# 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 = 17 sizeStates = 5 sizeConstants = 32 from math import * from numpy import * def createLegends(): legend_states = [""] * sizeStates legend_rates = [""] * sizeStates legend_algebraic = [""] * sizeAlgebraic legend_voi = "" legend_constants = [""] * sizeConstants legend_states[0] = "s in component synaptic_input (dimensionless)" legend_algebraic[15] = "sum_g_syn_e_s in component synaptic_coupling (nanoS)" legend_algebraic[0] = "V_public in component synaptic_input (millivolt)" legend_voi = "time in component environment (millisecond)" legend_states[1] = "V in component membrane (millivolt)" legend_constants[0] = "C in component membrane (picoF)" legend_constants[1] = "i_app in component membrane (picoA)" legend_algebraic[12] = "i_NaP in component persistent_sodium_current (picoA)" legend_algebraic[6] = "i_Na in component fast_sodium_current (picoA)" legend_algebraic[10] = "i_K in component potassium_current (picoA)" legend_algebraic[13] = "i_L in component leakage_current (picoA)" legend_algebraic[14] = "i_tonic_e in component tonic_current (picoA)" legend_algebraic[16] = "i_syn_e in component synaptic_input (picoA)" legend_constants[2] = "E_Na in component fast_sodium_current (millivolt)" legend_constants[3] = "g_Na in component fast_sodium_current (nanoS)" legend_algebraic[1] = "m_infinity in component fast_sodium_current_m_gate (dimensionless)" legend_states[2] = "n in component fast_sodium_current_n_gate (dimensionless)" legend_constants[4] = "theta_m in component fast_sodium_current_m_gate (millivolt)" legend_constants[5] = "sigma_m in component fast_sodium_current_m_gate (millivolt)" legend_algebraic[2] = "n_infinity in component fast_sodium_current_n_gate (dimensionless)" legend_algebraic[7] = "tau_n in component fast_sodium_current_n_gate (millisecond)" legend_constants[6] = "tau_n_max in component fast_sodium_current_n_gate (millisecond)" legend_constants[7] = "theta_n in component fast_sodium_current_n_gate (millivolt)" legend_constants[8] = "sigma_n in component fast_sodium_current_n_gate (millivolt)" legend_constants[9] = "g_K in component potassium_current (nanoS)" legend_constants[10] = "E_K in component potassium_current (millivolt)" legend_states[3] = "n in component potassium_current_n_gate (dimensionless)" legend_algebraic[3] = "n_infinity in component potassium_current_n_gate (dimensionless)" legend_algebraic[8] = "tau_n in component potassium_current_n_gate (millisecond)" legend_constants[11] = "tau_n_max in component potassium_current_n_gate (millisecond)" legend_constants[12] = "theta_n in component potassium_current_n_gate (millivolt)" legend_constants[13] = "sigma_n in component potassium_current_n_gate (millivolt)" legend_constants[14] = "g_NaP in component persistent_sodium_current (nanoS)" legend_algebraic[11] = "m_infinity in component persistent_sodium_current_m_gate (dimensionless)" legend_states[4] = "h in component persistent_sodium_current_h_gate (dimensionless)" legend_constants[15] = "theta_m in component persistent_sodium_current_m_gate (millivolt)" legend_constants[16] = "sigma_m in component persistent_sodium_current_m_gate (millivolt)" legend_algebraic[4] = "h_infinity in component persistent_sodium_current_h_gate (dimensionless)" legend_algebraic[9] = "tau_h in component persistent_sodium_current_h_gate (millisecond)" legend_constants[17] = "tau_h_max in component persistent_sodium_current_h_gate (millisecond)" legend_constants[18] = "theta_h in component persistent_sodium_current_h_gate (millivolt)" legend_constants[19] = "sigma_h in component persistent_sodium_current_h_gate (millivolt)" legend_constants[20] = "g_L in component leakage_current (nanoS)" legend_constants[21] = "E_L in component leakage_current (millivolt)" legend_constants[22] = "E_syn_e in component tonic_current (millivolt)" legend_constants[23] = "g_tonic_e in component tonic_current (nanoS)" legend_algebraic[5] = "s_infinity in component synaptic_input (dimensionless)" legend_constants[24] = "kr in component synaptic_input (dimensionless)" legend_constants[25] = "tau_s in component synaptic_input (millisecond)" legend_constants[26] = "sigma_s in component synaptic_input (millivolt)" legend_constants[27] = "theta_s in component synaptic_input (millivolt)" legend_constants[28] = "g_syn_e_1_2 in component synaptic_coupling (nanoS)" legend_constants[29] = "g_syn_e_1_3 in component synaptic_coupling (nanoS)" legend_constants[30] = "g_syn_e_1_4 in component synaptic_coupling (nanoS)" legend_constants[31] = "g_syn_e_1_5 in component synaptic_coupling (nanoS)" legend_rates[1] = "d/dt V in component membrane (millivolt)" legend_rates[2] = "d/dt n in component fast_sodium_current_n_gate (dimensionless)" legend_rates[3] = "d/dt n in component potassium_current_n_gate (dimensionless)" legend_rates[4] = "d/dt h in component persistent_sodium_current_h_gate (dimensionless)" legend_rates[0] = "d/dt s in component synaptic_input (dimensionless)" return (legend_states, legend_algebraic, legend_voi, legend_constants) def initConsts(): constants = [0.0] * sizeConstants; states = [0.0] * sizeStates; states[0] = 1 states[1] = -50.0 constants[0] = 21.0 constants[1] = 0.0 constants[2] = 50.0 constants[3] = 28.0 states[2] = 0.01 constants[4] = -34.0 constants[5] = -5.0 constants[6] = 10.0 constants[7] = -29.0 constants[8] = -4.0 constants[9] = 11.2 constants[10] = -85.0 states[3] = 0.01 constants[11] = 10.0 constants[12] = -29.0 constants[13] = -4.0 constants[14] = 2.8 states[4] = 0.46 constants[15] = -40.0 constants[16] = -6.0 constants[17] = 10000.0 constants[18] = -48.0 constants[19] = 6.0 constants[20] = 2.8 constants[21] = -57.5 constants[22] = 0.0 constants[23] = 0.0 constants[24] = 1.0 constants[25] = 5.0 constants[26] = -5.0 constants[27] = -10.0 constants[28] = 0.10 constants[29] = 0.10 constants[30] = 0.10 constants[31] = 0.10 return (states, constants) def computeRates(voi, states, constants): rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic algebraic[5] = 1.00000/(1.00000+exp((states[1]-constants[27])/constants[26])) rates[0] = ((1.00000-states[0])*algebraic[5]--(constants[24]*states[0]))/constants[25] algebraic[2] = 1.00000/(1.00000+exp((states[1]-constants[7])/constants[8])) algebraic[7] = constants[6]/cosh((states[1]-constants[7])/(2.00000*constants[8])) rates[2] = (algebraic[2]-states[2])/algebraic[7] algebraic[3] = 1.00000/(1.00000+exp((states[1]-constants[12])/constants[13])) algebraic[8] = constants[11]/cosh((states[1]-constants[12])/(2.00000*constants[13])) rates[3] = (algebraic[3]-states[3])/algebraic[8] algebraic[4] = 1.00000/(1.00000+exp((states[1]-constants[18])/constants[19])) algebraic[9] = constants[17]/cosh((states[1]-constants[18])/(2.00000*constants[19])) rates[4] = (algebraic[4]-states[4])/algebraic[9] algebraic[11] = 1.00000/(1.00000+exp((states[1]-constants[15])/constants[16])) algebraic[12] = constants[14]*algebraic[11]*states[4]*(states[1]-constants[2]) algebraic[1] = 1.00000/(1.00000+exp((states[1]-constants[4])/constants[5])) algebraic[6] = constants[3]*(power(algebraic[1], 3.00000))*(1.00000-states[2])*(states[1]-constants[2]) algebraic[10] = constants[9]*(power(states[3], 4.00000))*(states[1]-constants[10]) algebraic[13] = constants[20]*(states[1]-constants[21]) algebraic[14] = constants[23]*(states[1]-constants[22]) algebraic[15] = constants[28]*states[0]+constants[29]*states[0]+constants[30]*states[0]+constants[31]*states[0] algebraic[16] = algebraic[15]*(states[1]-constants[22]) rates[1] = (-(algebraic[12]+algebraic[6]+algebraic[10]+algebraic[13]+algebraic[14]+algebraic[16])+constants[1])/constants[0] return(rates) def computeAlgebraic(constants, states, voi): algebraic = array([[0.0] * len(voi)] * sizeAlgebraic) states = array(states) voi = array(voi) algebraic[5] = 1.00000/(1.00000+exp((states[1]-constants[27])/constants[26])) algebraic[2] = 1.00000/(1.00000+exp((states[1]-constants[7])/constants[8])) algebraic[7] = constants[6]/cosh((states[1]-constants[7])/(2.00000*constants[8])) algebraic[3] = 1.00000/(1.00000+exp((states[1]-constants[12])/constants[13])) algebraic[8] = constants[11]/cosh((states[1]-constants[12])/(2.00000*constants[13])) algebraic[4] = 1.00000/(1.00000+exp((states[1]-constants[18])/constants[19])) algebraic[9] = constants[17]/cosh((states[1]-constants[18])/(2.00000*constants[19])) algebraic[11] = 1.00000/(1.00000+exp((states[1]-constants[15])/constants[16])) algebraic[12] = constants[14]*algebraic[11]*states[4]*(states[1]-constants[2]) algebraic[1] = 1.00000/(1.00000+exp((states[1]-constants[4])/constants[5])) algebraic[6] = constants[3]*(power(algebraic[1], 3.00000))*(1.00000-states[2])*(states[1]-constants[2]) algebraic[10] = constants[9]*(power(states[3], 4.00000))*(states[1]-constants[10]) algebraic[13] = constants[20]*(states[1]-constants[21]) algebraic[14] = constants[23]*(states[1]-constants[22]) algebraic[15] = constants[28]*states[0]+constants[29]*states[0]+constants[30]*states[0]+constants[31]*states[0] algebraic[16] = algebraic[15]*(states[1]-constants[22]) algebraic[0] = states[1] 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)