# 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 = 4 sizeConstants = 24 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 (millisecond)" legend_states[0] = "V in component membrane (millivolt)" legend_constants[0] = "Cm in component membrane (femtofarad)" legend_algebraic[4] = "Ica in component Ica (femtoampere)" legend_algebraic[6] = "Is1 in component Is1 (femtoampere)" legend_algebraic[9] = "Is2 in component Is2 (femtoampere)" legend_algebraic[8] = "Il in component Il (femtoampere)" legend_algebraic[7] = "Ik in component Ik (femtoampere)" legend_constants[1] = "gCa in component Ica (picosiemens)" legend_constants[2] = "VCa in component Ica (millivolt)" legend_algebraic[0] = "m_infinity in component m (dimensionless)" legend_constants[3] = "vm in component m (millivolt)" legend_constants[4] = "sm in component m (millivolt)" legend_constants[5] = "gs1 in component Is1 (picosiemens)" legend_constants[6] = "VK in component Ik (millivolt)" legend_states[1] = "s1 in component s1 (dimensionless)" legend_algebraic[1] = "s1_infinity in component s1 (dimensionless)" legend_constants[7] = "autos1 in component s1 (dimensionless)" legend_constants[8] = "s1knot in component s1 (dimensionless)" legend_constants[9] = "tau_s1 in component s1 (millisecond)" legend_constants[10] = "vs1 in component s1 (millivolt)" legend_constants[11] = "ss1 in component s1 (millivolt)" legend_constants[12] = "gK in component Ik (picosiemens)" legend_states[2] = "n in component n (dimensionless)" legend_algebraic[2] = "n_infinity in component n (dimensionless)" legend_constants[13] = "tau_n_bar in component n (millisecond)" legend_algebraic[5] = "tau_n in component n (millisecond)" legend_constants[14] = "vn in component n (millivolt)" legend_constants[15] = "sn in component n (millivolt)" legend_constants[16] = "gl in component Il (picosiemens)" legend_constants[17] = "Vl in component Il (millivolt)" legend_constants[18] = "gs2 in component Is2 (picosiemens)" legend_states[3] = "s2 in component s2 (dimensionless)" legend_algebraic[3] = "s2_infinity in component s2 (dimensionless)" legend_constants[19] = "autos2 in component s2 (dimensionless)" legend_constants[20] = "s2knot in component s2 (dimensionless)" legend_constants[21] = "tau_s2 in component s2 (millisecond)" legend_constants[22] = "vs2 in component s2 (millivolt)" legend_constants[23] = "ss2 in component s2 (millivolt)" legend_rates[0] = "d/dt V in component membrane (millivolt)" legend_rates[1] = "d/dt s1 in component s1 (dimensionless)" legend_rates[2] = "d/dt n in component n (dimensionless)" legend_rates[3] = "d/dt s2 in component s2 (dimensionless)" return (legend_states, legend_algebraic, legend_voi, legend_constants) def initConsts(): constants = [0.0] * sizeConstants; states = [0.0] * sizeStates; states[0] = -40.0 constants[0] = 4525.0 constants[1] = 280.0 constants[2] = 100.0 constants[3] = -22.0 constants[4] = 7.5 constants[5] = 20.0 constants[6] = -80.0 states[1] = 0.9 constants[7] = 1 constants[8] = 1 constants[9] = 1000.0 constants[10] = -50.0 constants[11] = 5 constants[12] = 1300.0 states[2] = 0.0 constants[13] = 8.25 constants[14] = -9.0 constants[15] = 10.0 constants[16] = 25.0 constants[17] = -40.0 constants[18] = 16 states[3] = 0.5 constants[19] = 1 constants[20] = 0.49 constants[21] = 30000.0 constants[22] = -40.0 constants[23] = 15 return (states, constants) def computeRates(voi, states, constants): rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic algebraic[1] = 1.00000/(1.00000+exp((constants[10]-states[0])/constants[11])) rates[1] = constants[7]*((algebraic[1]-states[1])/constants[9])+(1.00000-constants[7])*(constants[8]-states[1]) algebraic[3] = 1.00000/(1.00000+exp((constants[22]-states[0])/constants[23])) rates[3] = constants[19]*((algebraic[3]-states[3])/constants[21])+(1.00000-constants[19])*(constants[20]-states[3]) algebraic[2] = 1.00000/(1.00000+exp((constants[14]-states[0])/constants[15])) algebraic[5] = constants[13]/(1.00000+exp((states[0]-constants[14])/constants[15])) rates[2] = (algebraic[2]-states[2])/algebraic[5] algebraic[0] = 1.00000/(1.00000+exp((constants[3]-states[0])/constants[4])) algebraic[4] = constants[1]*algebraic[0]*(states[0]-constants[2]) algebraic[6] = constants[5]*states[1]*(states[0]-constants[6]) algebraic[9] = constants[18]*states[3]*(states[0]-constants[6]) algebraic[8] = constants[16]*(states[0]-constants[17]) algebraic[7] = constants[12]*states[2]*(states[0]-constants[6]) rates[0] = -(algebraic[4]+algebraic[6]+algebraic[9]+algebraic[8]+algebraic[7])/constants[0] return(rates) def computeAlgebraic(constants, states, voi): algebraic = array([[0.0] * len(voi)] * sizeAlgebraic) states = array(states) voi = array(voi) algebraic[1] = 1.00000/(1.00000+exp((constants[10]-states[0])/constants[11])) algebraic[3] = 1.00000/(1.00000+exp((constants[22]-states[0])/constants[23])) algebraic[2] = 1.00000/(1.00000+exp((constants[14]-states[0])/constants[15])) algebraic[5] = constants[13]/(1.00000+exp((states[0]-constants[14])/constants[15])) algebraic[0] = 1.00000/(1.00000+exp((constants[3]-states[0])/constants[4])) algebraic[4] = constants[1]*algebraic[0]*(states[0]-constants[2]) algebraic[6] = constants[5]*states[1]*(states[0]-constants[6]) algebraic[9] = constants[18]*states[3]*(states[0]-constants[6]) algebraic[8] = constants[16]*(states[0]-constants[17]) algebraic[7] = constants[12]*states[2]*(states[0]-constants[6]) 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)