# 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 = 12 sizeStates = 4 sizeConstants = 5 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_states[0] = "V in component membrane (millivolt)" legend_constants[0] = "Cm in component membrane (microF)" legend_algebraic[4] = "i_Na in component sodium_channel (nanoA)" legend_algebraic[10] = "i_K in component potassium_channel (nanoA)" legend_algebraic[11] = "i_Leak in component leakage_current (nanoA)" legend_constants[1] = "g_Na_max in component sodium_channel (microS)" legend_algebraic[0] = "g_Na in component sodium_channel (microS)" legend_constants[2] = "E_Na in component sodium_channel (millivolt)" legend_states[1] = "m in component sodium_channel_m_gate (dimensionless)" legend_states[2] = "h in component sodium_channel_h_gate (dimensionless)" legend_algebraic[1] = "alpha_m in component sodium_channel_m_gate (per_second)" legend_algebraic[5] = "beta_m in component sodium_channel_m_gate (per_second)" legend_algebraic[2] = "alpha_h in component sodium_channel_h_gate (per_second)" legend_algebraic[6] = "beta_h in component sodium_channel_h_gate (per_second)" legend_algebraic[8] = "g_K1 in component potassium_channel (microS)" legend_algebraic[9] = "g_K2 in component potassium_channel (microS)" legend_states[3] = "n in component potassium_channel_n_gate (dimensionless)" legend_algebraic[3] = "alpha_n in component potassium_channel_n_gate (per_second)" legend_algebraic[7] = "beta_n in component potassium_channel_n_gate (per_second)" legend_constants[3] = "g_L in component leakage_current (microS)" legend_constants[4] = "E_L in component leakage_current (millivolt)" legend_rates[0] = "d/dt V in component membrane (millivolt)" legend_rates[1] = "d/dt m in component sodium_channel_m_gate (dimensionless)" legend_rates[2] = "d/dt h in component sodium_channel_h_gate (dimensionless)" legend_rates[3] = "d/dt n in component potassium_channel_n_gate (dimensionless)" return (legend_states, legend_algebraic, legend_voi, legend_constants) def initConsts(): constants = [0.0] * sizeConstants; states = [0.0] * sizeStates; states[0] = -87 constants[0] = 12 constants[1] = 400000 constants[2] = 40 states[1] = 0.01 states[2] = 0.8 states[3] = 0.01 constants[3] = 75 constants[4] = -60 return (states, constants) def computeRates(voi, states, constants): rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic algebraic[1] = (100.000*(-states[0]-48.0000))/(exp((-states[0]-48.0000)/15.0000)-1.00000) algebraic[5] = (120.000*(states[0]+8.00000))/(exp((states[0]+8.00000)/5.00000)-1.00000) rates[1] = algebraic[1]*(1.00000-states[1])-algebraic[5]*states[1] algebraic[2] = 170.000*exp((-states[0]-90.0000)/20.0000) algebraic[6] = 1000.00/(1.00000+exp((-states[0]-42.0000)/10.0000)) rates[2] = algebraic[2]*(1.00000-states[2])-algebraic[6]*states[2] algebraic[3] = (0.100000*(-states[0]-50.0000))/(exp((-states[0]-50.0000)/10.0000)-1.00000) algebraic[7] = 2.00000*exp((-states[0]-90.0000)/80.0000) rates[3] = algebraic[3]*(1.00000-states[3])-algebraic[7]*states[3] algebraic[0] = (power(states[1], 3.00000))*states[2]*constants[1] algebraic[4] = (algebraic[0]+140.000)*(states[0]-constants[2]) algebraic[8] = 1200.00*exp((-states[0]-90.0000)/50.0000)+15.0000*exp((states[0]+90.0000)/60.0000) algebraic[9] = 1200.00*(power(states[3], 4.00000)) algebraic[10] = (algebraic[8]+algebraic[9])*(states[0]+100.000) algebraic[11] = constants[3]*(states[0]-constants[4]) rates[0] = -(algebraic[4]+algebraic[10]+algebraic[11])/constants[0] return(rates) def computeAlgebraic(constants, states, voi): algebraic = array([[0.0] * len(voi)] * sizeAlgebraic) states = array(states) voi = array(voi) algebraic[1] = (100.000*(-states[0]-48.0000))/(exp((-states[0]-48.0000)/15.0000)-1.00000) algebraic[5] = (120.000*(states[0]+8.00000))/(exp((states[0]+8.00000)/5.00000)-1.00000) algebraic[2] = 170.000*exp((-states[0]-90.0000)/20.0000) algebraic[6] = 1000.00/(1.00000+exp((-states[0]-42.0000)/10.0000)) algebraic[3] = (0.100000*(-states[0]-50.0000))/(exp((-states[0]-50.0000)/10.0000)-1.00000) algebraic[7] = 2.00000*exp((-states[0]-90.0000)/80.0000) algebraic[0] = (power(states[1], 3.00000))*states[2]*constants[1] algebraic[4] = (algebraic[0]+140.000)*(states[0]-constants[2]) algebraic[8] = 1200.00*exp((-states[0]-90.0000)/50.0000)+15.0000*exp((states[0]+90.0000)/60.0000) algebraic[9] = 1200.00*(power(states[3], 4.00000)) algebraic[10] = (algebraic[8]+algebraic[9])*(states[0]+100.000) algebraic[11] = constants[3]*(states[0]-constants[4]) 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)