Generated Code
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The raw code is available.
# Size of variable arrays:
sizeAlgebraic = 2
sizeStates = 15
sizeConstants = 21
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] = "Arg in component Arg (micromolar)"
legend_algebraic[0] = "S in component Arg (flux)"
legend_states[1] = "Fe3 in component Fe3 (micromolar)"
legend_states[2] = "Fe3_Arg in component Fe3_Arg (micromolar)"
legend_states[3] = "Fe2_Arg in component Fe2_Arg (micromolar)"
legend_states[4] = "Fe2 in component Fe2 (micromolar)"
legend_constants[0] = "k1 in component model_constants (second_order_rate_constant)"
legend_constants[1] = "k_1 in component model_constants (first_order_rate_constant)"
legend_constants[2] = "k4 in component model_constants (second_order_rate_constant)"
legend_constants[3] = "k_4 in component model_constants (first_order_rate_constant)"
legend_states[5] = "Fe3_NO in component Fe3_NO (micromolar)"
legend_states[6] = "Fe2_NO in component Fe2_NO (micromolar)"
legend_constants[4] = "O2 in component model_constants (micromolar)"
legend_states[7] = "Fe3_NOHA in component Fe3_NOHA (micromolar)"
legend_states[8] = "NOHA in component NOHA (micromolar)"
legend_constants[5] = "k2 in component model_constants (first_order_rate_constant)"
legend_constants[6] = "k13 in component model_constants (second_order_rate_constant)"
legend_constants[7] = "k14 in component model_constants (first_order_rate_constant)"
legend_constants[8] = "k8 in component model_constants (first_order_rate_constant)"
legend_constants[9] = "k_8 in component model_constants (second_order_rate_constant)"
legend_constants[10] = "k3 in component model_constants (first_order_rate_constant)"
legend_states[9] = "Fe2_NOHA in component Fe2_NOHA (micromolar)"
legend_constants[11] = "k9 in component model_constants (first_order_rate_constant)"
legend_constants[12] = "k_9 in component model_constants (second_order_rate_constant)"
legend_states[10] = "Fe3_O2_Arg in component Fe3_O2_Arg (micromolar)"
legend_constants[13] = "k5 in component model_constants (second_order_rate_constant)"
legend_constants[14] = "k_5 in component model_constants (first_order_rate_constant)"
legend_constants[15] = "k6 in component model_constants (first_order_rate_constant)"
legend_constants[16] = "k7 in component model_constants (first_order_rate_constant)"
legend_states[11] = "Fe3_O2_NOHA in component Fe3_O2_NOHA (micromolar)"
legend_constants[17] = "k_10 in component model_constants (first_order_rate_constant)"
legend_constants[18] = "k10 in component model_constants (second_order_rate_constant)"
legend_constants[19] = "k11 in component model_constants (first_order_rate_constant)"
legend_constants[20] = "k12 in component model_constants (first_order_rate_constant)"
legend_states[12] = "NO in component NO (micromolar)"
legend_algebraic[1] = "dNOdt in component NO (flux)"
legend_states[13] = "citrulline in component citrulline (micromolar)"
legend_states[14] = "NO3 in component NO3 (micromolar)"
legend_rates[0] = "d/dt Arg in component Arg (micromolar)"
legend_rates[1] = "d/dt Fe3 in component Fe3 (micromolar)"
legend_rates[2] = "d/dt Fe3_Arg in component Fe3_Arg (micromolar)"
legend_rates[4] = "d/dt Fe2 in component Fe2 (micromolar)"
legend_rates[3] = "d/dt Fe2_Arg in component Fe2_Arg (micromolar)"
legend_rates[10] = "d/dt Fe3_O2_Arg in component Fe3_O2_Arg (micromolar)"
legend_rates[7] = "d/dt Fe3_NOHA in component Fe3_NOHA (micromolar)"
legend_rates[9] = "d/dt Fe2_NOHA in component Fe2_NOHA (micromolar)"
legend_rates[11] = "d/dt Fe3_O2_NOHA in component Fe3_O2_NOHA (micromolar)"
legend_rates[5] = "d/dt Fe3_NO in component Fe3_NO (micromolar)"
legend_rates[6] = "d/dt Fe2_NO in component Fe2_NO (micromolar)"
legend_rates[12] = "d/dt NO in component NO (micromolar)"
legend_rates[13] = "d/dt citrulline in component citrulline (micromolar)"
legend_rates[14] = "d/dt NO3 in component NO3 (micromolar)"
legend_rates[8] = "d/dt NOHA in component NOHA (micromolar)"
return (legend_states, legend_algebraic, legend_voi, legend_constants)
def initConsts():
constants = [0.0] * sizeConstants; states = [0.0] * sizeStates;
states[0] = 100.0
states[1] = 0.045
states[2] = 0.0
states[3] = 0.0
states[4] = 0.0
constants[0] = 0.1
constants[1] = 0.1
constants[2] = 1.89
constants[3] = 11.4
states[5] = 0.0
states[6] = 0.0
constants[4] = 172.0
states[7] = 0.0
states[8] = 0.0
constants[5] = 0.91
constants[6] = 0.033
constants[7] = 53.9
constants[8] = 0.1
constants[9] = 0.1
constants[10] = 0.91
states[9] = 0.0
constants[11] = 11.4
constants[12] = 1.89
states[10] = 0.0
constants[13] = 2.58
constants[14] = 98.0
constants[15] = 12.6
constants[16] = 0.91
states[11] = 0.0
constants[17] = 89.9
constants[18] = 3.33
constants[19] = 29.4
constants[20] = 0.91
states[12] = 0.0
states[13] = 0.0
states[14] = 0.0
return (states, constants)
def computeRates(voi, states, constants):
rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic
rates[1] = (constants[1]*states[2]+constants[7]*states[5]+constants[6]*states[6]*constants[4]+constants[8]*states[7])-(constants[0]*states[0]*states[1]+constants[5]*states[1]+constants[9]*states[8]*states[1])
rates[2] = constants[0]*states[1]*states[0]-(constants[1]*states[2]+constants[10]*states[2])
rates[4] = (constants[5]*states[1]+constants[3]*states[3]+constants[11]*states[9])-(constants[2]*states[4]*states[0]+constants[12]*states[4]*states[8])
rates[3] = (constants[10]*states[2]+constants[14]*states[10]+constants[2]*states[4]*states[0])-(constants[13]*states[3]*constants[4]+constants[3]*states[3])
rates[10] = constants[13]*states[3]*constants[4]-(constants[15]*states[10]+constants[14]*states[10])
rates[7] = (constants[15]*states[10]+constants[9]*states[1]*states[8])-(constants[16]*states[7]+constants[8]*states[7])
rates[9] = (constants[16]*states[7]+constants[17]*states[11]+constants[12]*states[4]*states[8])-(constants[11]*states[9]+constants[18]*states[9]*constants[4])
rates[11] = constants[18]*states[9]*constants[4]-(constants[19]*states[11]+constants[17]*states[11])
rates[5] = constants[19]*states[11]-(constants[7]*states[5]+constants[20]*states[5])
rates[6] = constants[20]*states[5]-constants[6]*states[6]*constants[4]
rates[12] = constants[7]*states[5]
rates[13] = constants[19]*states[11]
rates[14] = constants[6]*states[6]*constants[4]
rates[8] = (constants[8]*states[7]+constants[11]*states[9])-(constants[9]*states[1]*states[8]+constants[12]*states[4]*states[8])
algebraic[0] = (constants[0]*states[0]*states[1]+constants[2]*states[0]*states[4])-(constants[1]*states[2]+constants[3]*states[3])
rates[0] = (constants[1]*states[2]+constants[3]*states[3]+algebraic[0])-(constants[0]*states[0]*states[1]+constants[2]*states[0]*states[4])
return(rates)
def computeAlgebraic(constants, states, voi):
algebraic = array([[0.0] * len(voi)] * sizeAlgebraic)
states = array(states)
voi = array(voi)
algebraic[0] = (constants[0]*states[0]*states[1]+constants[2]*states[0]*states[4])-(constants[1]*states[2]+constants[3]*states[3])
algebraic[1] = constants[7]*states[5]
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)