# 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 = 5 sizeStates = 2 sizeConstants = 7 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 (second)" legend_algebraic[0] = "kappa_L1 in component rate_constants (per_second)" legend_constants[0] = "kappa_P1 in component rate_constants (per_second)" legend_algebraic[2] = "kappa_L2 in component rate_constants (per_second)" legend_constants[1] = "kappa_P2 in component rate_constants (per_second)" legend_constants[2] = "kappa_L2_0 in component rate_constants (per_second)" legend_constants[3] = "kappa_L2_1 in component rate_constants (per_second)" legend_algebraic[1] = "Kd_Ca in component rate_constants (nanomolar)" legend_constants[4] = "n in component rate_constants (dimensionless)" legend_states[0] = "Ca_i in component cytosolic_calcium (nanomolar)" legend_constants[5] = "Ca_o in component cytosolic_calcium (nanomolar)" legend_algebraic[3] = "Ca_i_ss in component cytosolic_calcium (nanomolar)" legend_constants[6] = "gamma in component cytosolic_calcium (dimensionless)" legend_states[1] = "Ca_s in component subspace_calcium (nanomolar)" legend_algebraic[4] = "Ca_s_ss in component subspace_calcium (nanomolar)" legend_rates[0] = "d/dt Ca_i in component cytosolic_calcium (nanomolar)" legend_rates[1] = "d/dt Ca_s in component subspace_calcium (nanomolar)" return (legend_states, legend_algebraic, legend_voi, legend_constants) def initConsts(): constants = [0.0] * sizeConstants; states = [0.0] * sizeStates; constants[0] = 0.132 constants[1] = 3.78 constants[2] = 0.054 constants[3] = 2.4 constants[4] = 3 states[0] = 100.0 constants[5] = 1000000.0 constants[6] = 0.24 states[1] = 10.0 return (states, constants) def computeRates(voi, states, constants): rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic algebraic[0] = custom_piecewise([greater_equal(voi , 0.00000) & less(voi , 30.0000), 5.00000e-06 , True, 2.00000e-05]) algebraic[1] = custom_piecewise([greater_equal(voi , 0.00000) & less(voi , 60.0000), 1.00000 , True, 0.500000]) algebraic[2] = constants[2]+constants[3]/(1.00000+algebraic[1]/states[0]**constants[4]) rates[0] = -(algebraic[0]+constants[0]+constants[6]*(algebraic[2]+constants[1]))*states[0]+constants[6]*algebraic[2]*states[1]+algebraic[0]*constants[5] rates[1] = (algebraic[2]+constants[1])*states[0]-algebraic[2]*states[1] return(rates) def computeAlgebraic(constants, states, voi): algebraic = array([[0.0] * len(voi)] * sizeAlgebraic) states = array(states) voi = array(voi) algebraic[0] = custom_piecewise([greater_equal(voi , 0.00000) & less(voi , 30.0000), 5.00000e-06 , True, 2.00000e-05]) algebraic[1] = custom_piecewise([greater_equal(voi , 0.00000) & less(voi , 60.0000), 1.00000 , True, 0.500000]) algebraic[2] = constants[2]+constants[3]/(1.00000+algebraic[1]/states[0]**constants[4]) algebraic[3] = constants[5]/(1.00000+constants[0]/algebraic[0]) algebraic[4] = algebraic[3]*(1.00000+constants[1]/algebraic[2]) return algebraic def custom_piecewise(cases): """Compute result of a piecewise function""" return select(cases[0::2],cases[1::2]) 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)