constant)" legend_constants[39] = "k39 in component model_parameters (first_order_rate_constant)" legend_constants[40] = "k40 in component model_parameters (first_order_rate_constant)" legend_constants[41] = "k41 in component model_parameters (first_order_rate_constant)" legend_constants[42] = "k42 in component model_parameters (first_order_rate_constant)" legend_constants[43] = "t_half in component model_parameters (minute)" legend_constants[44] = "k43 in component model_parameters (first_order_rate_constant)" legend_rates[0] = "d/dt BMK1 in component BMK1 (micromolar)" legend_rates[1] = "d/dt MRNA in component MRNA (micromolar)" legend_rates[2] = "d/dt NFATc in component NFATc (micromolar)" legend_rates[3] = "d/dt NFATn in component NFATn (micromolar)" legend_rates[4] = "d/dt NFATpc in component NFATpc (micromolar)" legend_rates[5] = "d/dt NFATpn in component NFATpn (micromolar)" legend_rates[6] = "d/dt GSK3betac in component GSK3betac (micromolar)" legend_rates[7] = "d/dt GSK3betan in component GSK3betan (micromolar)" legend_rates[8] = "d/dt CaNc in component CaNc (micromolar)" legend_rates[9] = "d/dt CaNc_star in component CaNc_star (micromolar)" legend_rates[10] = "d/dt CaNn_star in component CaNn_star (micromolar)" legend_rates[11] = "d/dt CaNn in component CaNn (micromolar)" legend_rates[12] = "d/dt CaM in component CaM (micromolar)" legend_rates[13] = "d/dt CaMCa in component CaMCa (micromolar)" legend_rates[14] = "d/dt MCIP in component MCIP (micromolar)" legend_rates[15] = "d/dt MCIPp in component MCIPp (micromolar)" legend_rates[16] = "d/dt MCIPpp in component MCIPpp (micromolar)" legend_rates[17] = "d/dt Comp1 in component Comp1 (micromolar)" legend_rates[18] = "d/dt Comp2 in component Comp2 (micromolar)" legend_rates[19] = "d/dt Comp3 in component Comp3 (micromolar)" legend_rates[20] = "d/dt P1433 in component P1433 (micromolar)" legend_rates[21] = "d/dt MCIP_BMK1 in component MCIP_BMK1 (micromolar)" legend_rates[22] = "d/dt MCIPp_CaNc_star in component MCIPp_CaNc_star (micromolar)" legend_rates[23] = "d/dt MCIPp_GSK3betac in component MCIPp_GSK3betac (micromolar)" legend_rates[24] = "d/dt MCIPpp_CaNc_star in component MCIPpp_CaNc_star (micromolar)" legend_rates[25] = "d/dt NFATpc_CaNc_star in component NFATpc_CaNc_star (micromolar)" legend_rates[26] = "d/dt NFATc_GSK3betac in component NFATc_GSK3betac (micromolar)" legend_rates[27] = "d/dt NFATpn_CaNn_star in component NFATpn_CaNn_star (micromolar)" legend_rates[28] = "d/dt NFATn_GSK3betan in component NFATn_GSK3betan (micromolar)" return (legend_states, legend_algebraic, legend_voi, legend_constants) def initConsts(): constants = [0.0] * sizeConstants; states = [0.0] * sizeStates; states[0] = 0.012 states[1] = 3.33E-4 states[2] = 2E-5 states[3] = 4.99E-4 states[4] = 4.94E-3 states[5] = 8.01E-5 states[6] = 0.17 states[7] = 0.339 states[8] = 0.91 states[9] = 0.0275 states[10] = 0.0568 states[11] = 0.0057 states[12] = 25.2 states[13] = 7.88E-7 states[14] = 2.15E-4 states[15] = 7.76E-3 states[16] = 0.0798 states[17] = 5.21E-3 states[18] = 0.283 states[19] = 0.014 states[20] = 0.708 states[21] = 2.14E-5 states[22] = 1.07E-4 states[23] = 1.1E-3 states[24] = 1.1E-3 states[25] = 8.15E-5 states[26] = 1.36E-6 states[27] = 2.27E-6 states[28] = 8.46E-5 constants[0] = 0.4 constants[1] = 0.1 constants[2] = 0.1 constants[3] = 0.05 constants[4] = 0.114 constants[5] = 0.0552 constants[6] = 0.2 constants[7] = 5 constants[8] = 100 constants[9] = 2760 constants[10] = 0.072 constants[11] = 50 constants[12] = 0.0567 constants[13] = 0.5 constants[14] = 0.1 constants[15] = 0.4 constants[16] = 0.1 constants[17] = 5 constants[18] = 0.1 constants[19] = 0.5 constants[20] = 0.1 constants[21] = 0.1 constants[22] = 0.1 constants[23] = 0.5 constants[24] = 0.5 constants[25] = 0.1 constants[26] = 0.1 constants[27] = 0.1 constants[28] = 0.1 constants[29] = 0.15 constants[30] = 0.15 constants[31] = 0.15 constants[32] = 0.1 constants[33] = 0.15 constants[34] = 0.1 constants[35] = 0.15 constants[36] = 0.1 constants[37] = 0.2 constants[38] = 0.1 constants[39] = 0.1 constants[40] = 0.1 constants[41] = 0.02 constants[42] = 0.03 constants[43] = 15 constants[44] = 0.03 return (states, constants) def computeRates(voi, states, constants): rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic algebraic[4] = constants[7]*states[12]*(power(constants[6], 4.00000))-constants[8]*states[13] rates[12] = -algebraic[4] algebraic[5] = constants[9]*states[13]*states[8]-constants[10]*states[9] rates[8] = -algebraic[5] rates[11] = -algebraic[5] rates[13] = algebraic[4]-algebraic[5] algebraic[6] = constants[11]*states[9]*states[14]-constants[12]*states[17] rates[17] = algebraic[6] algebraic[7] = constants[13]*states[20]*states[16]-constants[14]*states[18] rates[18] = algebraic[7] algebraic[8] = constants[15]*states[4]*states[20]-constants[16]*states[19] rates[19] = algebraic[8] rates[20] = -(algebraic[7]+algebraic[8]) algebraic[9] = constants[17]*states[14]*states[0]-constants[18]*states[21] algebraic[10] = constants[19]*states[21] rates[0] = algebraic[10]-algebraic[9] rates[21] = algebraic[9]-algebraic[10] algebraic[12] = constants[20]*states[15]*states[9]-constants[21]*states[22] algebraic[13] = constants[22]*states[22] rates[22] = algebraic[12]-algebraic[13] algebraic[3] = constants[4]*states[9]-constants[5]*states[10] algebraic[15] = constants[35]*states[5]*states[10]-constants[36]*states[27] algebraic[17] = constants[37]*states[27] rates[10] = (algebraic[3]+algebraic[17])-algebraic[15] algebraic[16] = constants[23]*states[15]*states[6]-constants[24]*states[23] algebraic[18] = constants[25]*states[23] rates[23] = algebraic[16]-algebraic[18] rates[27] = algebraic[15]-algebraic[17] algebraic[2] = constants[2]*states[6]-constants[3]*states[7] algebraic[21] = constants[38]*states[3]*states[7]-constants[39]*states[28] algebraic[23] = constants[40]*states[28] rates[7] = (algebraic[2]+algebraic[23])-algebraic[21] algebraic[22] = constants[26]*states[16]*states[9]-constants[27]*states[24] algebraic[24] = constants[28]*states[24] rates[24] = algebraic[22]-algebraic[24] rates[28] = algebraic[21]-algebraic[23] algebraic[19] = algebraic[15]+algebraic[17] algebraic[25] = algebraic[21]+algebraic[23] algebraic[1] = constants[1]*states[5] rates[5] = algebraic[25]-(algebraic[1]+algebraic[19]) algebraic[11] = algebraic[9]+algebraic[10] algebraic[14] = algebraic[12]+algebraic[13] algebraic[20] = algebraic[16]+algebraic[18] algebraic[27] = algebraic[22]+algebraic[24] rates[15] = (algebraic[11]+algebraic[27])-(algebraic[14]+algebraic[20]) rates[16] = algebraic[20]-(algebraic[7]+algebraic[27]) algebraic[28] = constants[41]*states[3]-constants[42]*states[1] algebraic[0] = constants[0]*states[2] rates[3] = (algebraic[0]+algebraic[19])-(algebraic[25]+algebraic[28]) algebraic[26] = constants[29]*states[4]*states[9]-constants[30]*states[25] algebraic[29] = constants[31]*states[25] rates[9] = (algebraic[5]+algebraic[13]+algebraic[24]+algebraic[29])-(algebraic[3]+algebraic[6]+algebraic[12]+algebraic[22]+algebraic[26]) rates[25] = algebraic[26]-algebraic[29] algebraic[30] = constants[44]*states[1]-(log(2.00000)/constants[43])*states[14] rates[1] = algebraic[30]-algebraic[28] rates[14] = algebraic[14]-(algebraic[6]+algebraic[11]+algebraic[30]) algebraic[32] = constants[32]*states[2]*states[6]-constants[33]*states[26] algebraic[33] = constants[34]*states[26] rates[6] = (algebraic[18]+algebraic[33])-(algebraic[2]+algebraic[16]+algebraic[32]) rates[26] = algebraic[32]-algebraic[33] algebraic[31] = algebraic[26]+algebraic[29] algebraic[34] = algebraic[32]+algebraic[33] rates[2] = algebraic[31]-(algebraic[0]+algebraic[34]) rates[4] = (algebraic[1]+algebraic[34])-(algebraic[8]+algebraic[31]) return(rates) def computeAlgebraic(constants, states, voi): algebraic = array([[0.0] * len(voi)] * sizeAlgebraic) states = array(states) voi = array(voi) algebraic[4] = constants[7]*states[12]*(power(constants[6], 4.00000))-constants[8]*states[13] algebraic[5] = constants[9]*states[13]*states[8]-constants[10]*states[9] algebraic[6] = constants[11]*states[9]*states[14]-constants[12]*states[17] algebraic[7] = constants[13]*states[20]*states[16]-constants[14]*states[18] algebraic[8] = constants[15]*states[4]*states[20]-constants[16]*states[19] algebraic[9] = constants[17]*states[14]*states[0]-constants[18]*states[21] algebraic[10] = constants[19]*states[21] algebraic[12] = constants[20]*states[15]*states[9]-constants[21]*states[22] algebraic[13] = constants[22]*states[22] algebraic[3] = constants[4]*states[9]-constants[5]*states[10] algebraic[15] = constants[35]*states[5]*states[10]-constants[36]*states[27] algebraic[17] = constants[37]*states[27] algebraic[16] = constants[23]*states[15]*states[6]-constants[24]*states[23] algebraic[18] = constants[25]*states[23] algebraic[2] = constants[2]*states[6]-constants[3]*states[7] algebraic[21] = constants[38]*states[3]*states[7]-constants[39]*states[28] algebraic[23] = constants[40]*states[28] algebraic[22] = constants[26]*states[16]*states[9]-constants[27]*states[24] algebraic[24] = constants[28]*states[24] algebraic[19] = algebraic[15]+algebraic[17] algebraic[25] = algebraic[21]+algebraic[23] algebraic[1] = constants[1]*states[5] algebraic[11] = algebraic[9]+algebraic[10] algebraic[14] = algebraic[12]+algebraic[13] algebraic[20] = algebraic[16]+algebraic[18] algebraic[27] = algebraic[22]+algebraic[24] algebraic[28] = constants[41]*states[3]-constants[42]*states[1] algebraic[0] = constants[0]*states[2] algebraic[26] = constants[29]*states[4]*states[9]-constants[30]*states[25] algebraic[29] = constants[31]*states[25] algebraic[30] = constants[44]*states[1]-(log(2.00000)/constants[43])*states[14] algebraic[32] = constants[32]*states[2]*states[6]-constants[33]*states[26] algebraic[33] = constants[34]*states[26] algebraic[31] = algebraic[26]+algebraic[29] algebraic[34] = algebraic[32]+algebraic[33] 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)