Generated Code
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The raw code is available.
# Size of variable arrays:
sizeAlgebraic = 0
sizeStates = 13
sizeConstants = 24
from math import *
from numpy import *
def createLegends():
legend_states = [""] * sizeStates
legend_rates = [""] * sizeStates
legend_algebraic = [""] * sizeAlgebraic
legend_voi = ""
legend_constants = [""] * sizeConstants
legend_voi = "t in component environment (s)"
legend_constants[0] = "kf1 in component EGF_EGFRtoEGFEGFR (per_um_s)"
legend_constants[1] = "kb1 in component EGF_EGFRtoEGFEGFR (per_s)"
legend_constants[2] = "kf2 in component EGF_EGFRtoEGFEGFR (per_s)"
legend_constants[3] = "kb2 in component EGF_EGFRtoEGFEGFR (per_s)"
legend_states[0] = "EGF in component EGF_EGFRtoEGFEGFR (um)"
legend_states[1] = "EGFR in component EGF_EGFRtoEGFEGFR (um)"
legend_states[2] = "EGF_EGFR in component EGF_EGFRtoEGFEGFR (um)"
legend_states[3] = "EGF_EGFR_INTERNAL in component EGF_EGFRtoEGFEGFR (um)"
legend_constants[4] = "km3 in component SHCtoSHCStar (um)"
legend_constants[5] = "kf4 in component SHCtoSHCStar (per_s)"
legend_constants[6] = "kb4 in component SHCtoSHCStar (per_s)"
legend_constants[7] = "kf5 in component SHCtoSHCStar (per_um_s)"
legend_constants[8] = "kb5 in component SHCtoSHCStar (per_s)"
legend_constants[9] = "kf6 in component SHCtoSHCStar (per_um_s)"
legend_constants[10] = "kb6 in component SHCtoSHCStar (per_s)"
legend_constants[11] = "kf8 in component SHCtoSHCStar (per_s)"
legend_constants[12] = "kb8 in component SHCtoSHCStar (per_s)"
legend_constants[13] = "kf10 in component SHCtoSHCStar (per_um_s)"
legend_constants[14] = "kb10 in component SHCtoSHCStar (per_s)"
legend_constants[15] = "km7 in component SHCtoSHCStar (um)"
legend_constants[16] = "km9 in component SHCtoSHCStar (um)"
legend_constants[17] = "Vmax7 in component SHCtoSHCStar (per_s)"
legend_constants[18] = "Vmax3 in component SHCtoSHCStar (per_s)"
legend_constants[19] = "Vmax9 in component SHCtoSHCStar (per_s)"
legend_states[4] = "SHC in component SHCtoSHCStar (um)"
legend_states[5] = "SHCstar in component SHCtoSHCStar (um)"
legend_states[6] = "SHCstar_SOS_GRB2 in component SHCtoSHCStar (um)"
legend_states[7] = "SOS_GRB2 in component SHCtoSHCStar (um)"
legend_states[8] = "SOS in component SHCtoSHCStar (um)"
legend_constants[20] = "GRB2 in component SHCtoSHCStar (um)"
legend_constants[21] = "MAPK in component SHCtoSHCStar (um)"
legend_states[9] = "SOSstar in component SHCtoSHCStar (um)"
legend_states[10] = "SOSstar_GRB2 in component SHCtoSHCStar (um)"
legend_constants[22] = "km7 in component GDPrasToGTPras (um)"
legend_constants[23] = "Vmax7 in component GDPrasToGTPras (per_s)"
legend_states[11] = "GDP_ras in component GDPrasToGTPras (um)"
legend_states[12] = "GTP_ras in component GDPrasToGTPras (um)"
legend_rates[0] = "d/dt EGF in component EGF_EGFRtoEGFEGFR (um)"
legend_rates[1] = "d/dt EGFR in component EGF_EGFRtoEGFEGFR (um)"
legend_rates[2] = "d/dt EGF_EGFR in component EGF_EGFRtoEGFEGFR (um)"
legend_rates[3] = "d/dt EGF_EGFR_INTERNAL in component EGF_EGFRtoEGFEGFR (um)"
legend_rates[5] = "d/dt SHCstar in component SHCtoSHCStar (um)"
legend_rates[4] = "d/dt SHC in component SHCtoSHCStar (um)"
legend_rates[6] = "d/dt SHCstar_SOS_GRB2 in component SHCtoSHCStar (um)"
legend_rates[7] = "d/dt SOS_GRB2 in component SHCtoSHCStar (um)"
legend_rates[8] = "d/dt SOS in component SHCtoSHCStar (um)"
legend_rates[9] = "d/dt SOSstar in component SHCtoSHCStar (um)"
legend_rates[10] = "d/dt SOSstar_GRB2 in component SHCtoSHCStar (um)"
legend_rates[11] = "d/dt GDP_ras in component GDPrasToGTPras (um)"
legend_rates[12] = "d/dt GTP_ras in component GDPrasToGTPras (um)"
return (legend_states, legend_algebraic, legend_voi, legend_constants)
def initConsts():
constants = [0.0] * sizeConstants; states = [0.0] * sizeStates;
constants[0] = 0.000007
constants[1] = 0.25
constants[2] = 0.002
constants[3] = 0.00033
states[0] = 0.16667
states[1] = 0.16667
states[2] = 0
states[3] = 0
constants[4] = 0.83333333333
constants[5] = 0.0016667
constants[6] = 0
constants[7] = 0.000000041667
constants[8] = 0.0168
constants[9] = 0.0000008333
constants[10] = 0.1
constants[11] = 0.001
constants[12] = 0
constants[13] = 0.000000041667
constants[14] = 0.0168
constants[15] = 0.40404
constants[16] = 2.564166667
constants[17] = 0.02
constants[18] = 0.2
constants[19] = 10
states[4] = 0.5
states[5] = 0
states[6] = 0
states[7] = 0
states[8] = 0.1
constants[20] = 1
constants[21] = 0.36
states[9] = 0
states[10] = 0
constants[22] = 0.50505
constants[23] = 0.02
states[11] = 1
states[12] = 0
return (states, constants)
def computeRates(voi, states, constants):
rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic
rates[0] = -constants[0]*states[0]*states[1]+constants[1]*states[2]
rates[1] = -constants[0]*states[0]*states[1]+constants[1]*states[2]
rates[2] = ((constants[0]*states[0]*states[1]-constants[1]*states[2])-constants[2]*states[2])+constants[3]*states[3]
rates[3] = constants[2]*states[2]-constants[3]*states[3]
rates[5] = ((states[2]*constants[18]*states[4])/(constants[4]+states[4])-constants[9]*states[5]*states[7])+constants[10]*states[6]
rates[4] = (constants[5]*states[5]-constants[6]*states[4])-(states[2]*constants[18]*states[4])/(constants[4]+states[4])
rates[6] = constants[9]*states[5]*states[7]-constants[10]*states[6]
rates[7] = ((-constants[9]*states[5]*states[7]+constants[10]*states[6])-constants[8]*states[7])+constants[7]*states[8]*constants[20]
rates[8] = (constants[11]*states[9]-constants[12]*states[8])-(constants[21]*constants[19]*states[8])/(constants[16]+states[8])
rates[9] = ((-constants[11]*states[9]+constants[12]*states[8]+(constants[21]*constants[19]*states[8])/(constants[16]+states[8]))-constants[13]*states[9]*constants[20])+constants[14]*states[10]
rates[10] = constants[13]*states[9]*constants[20]-constants[14]*states[10]
rates[11] = (-states[10]*constants[23]*states[11])/(constants[22]+states[11])
rates[12] = (states[10]*constants[23]*states[11])/(constants[22]+states[11])
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)