Generated Code
The following is python code generated by the CellML API from this CellML file. (Back to language selection)
The raw code is available.
# Size of variable arrays:
sizeAlgebraic = 0
sizeStates = 18
sizeConstants = 37
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] = "mostot in component total_concs (micromolar)"
legend_constants[1] = "e1tot in component total_concs (micromolar)"
legend_constants[2] = "e2tot in component total_concs (micromolar)"
legend_constants[3] = "mektot in component total_concs (micromolar)"
legend_constants[4] = "mekpasetot in component total_concs (micromolar)"
legend_constants[5] = "mapktot in component total_concs (micromolar)"
legend_constants[6] = "mapkpasetot in component total_concs (micromolar)"
legend_constants[7] = "a1 in component rate_constants (second_order_rate_constant_units)"
legend_constants[8] = "a2 in component rate_constants (second_order_rate_constant_units)"
legend_constants[9] = "a3 in component rate_constants (second_order_rate_constant_units)"
legend_constants[10] = "a4 in component rate_constants (second_order_rate_constant_units)"
legend_constants[11] = "a5 in component rate_constants (second_order_rate_constant_units)"
legend_constants[12] = "a6 in component rate_constants (second_order_rate_constant_units)"
legend_constants[13] = "a7 in component rate_constants (second_order_rate_constant_units)"
legend_constants[14] = "a8 in component rate_constants (second_order_rate_constant_units)"
legend_constants[15] = "a9 in component rate_constants (second_order_rate_constant_units)"
legend_constants[16] = "a10 in component rate_constants (second_order_rate_constant_units)"
legend_constants[17] = "d1 in component rate_constants (first_order_rate_constant_units)"
legend_constants[18] = "d2 in component rate_constants (first_order_rate_constant_units)"
legend_constants[19] = "d3 in component rate_constants (first_order_rate_constant_units)"
legend_constants[20] = "d4 in component rate_constants (first_order_rate_constant_units)"
legend_constants[21] = "d5 in component rate_constants (first_order_rate_constant_units)"
legend_constants[22] = "d6 in component rate_constants (first_order_rate_constant_units)"
legend_constants[23] = "d7 in component rate_constants (first_order_rate_constant_units)"
legend_constants[24] = "d8 in component rate_constants (first_order_rate_constant_units)"
legend_constants[25] = "d9 in component rate_constants (first_order_rate_constant_units)"
legend_constants[26] = "d10 in component rate_constants (first_order_rate_constant_units)"
legend_constants[27] = "k1 in component rate_constants (first_order_rate_constant_units)"
legend_constants[28] = "k2 in component rate_constants (first_order_rate_constant_units)"
legend_constants[29] = "k3 in component rate_constants (first_order_rate_constant_units)"
legend_constants[30] = "k4 in component rate_constants (first_order_rate_constant_units)"
legend_constants[31] = "k5 in component rate_constants (first_order_rate_constant_units)"
legend_constants[32] = "k6 in component rate_constants (first_order_rate_constant_units)"
legend_constants[33] = "k7 in component rate_constants (first_order_rate_constant_units)"
legend_constants[34] = "k8 in component rate_constants (first_order_rate_constant_units)"
legend_constants[35] = "k9 in component rate_constants (first_order_rate_constant_units)"
legend_constants[36] = "k10 in component rate_constants (first_order_rate_constant_units)"
legend_states[0] = "mos in component mos (micromolar)"
legend_states[1] = "mosstar in component mosstar (micromolar)"
legend_states[2] = "mose1 in component mose1 (micromolar)"
legend_states[3] = "mosstare2 in component mosstare2 (micromolar)"
legend_states[4] = "mekstarmosstar in component mekstarmosstar (micromolar)"
legend_states[5] = "mekmosstar in component mekmosstar (micromolar)"
legend_states[6] = "mekstar in component mekstar (micromolar)"
legend_states[7] = "mekstarstar in component mekstarstar (micromolar)"
legend_states[8] = "mekstarmekpase in component mekstarmekpase (micromolar)"
legend_states[9] = "mekstarstarmekpase in component mekstarstarmekpase (micromolar)"
legend_states[10] = "mapkmekstarstar in component mapkmekstarstar (micromolar)"
legend_states[11] = "mapkstarmekstarstar in component mapkstarmekstarstar (micromolar)"
legend_states[12] = "mek in component mek (micromolar)"
legend_states[13] = "mapkstar in component mapkstar (micromolar)"
legend_states[14] = "mapkstarstar in component mapkstarstar (micromolar)"
legend_states[15] = "mapkstarmapkpase in component mapkstarmapkpase (micromolar)"
legend_states[16] = "mapkstarstarmapkpase in component mapkstarstarmapkpase (micromolar)"
legend_states[17] = "mapk in component mapk (micromolar)"
legend_rates[0] = "d/dt mos in component mos (micromolar)"
legend_rates[2] = "d/dt mose1 in component mose1 (micromolar)"
legend_rates[1] = "d/dt mosstar in component mosstar (micromolar)"
legend_rates[3] = "d/dt mosstare2 in component mosstare2 (micromolar)"
legend_rates[12] = "d/dt mek in component mek (micromolar)"
legend_rates[5] = "d/dt mekmosstar in component mekmosstar (micromolar)"
legend_rates[6] = "d/dt mekstar in component mekstar (micromolar)"
legend_rates[8] = "d/dt mekstarmekpase in component mekstarmekpase (micromolar)"
legend_rates[4] = "d/dt mekstarmosstar in component mekstarmosstar (micromolar)"
legend_rates[7] = "d/dt mekstarstar in component mekstarstar (micromolar)"
legend_rates[9] = "d/dt mekstarstarmekpase in component mekstarstarmekpase (micromolar)"
legend_rates[17] = "d/dt mapk in component mapk (micromolar)"
legend_rates[10] = "d/dt mapkmekstarstar in component mapkmekstarstar (micromolar)"
legend_rates[13] = "d/dt mapkstar in component mapkstar (micromolar)"
legend_rates[11] = "d/dt mapkstarmekstarstar in component mapkstarmekstarstar (micromolar)"
legend_rates[14] = "d/dt mapkstarstar in component mapkstarstar (micromolar)"
legend_rates[15] = "d/dt mapkstarmapkpase in component mapkstarmapkpase (micromolar)"
legend_rates[16] = "d/dt mapkstarstarmapkpase in component mapkstarstarmapkpase (micromolar)"
return (legend_states, legend_algebraic, legend_voi, legend_constants)
def initConsts():
constants = [0.0] * sizeConstants; states = [0.0] * sizeStates;
constants[0] = 0.003
constants[1] = 0.0003
constants[2] = 0.0003
constants[3] = 1.2
constants[4] = 0.0003
constants[5] = 1.2
constants[6] = 0.12
constants[7] = 1000
constants[8] = 1000
constants[9] = 1000
constants[10] = 1000
constants[11] = 1000
constants[12] = 1000
constants[13] = 1000
constants[14] = 1000
constants[15] = 1000
constants[16] = 1000
constants[17] = 150
constants[18] = 150
constants[19] = 150
constants[20] = 150
constants[21] = 150
constants[22] = 150
constants[23] = 150
constants[24] = 150
constants[25] = 150
constants[26] = 150
constants[27] = 150
constants[28] = 150
constants[29] = 150
constants[30] = 150
constants[31] = 150
constants[32] = 150
constants[33] = 150
constants[34] = 150
constants[35] = 150
constants[36] = 150
states[0] = 0.003
states[1] = 0
states[2] = 0
states[3] = 0
states[4] = 0
states[5] = 0
states[6] = 0
states[7] = 0
states[8] = 0
states[9] = 0
states[10] = 0
states[11] = 0
states[12] = 1.2
states[13] = 0
states[14] = 0
states[15] = 0
states[16] = 0
states[17] = 1.2
return (states, constants)
def computeRates(voi, states, constants):
rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic
rates[0] = -constants[7]*(((((constants[0]-states[1])-states[2])-states[3])-states[5])-states[4])*(constants[1]-states[2])+constants[17]*states[2]+constants[28]*states[3]
rates[2] = constants[7]*(((((constants[0]-states[1])-states[2])-states[3])-states[5])-states[4])*(constants[1]-states[2])-(constants[17]+constants[27])*states[2]
rates[1] = (((-constants[8]*states[1]*(constants[2]-states[3])+constants[18]*states[3]+constants[27]*states[2]+(constants[29]+constants[19])*states[5])-constants[9]*states[1]*((((((((constants[3]-states[6])-states[7])-states[8])-states[9])-states[5])-states[4])-states[10])-states[11]))+(constants[31]+constants[21])*states[4])-constants[11]*states[6]*states[1]
rates[3] = constants[8]*states[1]*(constants[2]-states[3])-(constants[18]+constants[28])*states[3]
rates[12] = -constants[9]*((((((((constants[3]-states[6])-states[7])-states[8])-states[9])-states[5])-states[4])-states[10])-states[11])*states[1]+constants[19]*states[5]+constants[30]*states[8]
rates[5] = constants[9]*((((((((constants[3]-states[6])-states[7])-states[8])-states[9])-states[5])-states[4])-states[10])-states[11])*states[1]-(constants[19]+constants[29])*states[5]
rates[6] = (-constants[10]*states[6]*((constants[4]-states[8])-states[9])+constants[20]*states[8]+constants[29]*states[5]+constants[32]*states[9]+constants[21]*states[4])-constants[11]*states[6]*states[1]
rates[8] = constants[10]*states[6]*((constants[4]-states[8])-states[9])-(constants[20]+constants[30])*states[8]
rates[4] = constants[11]*states[6]*states[1]-(constants[21]+constants[31])*states[4]
rates[7] = ((((constants[31]*states[4]-constants[12]*states[7]*((constants[4]-states[8])-states[9]))+constants[22]*states[9])-constants[13]*states[7]*((((((constants[5]-states[13])-states[14])-states[15])-states[16])-states[10])-states[11]))+(constants[23]+constants[33])*states[10]+(constants[25]+constants[35])*states[11])-constants[15]*states[13]*states[7]
rates[9] = constants[12]*states[7]*((constants[4]-states[8])-states[9])-(constants[22]+constants[32])*states[9]
rates[17] = -constants[13]*((((((constants[5]-states[13])-states[14])-states[15])-states[16])-states[10])-states[11])*states[7]+constants[23]*states[10]+constants[34]*states[15]
rates[10] = constants[13]*((((((constants[5]-states[13])-states[14])-states[15])-states[16])-states[10])-states[11])*states[7]-(constants[23]+constants[33])*states[10]
rates[13] = (((constants[33]*states[10]-constants[14]*states[13]*((constants[6]-states[15])-states[16]))+constants[24]*states[15])-constants[15]*states[13]*states[7])+constants[25]*states[11]+constants[36]*states[16]
rates[11] = constants[15]*states[13]*states[7]-(constants[25]+constants[35])*states[11]
rates[14] = -constants[16]*states[14]*((constants[6]-states[15])-states[16])+constants[26]*states[16]+constants[35]*states[11]
rates[15] = constants[14]*states[13]*((constants[6]-states[15])-states[16])-(constants[24]+constants[34])*states[15]
rates[16] = constants[16]*states[14]*((constants[6]-states[15])-states[16])-(constants[26]+constants[36])*states[16]
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)