# 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 = 1 sizeStates = 3 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 (hour)" legend_states[0] = "M in component M (nanomolar)" legend_constants[0] = "vs in component M (flux)" legend_constants[1] = "vm in component M (flux)" legend_constants[2] = "Km in component M (nanomolar)" legend_constants[3] = "KI in component M (nanomolar)" legend_constants[4] = "n in component M (dimensionless)" legend_states[1] = "FN in component FN (nanomolar)" legend_states[2] = "FC in component FC (nanomolar)" legend_algebraic[0] = "Ft in component FC (nanomolar)" legend_constants[5] = "ks in component FC (first_order_rate_constant)" legend_constants[6] = "vd in component FC (flux)" legend_constants[7] = "Kd in component FC (nanomolar)" legend_constants[8] = "k1 in component parameters (first_order_rate_constant)" legend_constants[9] = "k2 in component parameters (first_order_rate_constant)" legend_rates[0] = "d/dt M in component M (nanomolar)" legend_rates[2] = "d/dt FC in component FC (nanomolar)" legend_rates[1] = "d/dt FN in component FN (nanomolar)" return (legend_states, legend_algebraic, legend_voi, legend_constants) def initConsts(): constants = [0.0] * sizeConstants; states = [0.0] * sizeStates; states[0] = 0.1 constants[0] = 1.6 constants[1] = 0.505 constants[2] = 0.5 constants[3] = 1.0 constants[4] = 4.0 states[1] = 0.1 states[2] = 0.1 constants[5] = 0.5 constants[6] = 1.4 constants[7] = 0.13 constants[8] = 0.5 constants[9] = 0.6 return (states, constants) def computeRates(voi, states, constants): rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic rates[0] = constants[0]*((power(constants[3], constants[4]))/(power(constants[3], constants[4])+power(states[1], constants[4])))-constants[1]*(states[0]/(constants[2]+states[0])) rates[2] = (constants[5]*states[0]+constants[9]*states[1])-(constants[6]*(states[2]/(constants[7]+states[2]))+constants[8]*states[2]) rates[1] = constants[8]*states[2]-constants[9]*states[1] return(rates) def computeAlgebraic(constants, states, voi): algebraic = array([[0.0] * len(voi)] * sizeAlgebraic) states = array(states) voi = array(voi) algebraic[0] = states[2]+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)