# 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 = 4 sizeConstants = 4 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_states[0] = "Ca in component Ca (micromolar)" legend_constants[0] = "k1 in component reaction_constants (second_order_rate_constant)" legend_constants[1] = "k1_ in component reaction_constants (first_order_rate_constant)" legend_constants[2] = "k2 in component reaction_constants (second_order_rate_constant)" legend_constants[3] = "k2_ in component reaction_constants (first_order_rate_constant)" legend_states[1] = "Trop in component Trop (micromolar)" legend_states[2] = "CaTrop in component CaTrop (micromolar)" legend_states[3] = "Ca2Trop in component Ca2Trop (micromolar)" legend_rates[0] = "d/dt Ca in component Ca (micromolar)" legend_rates[1] = "d/dt Trop in component Trop (micromolar)" legend_rates[2] = "d/dt CaTrop in component CaTrop (micromolar)" legend_rates[3] = "d/dt Ca2Trop in component Ca2Trop (micromolar)" return (legend_states, legend_algebraic, legend_voi, legend_constants) def initConsts(): constants = [0.0] * sizeConstants; states = [0.0] * sizeStates; states[0] = 0.05 constants[0] = 2.033E14 constants[1] = 2642.0 constants[2] = 1.017E14 constants[3] = 13.21 states[1] = 360.0 states[2] = 0.01 states[3] = 0.01 return (states, constants) def computeRates(voi, states, constants): rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic rates[0] = (constants[1]*states[2]+constants[3]*states[3])-(constants[0]*states[0]*states[1]+constants[2]*states[0]*states[2]) rates[1] = constants[1]*states[2]-constants[0]*states[0]*states[1] rates[2] = (constants[0]*states[0]*states[1]+constants[3]*states[3])-(constants[1]*states[2]+constants[2]*states[0]*states[2]) rates[3] = constants[2]*states[0]*states[2]-constants[3]*states[3] 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)