Generated Code
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The raw code is available.
# Size of variable arrays:
sizeAlgebraic = 0
sizeStates = 16
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 = "t in component environment (s)"
legend_constants[0] = "kM2T2_on in component Model (second_order_rate_constant)"
legend_constants[1] = "kM2T2_off in component Model (first_order_rate_constant)"
legend_constants[2] = "kM2T2_iso in component Model (first_order_rate_constant)"
legend_constants[3] = "kM2T2_negativeiso in component Model (first_order_rate_constant)"
legend_constants[4] = "kM2C1_on in component Model (second_order_rate_constant)"
legend_constants[5] = "kM2C1_off in component Model (first_order_rate_constant)"
legend_constants[6] = "kM2C1_cat in component Model (first_order_rate_constant)"
legend_constants[7] = "kMT1T2_on in component Model (second_order_rate_constant)"
legend_constants[8] = "kMT1T2_off in component Model (first_order_rate_constant)"
legend_constants[9] = "kMT1T2M2pro_on in component Model (second_order_rate_constant)"
legend_constants[10] = "kMT1T2M2pro_off in component Model (first_order_rate_constant)"
legend_constants[11] = "kM2_act in component Model (first_order_rate_constant)"
legend_constants[12] = "kMT1_shedeff in component Model (second_order_rate_constant)"
legend_constants[13] = "kMT1C1_cat in component Model (first_order_rate_constant)"
legend_constants[14] = "kMT1C1_on in component Model (second_order_rate_constant)"
legend_constants[15] = "kMT1C1_off in component Model (first_order_rate_constant)"
legend_constants[16] = "kMT1T2M2proMT1_on in component Model (second_order_rate_constant)"
legend_constants[17] = "kMT1T2M2proMT1_off in component Model (first_order_rate_constant)"
legend_states[0] = "M2T2 in component Model (M)"
legend_states[1] = "M2C1 in component Model (M)"
legend_states[2] = "MT1T2 in component Model (M)"
legend_states[3] = "MT1T2M2proMT1 in component Model (M)"
legend_states[4] = "MT1C1 in component Model (M)"
legend_states[5] = "M2 in component Model (M)"
legend_states[6] = "MT1 in component Model (M)"
legend_states[7] = "M2_p in component Model (M)"
legend_states[8] = "T2 in component Model (M)"
legend_states[9] = "C1_D in component Model (M)"
legend_states[10] = "C1 in component Model (M)"
legend_states[11] = "MT1_cat in component Model (M)"
legend_states[12] = "MT1_t in component Model (M)"
legend_states[13] = "MT1T2M2pro in component Model (M)"
legend_constants[18] = "qMT1 in component Model (flux)"
legend_constants[19] = "qT2 in component Model (flux)"
legend_constants[20] = "qpro in component Model (flux)"
legend_states[14] = "MT1T2_star in component Model (um)"
legend_states[15] = "M2T2_star in component Model (um)"
legend_rates[5] = "d/dt M2 in component Model (M)"
legend_rates[6] = "d/dt MT1 in component Model (M)"
legend_rates[12] = "d/dt MT1_t in component Model (M)"
legend_rates[4] = "d/dt MT1C1 in component Model (M)"
legend_rates[2] = "d/dt MT1T2 in component Model (M)"
legend_rates[13] = "d/dt MT1T2M2pro in component Model (M)"
legend_rates[3] = "d/dt MT1T2M2proMT1 in component Model (M)"
legend_rates[10] = "d/dt C1 in component Model (M)"
legend_rates[9] = "d/dt C1_D in component Model (M)"
legend_rates[11] = "d/dt MT1_cat in component Model (M)"
legend_rates[8] = "d/dt T2 in component Model (M)"
legend_rates[7] = "d/dt M2_p in component Model (M)"
legend_rates[0] = "d/dt M2T2 in component Model (M)"
legend_rates[15] = "d/dt M2T2_star in component Model (um)"
legend_rates[1] = "d/dt M2C1 in component Model (M)"
legend_rates[14] = "d/dt MT1T2_star in component Model (um)"
return (legend_states, legend_algebraic, legend_voi, legend_constants)
def initConsts():
constants = [0.0] * sizeConstants; states = [0.0] * sizeStates;
constants[0] = 5900000
constants[1] = 6.3
constants[2] = 33
constants[3] = 0.00000002
constants[4] = 2600
constants[5] = 0.0021
constants[6] = 0.0045
constants[7] = 2980000
constants[8] = 0.202
constants[9] = 140000
constants[10] = 0.0047
constants[11] = 0.02
constants[12] = 2800
constants[13] = 0.00197
constants[14] = 1000
constants[15] = 1
constants[16] = 3000
constants[17] = 0.0009
states[0] = 0.0000000072
states[1] = 0.0000085
states[2] = 0.00000000139
states[3] = 0.00000000056
states[4] = 0.0000029
states[5] = 0
states[6] = 0
states[7] = 0
states[8] = 0
states[9] = 0
states[10] = 0
states[11] = 0
states[12] = 0
states[13] = 0
constants[18] = 0
constants[19] = 0
constants[20] = 0
states[14] = 0
states[15] = 0
return (states, constants)
def computeRates(voi, states, constants):
rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic
rates[5] = ((-constants[0]*states[5]*states[8]+constants[1]*states[0])-constants[4]*states[5]*states[10])+(constants[5]+constants[6])*states[1]+constants[11]*states[3]
rates[6] = ((((((constants[18]-constants[12]*states[6]*states[6])-constants[7]*states[6]*states[8])+constants[8]*states[2])-constants[14]*states[6]*states[10])+(constants[15]+constants[13])*states[4])-constants[16]*states[6]*states[13])+constants[17]*states[3]+constants[11]*states[3]
rates[12] = constants[12]*states[6]*states[6]
rates[4] = constants[14]*states[6]*states[10]-(constants[15]+constants[13])*states[4]
rates[2] = ((constants[7]*states[6]*states[8]-constants[8]*states[2])-constants[9]*states[2]*states[7])+constants[10]*states[13]
rates[13] = ((constants[9]*states[2]*states[7]-constants[10]*states[13])-constants[16]*states[6]*states[13])+constants[17]*states[3]
rates[3] = (constants[16]*states[6]*states[13]-constants[17]*states[3])-constants[11]*states[3]
rates[10] = ((-constants[14]*states[6]*states[10]+constants[15]*states[4])-constants[4]*states[5]*states[10])+constants[5]*states[1]
rates[9] = constants[6]*states[1]+constants[13]*states[4]
rates[11] = constants[12]*states[6]*states[6]
rates[8] = ((-constants[0]*states[5]*states[8]+constants[1]*states[0]+constants[19])-constants[7]*states[6]*states[8])+constants[8]*states[2]
rates[7] = (constants[20]-constants[9]*states[2]*states[7])+constants[10]*states[13]
rates[0] = ((constants[0]*states[5]*states[8]-constants[1]*states[0])-constants[2]*states[0])+constants[3]*states[15]
rates[15] = constants[2]*states[0]-constants[3]*states[15]
rates[1] = constants[4]*states[5]*states[10]-(constants[5]+constants[6])*states[1]
rates[14] = constants[11]*states[3]
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)