# 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 = 9 sizeStates = 5 sizeConstants = 20 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_constants[0] = "tau_c in component nucleotides (second)" legend_constants[1] = "eta in component nucleotides (dimensionless)" legend_constants[2] = "v in component nucleotides (dimensionless)" legend_constants[3] = "k in component nucleotides (dimensionless)" legend_algebraic[0] = "phi in component nucleotides (dimensionless)" legend_states[0] = "ADP in component nucleotides (dimensionless)" legend_states[1] = "ATP in component nucleotides (dimensionless)" legend_constants[4] = "C_m in component membrane (femtofarad)" legend_algebraic[3] = "I_Ca in component Ca_current (femtoampere)" legend_algebraic[4] = "I_K in component K_current (femtoampere)" legend_algebraic[7] = "I_KCa in component Ca_activated_K_current (femtoampere)" legend_algebraic[8] = "I_KATP in component ATP_sensitive_K_current (femtoampere)" legend_states[2] = "V in component membrane (millivolt)" legend_constants[5] = "g_Ca_ in component Ca_current (picosiemens)" legend_constants[6] = "V_Ca in component Ca_current (millivolt)" legend_constants[7] = "v_m in component Ca_current (millivolt)" legend_constants[8] = "s_m in component Ca_current (millivolt)" legend_algebraic[1] = "m_infinity in component Ca_current (dimensionless)" legend_constants[9] = "g_K_ in component K_current (picosiemens)" legend_constants[10] = "V_K in component K_current (millivolt)" legend_states[3] = "n in component K_channel_activation (dimensionless)" legend_constants[11] = "g_KCa_ in component Ca_activated_K_current (picosiemens)" legend_constants[12] = "k_D in component Ca_activated_K_current (micromolar)" legend_states[4] = "c in component cytosolic_Ca (micromolar)" legend_algebraic[6] = "omega in component Ca_activated_K_current (dimensionless)" legend_constants[13] = "g_KATP_ in component ATP_sensitive_K_current (picosiemens)" legend_constants[14] = "tau_n in component K_channel_activation (millisecond)" legend_constants[15] = "v_n in component K_channel_activation (millivolt)" legend_constants[16] = "s_n in component K_channel_activation (millivolt)" legend_algebraic[2] = "n_infinity in component K_channel_activation (dimensionless)" legend_algebraic[5] = "J_mem in component Ca_influx (micromolar_per_ms)" legend_constants[17] = "f in component Ca_influx (dimensionless)" legend_constants[18] = "alpha in component Ca_influx (micromolar_per_fA_ms)" legend_constants[19] = "k_c in component Ca_influx (per_millisecond)" legend_rates[1] = "d/dt ATP in component nucleotides (dimensionless)" legend_rates[0] = "d/dt ADP in component nucleotides (dimensionless)" legend_rates[2] = "d/dt V in component membrane (millivolt)" legend_rates[3] = "d/dt n in component K_channel_activation (dimensionless)" legend_rates[4] = "d/dt c in component cytosolic_Ca (micromolar)" return (legend_states, legend_algebraic, legend_voi, legend_constants) def initConsts(): constants = [0.0] * sizeConstants; states = [0.0] * sizeStates; constants[0] = 1200 constants[1] = 185 constants[2] = 10 constants[3] = 20 states[0] = 0.085817 states[1] = 2.1047 constants[4] = 5300 states[2] = -67.018 constants[5] = 1200 constants[6] = 25 constants[7] = -20 constants[8] = 12 constants[9] = 3000 constants[10] = -75 states[3] = 0.00011 constants[11] = 300 constants[12] = 0.3 states[4] = 0.15666 constants[13] = 350 constants[14] = 16 constants[15] = -16 constants[16] = 5.6 constants[17] = 0.001 constants[18] = 0.00000225 constants[19] = 0.1 return (states, constants) def computeRates(voi, states, constants): rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic algebraic[0] = states[1]*(power(1.00000+constants[3]*states[0], 2.00000)) rates[1] = (constants[2]-algebraic[0])/(1000.00*constants[0]) rates[0] = (algebraic[0]-constants[1]*states[0])/(1000.00*constants[0]) algebraic[2] = 1.00000/(1.00000+exp((constants[15]-states[2])/constants[16])) rates[3] = (algebraic[2]-states[3])/constants[14] algebraic[1] = 1.00000/(1.00000+exp((constants[7]-states[2])/constants[8])) algebraic[3] = constants[5]*algebraic[1]*(states[2]-constants[6]) algebraic[5] = -constants[17]*(constants[18]*algebraic[3]+constants[19]*states[4]) rates[4] = algebraic[5] algebraic[4] = constants[9]*states[3]*(states[2]-constants[10]) algebraic[6] = 1.00000/(1.00000+constants[12]/states[4]) algebraic[7] = constants[11]*algebraic[6]*(states[2]-constants[10]) algebraic[8] = ((states[2]-constants[10])*constants[13])/states[1] rates[2] = -(algebraic[3]+algebraic[4]+algebraic[7]+algebraic[8])/constants[4] return(rates) def computeAlgebraic(constants, states, voi): algebraic = array([[0.0] * len(voi)] * sizeAlgebraic) states = array(states) voi = array(voi) algebraic[0] = states[1]*(power(1.00000+constants[3]*states[0], 2.00000)) algebraic[2] = 1.00000/(1.00000+exp((constants[15]-states[2])/constants[16])) algebraic[1] = 1.00000/(1.00000+exp((constants[7]-states[2])/constants[8])) algebraic[3] = constants[5]*algebraic[1]*(states[2]-constants[6]) algebraic[5] = -constants[17]*(constants[18]*algebraic[3]+constants[19]*states[4]) algebraic[4] = constants[9]*states[3]*(states[2]-constants[10]) algebraic[6] = 1.00000/(1.00000+constants[12]/states[4]) algebraic[7] = constants[11]*algebraic[6]*(states[2]-constants[10]) algebraic[8] = ((states[2]-constants[10])*constants[13])/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)