# 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 = 4 sizeStates = 3 sizeConstants = 17 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 (hour)" legend_algebraic[0] = "Qv in component v (per_second)" legend_states[0] = "Vv in component v (mV)" legend_constants[0] = "tau_v in component v (second)" legend_constants[1] = "v_vm in component v (mV_second)" legend_algebraic[1] = "Qm in component m (per_second)" legend_constants[2] = "Qmax in component model_parameters (per_second)" legend_algebraic[3] = "D in component D (mV)" legend_constants[3] = "theta in component model_parameters (mV)" legend_constants[4] = "sigma in component model_parameters (mV)" legend_constants[16] = "Qa in component a (per_second)" legend_constants[14] = "Va in component a (mV)" legend_constants[5] = "Vao in component a (mV)" legend_states[1] = "Vm in component m (mV)" legend_constants[6] = "tau_m in component m (second)" legend_constants[7] = "v_mv in component m (mV_second)" legend_constants[8] = "v_maQao in component m (mV)" legend_states[2] = "H in component H (nM)" legend_constants[9] = "chi in component H (hour)" legend_constants[10] = "mu in component H (nM_second)" legend_algebraic[2] = "C in component D (dimensionless)" legend_constants[11] = "c0 in component D (dimensionless)" legend_constants[15] = "omega in component D (per_hour)" legend_constants[12] = "v_vc in component D (mV)" legend_constants[13] = "v_vh in component D (mV_per_nM)" legend_rates[0] = "d/dt Vv in component v (mV)" legend_rates[1] = "d/dt Vm in component m (mV)" legend_rates[2] = "d/dt H in component H (nM)" return (legend_states, legend_algebraic, legend_voi, legend_constants) def initConsts(): constants = [0.0] * sizeConstants; states = [0.0] * sizeStates; states[0] = 0.0 constants[0] = 10.0 constants[1] = -1.9 constants[2] = 100.0 constants[3] = 10.0 constants[4] = 3.0 constants[5] = 1.0 states[1] = 0.0 constants[6] = 10.0 constants[7] = -1.9 constants[8] = 1.0 states[2] = 15.0 constants[9] = 10.8 constants[10] = 3.6 constants[11] = 1.0 constants[12] = -6.3 constants[13] = 0.19 constants[14] = constants[5] constants[15] = (2.00000* pi)/24.0000 constants[16] = constants[2]/(1.00000+exp(-(constants[14]-constants[3])/constants[4])) return (states, constants) def computeRates(voi, states, constants): rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic algebraic[0] = constants[2]/(1.00000+exp(-(states[0]-constants[3])/constants[4])) rates[1] = ((constants[8]+constants[7]*algebraic[0])-states[1])/(constants[6]/3600.00) algebraic[1] = constants[2]/(1.00000+exp(-(states[1]-constants[3])/constants[4])) rates[2] = (constants[10]*algebraic[1]-states[2])/constants[9] algebraic[2] = constants[11]+cos(constants[15]*voi) algebraic[3] = constants[12]*algebraic[2]+constants[13]*states[2] rates[0] = ((constants[1]*algebraic[1]+algebraic[3])-states[0])/(constants[0]/3600.00) return(rates) def computeAlgebraic(constants, states, voi): algebraic = array([[0.0] * len(voi)] * sizeAlgebraic) states = array(states) voi = array(voi) algebraic[0] = constants[2]/(1.00000+exp(-(states[0]-constants[3])/constants[4])) algebraic[1] = constants[2]/(1.00000+exp(-(states[1]-constants[3])/constants[4])) algebraic[2] = constants[11]+cos(constants[15]*voi) algebraic[3] = constants[12]*algebraic[2]+constants[13]*states[2] 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)