Generated Code
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The raw code is available.
# Size of variable arrays:
sizeAlgebraic = 3
sizeStates = 11
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_constants[0] = "EGF in component EGF (dimensionless)"
legend_constants[1] = "inhibitor in component inhibitor (dimensionless)"
legend_constants[2] = "pro_EGFR in component pro_EGFR (dimensionless)"
legend_states[0] = "EGFR in component EGFR (dimensionless)"
legend_states[1] = "EGF_EGFR in component EGF_EGFR (dimensionless)"
legend_states[2] = "EGFR_i in component EGFR_i (dimensionless)"
legend_constants[3] = "EGF_binding_kb in component model_parameters (first_order_rate_constant)"
legend_constants[4] = "EGF_binding_kf in component model_parameters (first_order_rate_constant)"
legend_constants[5] = "inhibitor_binding_kb in component model_parameters (first_order_rate_constant)"
legend_constants[6] = "inhibitor_binding_kf in component model_parameters (first_order_rate_constant)"
legend_constants[7] = "EGFR_turnover in component model_parameters (first_order_rate_constant)"
legend_states[3] = "EGF_EGFR_i in component EGF_EGFR_i (dimensionless)"
legend_constants[8] = "k1_EGFR_phosphorylation in component model_parameters (first_order_rate_constant)"
legend_states[4] = "pEGFR in component pEGFR (dimensionless)"
legend_states[5] = "pEGFR_Akt in component pEGFR_Akt (dimensionless)"
legend_states[6] = "Akt in component Akt (dimensionless)"
legend_constants[9] = "k1_pEGFR_degradation in component model_parameters (first_order_rate_constant)"
legend_constants[10] = "k1_Akt_phosphorylation in component model_parameters (first_order_rate_constant)"
legend_constants[11] = "k1_pEGFR_Akt in component model_parameters (first_order_rate_constant)"
legend_constants[12] = "k2_pEGFR_Akt in component model_parameters (first_order_rate_constant)"
legend_states[7] = "pAkt in component pAkt (dimensionless)"
legend_constants[13] = "k1_pAkt_dephosphorylation in component model_parameters (first_order_rate_constant)"
legend_states[8] = "S6 in component S6 (dimensionless)"
legend_states[9] = "pAkt_S6 in component pAkt_S6 (dimensionless)"
legend_constants[14] = "k1_pAkt_S6 in component model_parameters (first_order_rate_constant)"
legend_constants[15] = "k2_pAkt_S6 in component model_parameters (first_order_rate_constant)"
legend_constants[16] = "k1_S6_phosphorylation in component model_parameters (first_order_rate_constant)"
legend_states[10] = "pS6 in component pS6 (dimensionless)"
legend_constants[17] = "k1_pS6_dephosphorylation in component model_parameters (first_order_rate_constant)"
legend_algebraic[0] = "pEGFR_total in component pEGFR_total (dimensionless)"
legend_constants[18] = "pEGFR_scalefactor in component pEGFR_total (dimensionless)"
legend_algebraic[1] = "pAkt_total in component pAkt_total (dimensionless)"
legend_constants[19] = "pAkt_scalefactor in component pAkt_total (dimensionless)"
legend_algebraic[2] = "pS6_total in component pS6_total (dimensionless)"
legend_constants[20] = "pS6_scalefactor in component pS6_total (dimensionless)"
legend_rates[0] = "d/dt EGFR in component EGFR (dimensionless)"
legend_rates[1] = "d/dt EGF_EGFR in component EGF_EGFR (dimensionless)"
legend_rates[2] = "d/dt EGFR_i in component EGFR_i (dimensionless)"
legend_rates[3] = "d/dt EGF_EGFR_i in component EGF_EGFR_i (dimensionless)"
legend_rates[4] = "d/dt pEGFR in component pEGFR (dimensionless)"
legend_rates[5] = "d/dt pEGFR_Akt in component pEGFR_Akt (dimensionless)"
legend_rates[6] = "d/dt Akt in component Akt (dimensionless)"
legend_rates[7] = "d/dt pAkt in component pAkt (dimensionless)"
legend_rates[9] = "d/dt pAkt_S6 in component pAkt_S6 (dimensionless)"
legend_rates[8] = "d/dt S6 in component S6 (dimensionless)"
legend_rates[10] = "d/dt pS6 in component pS6 (dimensionless)"
return (legend_states, legend_algebraic, legend_voi, legend_constants)
def initConsts():
constants = [0.0] * sizeConstants; states = [0.0] * sizeStates;
constants[0] = 30.0
constants[1] = 15.0
constants[2] = 6.81902e-4
states[0] = 68190.000000002
states[1] = 0.0
states[2] = 0.0
constants[3] = 4.07490e-2
constants[4] = 6.73816e-3
constants[5] = 5.25097e-5
constants[6] = 2.434663e-5
constants[7] = 1.06386129269658e-4
states[3] = 0.0
constants[8] = 1.92391e-2
states[4] = 0.0
states[5] = 0.0
states[6] = 4.33090e-2
constants[9] = 9.97194e-2
constants[10] = 3.05684e-2
constants[11] = 1.55430e-5
constants[12] = 5.17473e-3
states[7] = 0.0
constants[13] = 3.27962e-2
states[8] = 3.54317e0
states[9] = 0.0
constants[14] = 2.10189e-6
constants[15] = 5.17940e-15
constants[16] = 1.21498e-3
states[10] = 0.0
constants[17] = 1.13102e-3
constants[18] = 1.81735e-4
constants[19] = 6.00588e1
constants[20] = 4.98862e4
return (states, constants)
def computeRates(voi, states, constants):
rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic
rates[0] = (constants[3]*states[1]+constants[5]*states[2]+constants[7]*(constants[2]-states[0]))-(constants[4]*constants[0]*states[0]+constants[6]*constants[1]*states[0])
rates[1] = (constants[4]*constants[0]*states[0]+constants[5]*states[3])-(constants[3]*states[1]+constants[6]*constants[1]*states[1]+constants[8]*states[1])
rates[2] = (constants[3]*states[3]+constants[6]*constants[1]*states[0])-(constants[4]*constants[0]*states[2]+constants[5]*states[2]+constants[7]*states[2])
rates[3] = (constants[4]*constants[0]*states[2]+constants[6]*constants[1]*states[1])-(constants[3]*states[3]+constants[5]*states[3])
rates[4] = (constants[8]*states[1]+constants[10]*states[5]+constants[12]*states[5])-(constants[9]*states[4]+constants[11]*states[4]*states[6])
rates[5] = constants[11]*states[4]*states[6]-(constants[12]*states[5]+constants[10]*states[5])
rates[6] = (constants[12]*states[5]+constants[13]*states[7])-constants[11]*states[4]*states[6]
rates[7] = (constants[10]*states[5]+constants[15]*states[9]+constants[16]*states[9])-(constants[13]*states[7]+constants[14]*states[7]*states[8])
rates[9] = constants[14]*states[7]*states[8]-(constants[15]*states[9]+constants[16]*states[9])
rates[8] = (constants[15]*states[9]+constants[17]*states[10])-constants[14]*states[7]*states[8]
rates[10] = constants[16]*states[9]-constants[17]*states[10]
return(rates)
def computeAlgebraic(constants, states, voi):
algebraic = array([[0.0] * len(voi)] * sizeAlgebraic)
states = array(states)
voi = array(voi)
algebraic[0] = (states[4]+states[5])*constants[18]
algebraic[1] = (states[7]+states[9])*constants[19]
algebraic[2] = states[10]*constants[20]
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)