# 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 = 3 sizeStates = 4 sizeConstants = 23 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] = "RA in component RA (nanomolar)" legend_constants[21] = "v_s1 in component v_s1 (flux)" legend_constants[0] = "k_d1 in component model_parameters (second_order_rate_constant)" legend_constants[1] = "C in component RA (nanomolar)" legend_constants[2] = "k_d5 in component RA (first_order_rate_constant)" legend_states[1] = "M_C in component M_C (nanomolar)" legend_constants[3] = "V_0 in component M_C (flux)" legend_constants[4] = "V_sC in component M_C (flux)" legend_states[2] = "F in component F (nanomolar)" legend_constants[5] = "n in component M_C (dimensionless)" legend_constants[6] = "K_A in component M_C (nanomolar)" legend_constants[7] = "k_d3 in component model_parameters (first_order_rate_constant)" legend_states[3] = "C in component C (nanomolar)" legend_constants[8] = "k_s2 in component model_parameters (first_order_rate_constant)" legend_constants[9] = "k_d2 in component model_parameters (first_order_rate_constant)" legend_constants[10] = "k_s3 in component model_parameters (first_order_rate_constant)" legend_constants[22] = "M_F in component M_F (nanomolar)" legend_constants[11] = "m in component F (dimensionless)" legend_constants[12] = "K_I in component F (nanomolar)" legend_constants[13] = "k_d4 in component model_parameters (first_order_rate_constant)" legend_constants[14] = "k_s1 in component model_parameters (first_order_rate_constant)" legend_constants[15] = "RALDH2_0 in component model_parameters (nanomolar)" legend_constants[16] = "x in component model_parameters (dimensionless)" legend_constants[17] = "L in component model_parameters (dimensionless)" legend_constants[18] = "M_0 in component model_parameters (nanomolar)" legend_algebraic[0] = "alpha_1 in component alpha_1 (dimensionless)" legend_constants[19] = "K_r1 in component model_parameters (nanomolar)" legend_algebraic[1] = "alpha_2 in component alpha_2 (dimensionless)" legend_constants[20] = "K_r2 in component model_parameters (nanomolar)" legend_algebraic[2] = "rho in component rho (dimensionless)" legend_rates[0] = "d/dt RA in component RA (nanomolar)" legend_rates[1] = "d/dt M_C in component M_C (nanomolar)" legend_rates[3] = "d/dt C in component C (nanomolar)" legend_rates[2] = "d/dt F in component F (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 constants[1] = 0.1 constants[2] = 0 states[1] = 0.1 constants[3] = 0.365 constants[4] = 7.1 states[2] = 0.0001 constants[5] = 2 constants[6] = 0.2 constants[7] = 1 states[3] = 0.1 constants[8] = 1 constants[9] = 0.28 constants[10] = 1 constants[11] = 2 constants[12] = 0.2 constants[13] = 1 constants[14] = 1 constants[15] = 7.1 constants[16] = 15 constants[17] = 50 constants[18] = 5 constants[19] = 1 constants[20] = 1 constants[21] = constants[14]*constants[15]*(1.00000-constants[16]/constants[17]) constants[22] = (constants[18]*constants[16])/constants[17] return (states, constants) def computeRates(voi, states, constants): rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic rates[0] = (constants[21]-constants[0]*constants[1]*states[0])-constants[2]*states[0] rates[1] = (constants[3]+(constants[4]*(power(states[2], constants[5])))/(power(constants[6], constants[5])+power(states[2], constants[5])))-constants[7]*states[1] rates[3] = constants[8]*states[1]-constants[9]*states[3] rates[2] = (constants[10]*constants[22]*(power(constants[12], constants[11])))/(power(constants[12], constants[11])+power(states[0], constants[11]))-constants[13]*states[2] return(rates) def computeAlgebraic(constants, states, voi): algebraic = array([[0.0] * len(voi)] * sizeAlgebraic) states = array(states) voi = array(voi) algebraic[0] = states[0]/(states[0]+constants[19]) algebraic[1] = states[2]/(states[2]+constants[20]) algebraic[2] = algebraic[1]/algebraic[0] 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)