# 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 = 8 sizeStates = 3 sizeConstants = 22 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 (ms)" legend_states[0] = "u in component membrane (dimensionless)" legend_constants[0] = "Cm in component membrane (uF_per_cm2)" legend_algebraic[0] = "Vm in component membrane (mV)" legend_constants[1] = "V_0 in component membrane (mV)" legend_constants[2] = "V_fi in component membrane (mV)" legend_algebraic[2] = "J_fi in component fast_inward_current (per_ms)" legend_algebraic[4] = "J_so in component slow_outward_current (per_ms)" legend_algebraic[6] = "J_si in component slow_inward_current (per_ms)" legend_algebraic[7] = "Istim in component stimulus_protocol (per_ms)" legend_algebraic[1] = "p in component p (dimensionless)" legend_constants[3] = "u_c in component p (dimensionless)" legend_algebraic[3] = "q in component q (dimensionless)" legend_constants[4] = "u_v in component q (dimensionless)" legend_constants[21] = "tau_d in component fast_inward_current (ms)" legend_constants[5] = "g_fi_max in component fast_inward_current (mS_per_cm2)" legend_states[1] = "v in component fast_inward_current_v_gate (dimensionless)" legend_algebraic[5] = "tau_v_minus in component fast_inward_current_v_gate (ms)" legend_constants[6] = "tau_v1_minus in component fast_inward_current_v_gate (ms)" legend_constants[7] = "tau_v2_minus in component fast_inward_current_v_gate (ms)" legend_constants[8] = "tau_v_plus in component fast_inward_current_v_gate (ms)" legend_constants[9] = "tau_0 in component slow_outward_current (ms)" legend_constants[10] = "tau_r in component slow_outward_current (ms)" legend_constants[11] = "tau_si in component slow_inward_current (ms)" legend_constants[12] = "u_csi in component slow_inward_current (dimensionless)" legend_constants[13] = "k in component slow_inward_current (dimensionless)" legend_states[2] = "w in component slow_inward_current_w_gate (dimensionless)" legend_constants[14] = "tau_w_minus in component slow_inward_current_w_gate (ms)" legend_constants[15] = "tau_w_plus in component slow_inward_current_w_gate (ms)" legend_constants[16] = "IstimStart in component stimulus_protocol (ms)" legend_constants[17] = "IstimEnd in component stimulus_protocol (ms)" legend_constants[18] = "IstimAmplitude in component stimulus_protocol (per_ms)" legend_constants[19] = "IstimPeriod in component stimulus_protocol (ms)" legend_constants[20] = "IstimPulseDuration in component stimulus_protocol (ms)" legend_rates[0] = "d/dt u in component membrane (dimensionless)" legend_rates[1] = "d/dt v in component fast_inward_current_v_gate (dimensionless)" legend_rates[2] = "d/dt w in component slow_inward_current_w_gate (dimensionless)" return (legend_states, legend_algebraic, legend_voi, legend_constants) def initConsts(): constants = [0.0] * sizeConstants; states = [0.0] * sizeStates; states[0] = 0 constants[0] = 1 constants[1] = -85 constants[2] = 15 constants[3] = 0.13 constants[4] = 0.04 constants[5] = 4 states[1] = 1 constants[6] = 1250 constants[7] = 19.6 constants[8] = 3.33 constants[9] = 12.5 constants[10] = 33.33 constants[11] = 29 constants[12] = 0.85 constants[13] = 10 states[2] = 1 constants[14] = 41 constants[15] = 870 constants[16] = 10 constants[17] = 50000 constants[18] = -0.2 constants[19] = 1000 constants[20] = 1 constants[21] = constants[0]/constants[5] return (states, constants) def computeRates(voi, states, constants): rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic algebraic[1] = custom_piecewise([less(states[0] , constants[3]), 0.00000 , True, 1.00000]) rates[2] = ((1.00000-algebraic[1])*(1.00000-states[2]))/constants[14]-(algebraic[1]*states[2])/constants[15] algebraic[3] = custom_piecewise([less(states[0] , constants[4]), 0.00000 , True, 1.00000]) algebraic[5] = algebraic[3]*constants[6]+(1.00000-algebraic[3])*constants[7] rates[1] = ((1.00000-algebraic[1])*(1.00000-states[1]))/algebraic[5]-(algebraic[1]*states[1])/constants[8] algebraic[2] = (-states[1]*algebraic[1]*(1.00000-states[0])*(states[0]-constants[3]))/constants[21] algebraic[4] = (states[0]*(1.00000-algebraic[1]))/constants[9]+algebraic[1]/constants[10] algebraic[6] = (-states[2]*(1.00000+tanh(constants[13]*(states[0]-constants[12]))))/(2.00000*constants[11]) algebraic[7] = custom_piecewise([greater_equal(voi , constants[16]) & less_equal(voi , constants[17]) & less_equal((voi-constants[16])-floor((voi-constants[16])/constants[19])*constants[19] , constants[20]), constants[18] , True, 0.00000]) rates[0] = -(algebraic[2]+algebraic[4]+algebraic[6]+algebraic[7]) return(rates) def computeAlgebraic(constants, states, voi): algebraic = array([[0.0] * len(voi)] * sizeAlgebraic) states = array(states) voi = array(voi) algebraic[1] = custom_piecewise([less(states[0] , constants[3]), 0.00000 , True, 1.00000]) algebraic[3] = custom_piecewise([less(states[0] , constants[4]), 0.00000 , True, 1.00000]) algebraic[5] = algebraic[3]*constants[6]+(1.00000-algebraic[3])*constants[7] algebraic[2] = (-states[1]*algebraic[1]*(1.00000-states[0])*(states[0]-constants[3]))/constants[21] algebraic[4] = (states[0]*(1.00000-algebraic[1]))/constants[9]+algebraic[1]/constants[10] algebraic[6] = (-states[2]*(1.00000+tanh(constants[13]*(states[0]-constants[12]))))/(2.00000*constants[11]) algebraic[7] = custom_piecewise([greater_equal(voi , constants[16]) & less_equal(voi , constants[17]) & less_equal((voi-constants[16])-floor((voi-constants[16])/constants[19])*constants[19] , constants[20]), constants[18] , True, 0.00000]) algebraic[0] = constants[1]+states[0]*(constants[2]-constants[1]) 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)