Generated Code
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The raw code is available.
# Size of variable arrays:
sizeAlgebraic = 0
sizeStates = 10
sizeConstants = 30
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] = "kf2 in component GEF (per_s)"
legend_constants[1] = "kb2 in component GEF (per_s)"
legend_constants[2] = "kf5 in component GEF (per_um_s)"
legend_constants[3] = "kb5 in component GEF (per_s)"
legend_constants[4] = "kf7 in component GEF (per_s)"
legend_constants[5] = "kb7 in component GEF (per_s)"
legend_constants[6] = "kf8 in component GEF (per_um_s)"
legend_constants[7] = "kb8 in component GEF (per_s)"
legend_constants[8] = "km1 in component GEF (um)"
legend_constants[9] = "Vmax1 in component GEF (per_s)"
legend_constants[10] = "km6 in component GEF (um)"
legend_constants[11] = "Vmax6 in component GEF (per_s)"
legend_states[0] = "GEF_inact in component GEF (um)"
legend_states[1] = "GEF in component GEF (um)"
legend_constants[12] = "PKA in component undefinedVariables (um)"
legend_states[2] = "Ca4CAM in component GEF (um)"
legend_constants[13] = "PKC in component undefinedVariables (um)"
legend_states[3] = "Gby in component GEF (um)"
legend_states[4] = "CaM_GEF in component GEF (um)"
legend_states[5] = "Gby_GEF in component GEF (um)"
legend_constants[14] = "kf12 in component GTPRAS (per_s)"
legend_constants[15] = "kb12 in component GTPRAS (per_s)"
legend_constants[16] = "km9 in component GTPRAS (um)"
legend_constants[17] = "Vmax9 in component GTPRAS (per_s)"
legend_constants[18] = "km10 in component GTPRAS (um)"
legend_constants[19] = "Vmax10 in component GTPRAS (per_s)"
legend_constants[20] = "km11 in component GTPRAS (um)"
legend_constants[21] = "Vmax11 in component GTPRAS (per_s)"
legend_constants[22] = "km13 in component GTPRAS (um)"
legend_constants[23] = "Vmax13 in component GTPRAS (per_s)"
legend_states[6] = "GTP_RAS in component GTPRAS (um)"
legend_states[7] = "GDP_RAS in component GTPRAS (um)"
legend_states[8] = "GAP in component GAP (um)"
legend_constants[24] = "kf4 in component GAP (per_s)"
legend_constants[25] = "kb4 in component GAP (per_s)"
legend_constants[26] = "km3 in component GAP (um)"
legend_constants[27] = "Vmax3 in component GAP (per_s)"
legend_states[9] = "GAPstar in component GAP (um)"
legend_constants[28] = "Ca4CAM in component undefinedVariables (um)"
legend_constants[29] = "Gby in component undefinedVariables (um)"
legend_rates[0] = "d/dt GEF_inact in component GEF (um)"
legend_rates[1] = "d/dt GEF in component GEF (um)"
legend_rates[3] = "d/dt Gby in component GEF (um)"
legend_rates[4] = "d/dt CaM_GEF in component GEF (um)"
legend_rates[2] = "d/dt Ca4CAM in component GEF (um)"
legend_rates[5] = "d/dt Gby_GEF in component GEF (um)"
legend_rates[6] = "d/dt GTP_RAS in component GTPRAS (um)"
legend_rates[7] = "d/dt GDP_RAS in component GTPRAS (um)"
legend_rates[8] = "d/dt GAP in component GAP (um)"
legend_rates[9] = "d/dt GAPstar in component GAP (um)"
return (legend_states, legend_algebraic, legend_voi, legend_constants)
def initConsts():
constants = [0.0] * sizeConstants; states = [0.0] * sizeStates;
constants[0] = 1
constants[1] = 0
constants[2] = 0.0001
constants[3] = 1
constants[4] = 1
constants[5] = 0
constants[6] = 0.00001
constants[7] = 1
constants[8] = 7.5
constants[9] = 9
constants[10] = 3.33333333333
constants[11] = 4
states[0] = 0.1
states[1] = 0
constants[12] = 1
states[2] = 1
constants[13] = 1
states[3] = 1
states[4] = 0
states[5] = 0
constants[14] = 0.0001
constants[15] = 0
constants[16] = 0.50505
constants[17] = 0.02
constants[18] = 0.50505
constants[19] = 0.02
constants[20] = 0.50505
constants[21] = 0.02
constants[22] = 1.0104
constants[23] = 10
states[6] = 0
states[7] = 0.2
states[8] = 0.002
constants[24] = 0.1
constants[25] = 0
constants[26] = 3.33333333333
constants[27] = 4
states[9] = 0
constants[28] = 1
constants[29] = 1
return (states, constants)
def computeRates(voi, states, constants):
rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic
rates[0] = (((constants[12]*constants[9]*states[1])/(constants[8]+states[1])+(constants[13]*constants[11]*states[1])/(constants[10]+states[1]))-constants[0]*states[0])-constants[4]*states[0]
rates[1] = (((-((((constants[12]*constants[9]*states[1])/(constants[8]+states[1])+(constants[13]*constants[11]*states[1])/(constants[10]+states[1]))-constants[0]*states[0])-constants[4]*states[0])-constants[2]*states[2]*states[1])+constants[3]*states[4])-constants[6]*states[1]*states[3])+constants[7]*states[5]
rates[3] = -constants[6]*states[1]*states[3]+constants[7]*states[5]
rates[4] = -constants[3]*states[4]+constants[2]*states[1]*states[2]
rates[2] = -(-constants[3]*states[4]+constants[2]*states[1]*states[2])
rates[5] = -(-constants[6]*states[1]*states[3]+constants[7]*states[5])
rates[6] = ((-states[8]*constants[23]*states[6])/(constants[22]+states[6])-constants[14]*states[6])+(states[0]*constants[19]*states[7])/(constants[18]+states[7])+(states[5]*constants[21]*states[7])/(constants[20]+states[7])+(states[4]*constants[17]*states[7])/(constants[16]+states[7])
rates[7] = -(((-states[8]*constants[23]*states[6])/(constants[22]+states[6])-constants[14]*states[6])+(states[0]*constants[19]*states[7])/(constants[18]+states[7])+(states[5]*constants[21]*states[7])/(constants[20]+states[7])+(states[4]*constants[17]*states[7])/(constants[16]+states[7]))
rates[8] = (-constants[13]*constants[27]*states[8])/(constants[26]+states[8])+constants[24]*states[9]
rates[9] = (constants[13]*constants[27]*states[8])/(constants[26]+states[8])-constants[24]*states[9]
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)