# 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 = 0 sizeStates = 7 sizeConstants = 10 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 (minute)" legend_states[0] = "Ca_cyt in component Ca_cyt (micromolar)" legend_states[1] = "J_ERch in component J_ERch (micromolar)" legend_states[2] = "J_ERpump in component J_ERpump (micromolar)" legend_states[3] = "J_ERleak in component J_ERleak (micromolar)" legend_states[4] = "J_in in component J_in (micromolar)" legend_states[5] = "J_out in component J_out (micromolar)" legend_states[6] = "Ca_ER in component Ca_ER (micromolar)" legend_constants[0] = "beta in component J_ERch (dimensionless)" legend_constants[1] = "k_0ch in component J_ERch (micromolar_per_minute)" legend_constants[2] = "K_chcyt in component J_ERch (micromolar)" legend_constants[3] = "K_chER in component J_ERch (micromolar)" legend_constants[4] = "K_ERpump in component J_ERpump (micromolar)" legend_constants[5] = "K_pump in component J_ERpump (micromolar)" legend_constants[6] = "K_ERleak in component J_ERleak (per_minute)" legend_constants[7] = "K_0in in component J_in (micromolar_per_minute)" legend_constants[8] = "K_out in component J_out (per_minute)" legend_rates[0] = "d/dt Ca_cyt in component Ca_cyt (micromolar)" legend_rates[6] = "d/dt Ca_ER in component Ca_ER (micromolar)" legend_rates[1] = "d/dt J_ERch in component J_ERch (micromolar)" legend_rates[2] = "d/dt J_ERpump in component J_ERpump (micromolar)" legend_rates[3] = "d/dt J_ERleak in component J_ERleak (micromolar)" legend_rates[4] = "d/dt J_in in component J_in (micromolar)" legend_rates[5] = "d/dt J_out in component J_out (micromolar)" return (legend_states, legend_algebraic, legend_voi, legend_constants) def initConsts(): constants = [0.0] * sizeConstants; states = [0.0] * sizeStates; states[0] = 0.01 states[1] = 0.1 states[2] = 0.1 states[3] = 0.1 states[4] = 0.1 states[5] = 0.1 states[6] = 20 constants[0] = 1.7 constants[1] = 325 constants[2] = 0.45 constants[3] = 1 constants[4] = 25 constants[5] = 0.5 constants[6] = 1 constants[7] = 1.7 constants[8] = 10 constants[9] = constants[7]*1.00000 return (states, constants) def computeRates(voi, states, constants): rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic rates[4] = constants[9] rates[0] = (((states[1]-states[2])+states[3]+states[4])-states[5])*1.00000 rates[6] = ((states[2]-states[3])-states[1])*1.00000 rates[1] = constants[0]*constants[1]*(((power(states[0], 4.00000))/(power(constants[2], 4.00000)+power(states[0], 4.00000)))*((power(states[6], 2.00000))/(power(constants[3], 2.00000)+power(states[6], 2.00000))))*1.00000 rates[2] = constants[4]*((power(states[0], 2.00000))/(power(constants[5], 2.00000)+power(states[0], 2.00000))) rates[3] = ((constants[6]*states[6])/1.00000)*1.00000 rates[5] = ((constants[8]*states[0])/1.00000)*1.00000 return(rates) def computeAlgebraic(constants, states, voi): algebraic = array([[0.0] * len(voi)] * sizeAlgebraic) states = array(states) voi = array(voi) 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)