# 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 = 10 sizeStates = 5 sizeConstants = 27 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 (second)" legend_constants[0] = "k_0 in component Constants (flux)" legend_constants[1] = "k_1 in component Constants (per_second)" legend_constants[2] = "k_2 in component Constants (per_second)" legend_constants[3] = "k_3 in component Constants (per_second)" legend_constants[4] = "k_4 in component Constants (per_second)" legend_constants[5] = "k_5 in component Constants (per_second)" legend_constants[6] = "k_6 in component Constants (per_second)" legend_constants[7] = "k_7 in component Constants (per_second)" legend_constants[8] = "k_8 in component Constants (flux)" legend_constants[9] = "k_9 in component Constants (flux)" legend_constants[10] = "k_10 in component Constants (flux)" legend_constants[11] = "k_11 in component Constants (flux)" legend_constants[12] = "C_PLC_T in component Constants (micromolar)" legend_constants[13] = "K_D in component Constants (micromolar)" legend_constants[14] = "K_P in component Constants (micromolar)" legend_constants[15] = "K_R in component Constants (micromolar)" legend_constants[16] = "K_G in component Constants (micromolar)" legend_constants[17] = "K_S in component Constants (micromolar)" legend_constants[18] = "K_ER in component Constants (micromolar)" legend_constants[19] = "K_C1 in component Constants (micromolar)" legend_constants[20] = "K_C2 in component Constants (micromolar)" legend_constants[21] = "beta in component Constants (dimensionless)" legend_constants[22] = "lambda in component Constants (dimensionless)" legend_constants[23] = "rho in component Constants (dimensionless)" legend_constants[24] = "n in component Constants (dimensionless)" legend_constants[25] = "m in component Constants (dimensionless)" legend_constants[26] = "w in component Constants (dimensionless)" legend_algebraic[1] = "R_APLC in component R_values (dimensionless)" legend_algebraic[8] = "R_PKC in component R_values (dimensionless)" legend_algebraic[3] = "R_G in component R_values (dimensionless)" legend_algebraic[9] = "R_DG in component R_values (dimensionless)" legend_algebraic[0] = "R_IP_3 in component R_values (dimensionless)" legend_algebraic[2] = "R_Cyt1 in component R_values (dimensionless)" legend_algebraic[4] = "R_Cyt2 in component R_values (dimensionless)" legend_algebraic[6] = "R_ER in component R_values (dimensionless)" legend_states[0] = "APLC in component APLC (micromolar)" legend_algebraic[7] = "DG in component DG (micromolar)" legend_states[1] = "C_cyt in component C_cyt (micromolar)" legend_states[2] = "G in component G_GTP (micromolar)" legend_states[3] = "IP_3 in component IP_3 (micromolar)" legend_states[4] = "C_ER in component C_ER (micromolar)" legend_algebraic[5] = "PLC in component APLC (micromolar)" legend_rates[2] = "d/dt G in component G_GTP (micromolar)" legend_rates[0] = "d/dt APLC in component APLC (micromolar)" legend_rates[3] = "d/dt IP_3 in component IP_3 (micromolar)" legend_rates[1] = "d/dt C_cyt in component C_cyt (micromolar)" legend_rates[4] = "d/dt C_ER in component C_ER (micromolar)" return (legend_states, legend_algebraic, legend_voi, legend_constants) def initConsts(): constants = [0.0] * sizeConstants; states = [0.0] * sizeStates; constants[0] = 1e-4 constants[1] = 3.4 constants[2] = 4 constants[3] = 4.5 constants[4] = 1.2 constants[5] = 0.12 constants[6] = 14 constants[7] = 2 constants[8] = 10.5 constants[9] = 0.6 constants[10] = 3 constants[11] = 0.26 constants[12] = 0.01 constants[13] = 0.01 constants[14] = 0.004 constants[15] = 0.2 constants[16] = 0.025 constants[17] = 0.025 constants[18] = 0.075 constants[19] = 1 constants[20] = 2 constants[21] = 0.05 constants[22] = 0.001 constants[23] = 0.2 constants[24] = 4 constants[25] = 2 constants[26] = 3 states[0] = 0.001 states[1] = 0.2 states[2] = 0.001 states[3] = 0.001 states[4] = 1 return (states, constants) def computeRates(voi, states, constants): rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic rates[3] = constants[6]*states[0]-constants[7]*states[3] algebraic[0] = (power(states[3], 3.00000))/(power(constants[17], 3.00000)+power(states[3], 3.00000)) algebraic[2] = states[1]/(constants[19]+states[1]) algebraic[4] = states[1]/(constants[20]+states[1]) algebraic[6] = (power(states[4], constants[26]))/(power(constants[18], constants[26])+power(states[4], constants[26])) rates[1] = constants[21]*((constants[23]*(constants[8]*algebraic[0]*algebraic[6]-constants[9]*algebraic[2])-constants[10]*algebraic[4])+constants[11]) rates[4] = constants[22]*(-constants[8]*algebraic[0]*algebraic[6]+constants[9]*algebraic[2]) algebraic[1] = states[0]/(constants[14]+states[0]) algebraic[7] = states[3] algebraic[8] = ((algebraic[7]/(constants[13]+algebraic[7]))*states[1])/(constants[15]+states[1]) rates[2] = ((constants[0]+constants[1]*states[2])-constants[2]*algebraic[1]*states[2])-constants[3]*algebraic[8]*states[2] algebraic[3] = (power(states[2], constants[24]))/(power(constants[16], constants[24])+power(states[2], constants[24])) algebraic[9] = (power(algebraic[7], constants[25]))/(power(constants[13], constants[25])+power(algebraic[7], constants[25])) algebraic[5] = constants[12]-states[0] rates[0] = constants[4]*algebraic[3]*algebraic[9]*algebraic[5]-constants[5]*states[0] return(rates) def computeAlgebraic(constants, states, voi): algebraic = array([[0.0] * len(voi)] * sizeAlgebraic) states = array(states) voi = array(voi) algebraic[0] = (power(states[3], 3.00000))/(power(constants[17], 3.00000)+power(states[3], 3.00000)) algebraic[2] = states[1]/(constants[19]+states[1]) algebraic[4] = states[1]/(constants[20]+states[1]) algebraic[6] = (power(states[4], constants[26]))/(power(constants[18], constants[26])+power(states[4], constants[26])) algebraic[1] = states[0]/(constants[14]+states[0]) algebraic[7] = states[3] algebraic[8] = ((algebraic[7]/(constants[13]+algebraic[7]))*states[1])/(constants[15]+states[1]) algebraic[3] = (power(states[2], constants[24]))/(power(constants[16], constants[24])+power(states[2], constants[24])) algebraic[9] = (power(algebraic[7], constants[25]))/(power(constants[13], constants[25])+power(algebraic[7], constants[25])) algebraic[5] = constants[12]-states[0] 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)