# 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 = 11 sizeStates = 4 sizeConstants = 23 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] = "C in component membrane (picofarad)" legend_algebraic[5] = "I_Ca in component I_Ca (picoampere)" legend_algebraic[0] = "I_K in component I_K (picoampere)" legend_algebraic[7] = "I_SK in component I_SK (picoampere)" legend_algebraic[10] = "I_DA in component I_DA (picoampere)" legend_constants[1] = "gK in component I_K (nanosiemens)" legend_constants[2] = "VK in component model_parameters (millivolt)" legend_states[1] = "n in component n (dimensionless)" legend_algebraic[1] = "n_infinity in component n (dimensionless)" legend_constants[3] = "lambda in component n (dimensionless)" legend_constants[4] = "tau_n in component n (millisecond)" legend_constants[5] = "vn in component n (millivolt)" legend_constants[6] = "sn in component n (millivolt)" legend_constants[7] = "gCa in component I_Ca (nanosiemens)" legend_constants[8] = "VCa in component model_parameters (millivolt)" legend_algebraic[4] = "m_infinity in component m (dimensionless)" legend_constants[9] = "vm in component m (millivolt)" legend_constants[10] = "sm in component m (millivolt)" legend_constants[11] = "gSK in component I_SK (nanosiemens)" legend_algebraic[6] = "s_infinity in component I_SK (dimensionless)" legend_constants[12] = "ks in component I_SK (micromolar)" legend_states[2] = "Ca in component Ca (micromolar)" legend_algebraic[9] = "I_BK in component I_DA (picoampere)" legend_constants[13] = "gBK in component I_DA (nanosiemens)" legend_algebraic[8] = "f_infinity in component f (dimensionless)" legend_constants[14] = "vf in component f (millivolt)" legend_constants[15] = "sf in component f (millivolt)" legend_states[3] = "h in component h (dimensionless)" legend_algebraic[2] = "h_infinity in component h (dimensionless)" legend_constants[16] = "tau_h in component h (millisecond)" legend_constants[17] = "vh in component h (millivolt)" legend_constants[18] = "sh in component h (millivolt)" legend_constants[19] = "fc in component Ca (dimensionless)" legend_constants[20] = "alpha in component Ca (micromolar_femtocoulomb)" legend_constants[21] = "kc in component Ca (first_order_rate_constant)" legend_algebraic[3] = "PRL in component PRL (dimensionless)" legend_constants[22] = "kPRL in component PRL (micromolar_4)" legend_rates[0] = "d/dt V in component membrane (millivolt)" legend_rates[1] = "d/dt n in component n (dimensionless)" legend_rates[3] = "d/dt h in component h (dimensionless)" legend_rates[2] = "d/dt Ca in component Ca (micromolar)" return (legend_states, legend_algebraic, legend_voi, legend_constants) def initConsts(): constants = [0.0] * sizeConstants; states = [0.0] * sizeStates; states[0] = -60 constants[0] = 10 constants[1] = 4 constants[2] = -75 states[1] = 0.1 constants[3] = 0.7 constants[4] = 30 constants[5] = -5 constants[6] = 10 constants[7] = 2 constants[8] = 50 constants[9] = -20 constants[10] = 12 constants[11] = 1.7 constants[12] = 0.5 states[2] = 0.1 constants[13] = 0.2 constants[14] = -20 constants[15] = 5.6 states[3] = 0.1 constants[16] = 20 constants[17] = -60 constants[18] = 5 constants[19] = 0.01 constants[20] = 0.0015 constants[21] = 0.16 constants[22] = 1 return (states, constants) def computeRates(voi, states, constants): rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic algebraic[1] = 1.00000/(1.00000+exp((constants[5]-states[0])/constants[6])) rates[1] = (constants[3]*(algebraic[1]-states[1]))/constants[4] algebraic[2] = 1.00000/(1.00000+exp((states[0]-constants[17])/constants[18])) rates[3] = (algebraic[2]-states[3])/constants[16] algebraic[4] = 1.00000/(1.00000+exp((constants[9]-states[0])/constants[10])) algebraic[5] = constants[7]*algebraic[4]*(states[0]-constants[8]) rates[2] = -constants[19]*(constants[20]*algebraic[5]+constants[21]*states[2]) algebraic[0] = constants[1]*states[1]*(states[0]-constants[2]) algebraic[6] = (power(states[2], 2.00000))/(power(states[2], 2.00000)+power(constants[12], 2.00000)) algebraic[7] = constants[11]*algebraic[6]*(states[0]-constants[2]) algebraic[8] = 1.00000/(1.00000+exp((constants[14]-states[0])/constants[15])) algebraic[9] = constants[13]*algebraic[8]*(states[0]-constants[2]) algebraic[10] = algebraic[9] rates[0] = -(algebraic[5]+algebraic[0]+algebraic[7]+algebraic[10])/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[5]-states[0])/constants[6])) algebraic[2] = 1.00000/(1.00000+exp((states[0]-constants[17])/constants[18])) algebraic[4] = 1.00000/(1.00000+exp((constants[9]-states[0])/constants[10])) algebraic[5] = constants[7]*algebraic[4]*(states[0]-constants[8]) algebraic[0] = constants[1]*states[1]*(states[0]-constants[2]) algebraic[6] = (power(states[2], 2.00000))/(power(states[2], 2.00000)+power(constants[12], 2.00000)) algebraic[7] = constants[11]*algebraic[6]*(states[0]-constants[2]) algebraic[8] = 1.00000/(1.00000+exp((constants[14]-states[0])/constants[15])) algebraic[9] = constants[13]*algebraic[8]*(states[0]-constants[2]) algebraic[10] = algebraic[9] algebraic[3] = constants[22]*(power(states[2], 4.00000)) 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)