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 = 9
sizeConstants = 40
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 (hour)"
legend_states[0] = "pRB in component pRB (CONC)"
legend_constants[0] = "k1 in component model_parameters (dimensionless)"
legend_states[1] = "E2F1 in component E2F1 (CONC)"
legend_constants[1] = "km1 in component model_parameters (dimensionless)"
legend_constants[2] = "j11 in component model_parameters (dimensionless)"
legend_constants[3] = "j61 in component model_parameters (dimensionless)"
legend_constants[4] = "k16 in component model_parameters (dimensionless)"
legend_states[2] = "CycDa in component CycDa (CONC)"
legend_constants[5] = "k61 in component model_parameters (dimensionless)"
legend_states[3] = "pRBp in component pRBp (CONC)"
legend_constants[6] = "phi_pRB in component model_parameters (dimensionless)"
legend_constants[7] = "kp in component model_parameters (dimensionless)"
legend_constants[8] = "k2 in component model_parameters (dimensionless)"
legend_constants[9] = "a in component model_parameters (dimensionless)"
legend_constants[10] = "km2 in component model_parameters (dimensionless)"
legend_constants[11] = "j12 in component model_parameters (dimensionless)"
legend_constants[12] = "j62 in component model_parameters (dimensionless)"
legend_constants[13] = "phi_E2F1 in component model_parameters (dimensionless)"
legend_constants[14] = "k34 in component model_parameters (dimensionless)"
legend_states[4] = "CycDi in component CycDi (CONC)"
legend_constants[15] = "km4 in component model_parameters (dimensionless)"
legend_constants[16] = "k43 in component model_parameters (dimensionless)"
legend_constants[17] = "phi_CycDa in component model_parameters (dimensionless)"
legend_constants[18] = "k3 in component model_parameters (dimensionless)"
legend_states[5] = "AP1 in component AP1 (CONC)"
legend_constants[19] = "k23 in component model_parameters (dimensionless)"
legend_constants[20] = "j13 in component model_parameters (dimensionless)"
legend_constants[21] = "j63 in component model_parameters (dimensionless)"
legend_constants[22] = "phi_CycDi in component model_parameters (dimensionless)"
legend_constants[23] = "Fm in component model_parameters (dimensionless)"
legend_constants[24] = "k25 in component model_parameters (dimensionless)"
legend_constants[25] = "j15 in component model_parameters (dimensionless)"
legend_constants[26] = "j65 in component model_parameters (dimensionless)"
legend_constants[27] = "phi_AP1 in component model_parameters (dimensionless)"
legend_constants[28] = "k67 in component model_parameters (dimensionless)"
legend_states[6] = "CycEa in component CycEa (CONC)"
legend_constants[29] = "k76 in component model_parameters (dimensionless)"
legend_states[7] = "pRBpp in component pRBpp (CONC)"
legend_constants[30] = "phi_pRBp in component model_parameters (dimensionless)"
legend_constants[31] = "phi_pRBpp in component model_parameters (dimensionless)"
legend_states[8] = "CycEi in component CycEi (CONC)"
legend_constants[32] = "k28 in component model_parameters (dimensionless)"
legend_constants[33] = "j18 in component model_parameters (dimensionless)"
legend_constants[34] = "j68 in component model_parameters (dimensionless)"
legend_constants[35] = "k98 in component model_parameters (dimensionless)"
legend_constants[36] = "k89 in component model_parameters (dimensionless)"
legend_constants[37] = "km9 in component model_parameters (dimensionless)"
legend_constants[38] = "phi_CycEi in component model_parameters (dimensionless)"
legend_constants[39] = "phi_CycEa in component model_parameters (dimensionless)"
legend_rates[0] = "d/dt pRB in component pRB (CONC)"
legend_rates[1] = "d/dt E2F1 in component E2F1 (CONC)"
legend_rates[2] = "d/dt CycDa in component CycDa (CONC)"
legend_rates[4] = "d/dt CycDi in component CycDi (CONC)"
legend_rates[5] = "d/dt AP1 in component AP1 (CONC)"
legend_rates[3] = "d/dt pRBp in component pRBp (CONC)"
legend_rates[7] = "d/dt pRBpp in component pRBpp (CONC)"
legend_rates[8] = "d/dt CycEi in component CycEi (CONC)"
legend_rates[6] = "d/dt CycEa in component CycEa (CONC)"
return (legend_states, legend_algebraic, legend_voi, legend_constants)
def initConsts():
constants = [0.0] * sizeConstants; states = [0.0] * sizeStates;
states[0] = 0
constants[0] = 1
states[1] = 0
constants[1] = 0.5
constants[2] = 0.5
constants[3] = 5
constants[4] = 0.4
states[2] = 0
constants[5] = 0.3
states[3] = 0
constants[6] = 0.005
constants[7] = 0.05
constants[8] = 1.6
constants[9] = 0.04
constants[10] = 4
constants[11] = 5
constants[12] = 8
constants[13] = 0.1
constants[14] = 0.04
states[4] = 0
constants[15] = 0.3
constants[16] = 0.01
constants[17] = 0.03
constants[18] = 0.05
states[5] = 0
constants[19] = 0.3
constants[20] = 0.002
constants[21] = 2
constants[22] = 0.023
constants[23] = 0
constants[24] = 0.9
constants[25] = 0.001
constants[26] = 6
constants[27] = 0.01
constants[28] = 0.7
states[6] = 0
constants[29] = 0.1
states[7] = 0
constants[30] = 0.06
constants[31] = 0.04
states[8] = 0
constants[32] = 0.06
constants[33] = 0.6
constants[34] = 7
constants[35] = 0.01
constants[36] = 0.07
constants[37] = 0.005
constants[38] = 0.06
constants[39] = 0.05
return (states, constants)
def computeRates(voi, states, constants):
rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic
rates[0] = ((constants[0]*(states[1]/(constants[1]+states[1]))*(constants[2]/(constants[2]*states[0]))*(constants[3]/(constants[3]*states[3]))-constants[4]*states[0]*states[2])+constants[5]*states[3])-constants[6]*states[0]
rates[1] = (constants[7]+constants[8]*((power(constants[9], 2.00000)+power(states[1], 2.00000))/(power(constants[10], 2.00000)+power(states[1], 2.00000)))*(constants[11]/(constants[11]+states[3]))*(constants[12]/(constants[12]+states[3])))-constants[13]*states[1]
rates[2] = ((constants[14]*states[4]*states[2])/(constants[15]+states[2])-constants[14]*states[2])-constants[17]*states[2]
rates[4] = ((constants[18]*states[5]+constants[19]*states[1]*(constants[20]/(constants[20]+states[0]))*(constants[21]/(constants[21]+states[3]))+constants[16]*states[2])-constants[14]*states[4]*(states[2]/(constants[15]+states[2])))-constants[22]*states[4]
rates[5] = (constants[23]+constants[24]*states[1]*(constants[25]/(constants[25]+states[0]))*(constants[26]/(constants[26]+states[3])))-constants[27]*states[5]
rates[3] = (((constants[4]*states[0]*states[2]-constants[5]*states[3])-constants[28]*states[3]*states[6])+constants[29]*states[7])-constants[30]*states[3]
rates[7] = (constants[28]*states[3]*states[6]-constants[29]*states[7])-constants[31]*states[7]
rates[8] = ((constants[32]*states[1]*(constants[33]/(constants[33]+states[0]))*(constants[34]/(constants[34]+states[3]))+constants[35]*states[6])-constants[36]*states[8]*(states[6]/(constants[37]+states[6])))-constants[38]*states[8]
rates[6] = (constants[36]*states[8]*(states[6]/(constants[37]+states[6]))-constants[35]*states[6])-constants[39]*states[6]
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)