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 = 30
sizeStates = 18
sizeConstants = 33
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_states[0] = "q_ATP in component environment (fmol)"
legend_states[1] = "q_AC in component environment (fmol)"
legend_states[2] = "q_cAMP in component environment (fmol)"
legend_states[3] = "q_AC_ATP in component environment (fmol)"
legend_states[4] = "q_FSK in component environment (fmol)"
legend_states[5] = "q_FSK_AC in component environment (fmol)"
legend_states[6] = "q_FSK_AC_ATP in component environment (fmol)"
legend_states[7] = "q_Gsa_GTP in component environment (fmol)"
legend_states[8] = "q_Gsa_GTP_AC in component environment (fmol)"
legend_states[9] = "q_Gsa_GTP_AC_ATP in component environment (fmol)"
legend_states[10] = "q_PDE in component environment (fmol)"
legend_states[11] = "q_PDEinh in component environment (fmol)"
legend_states[12] = "q_PDE_cAMP in component environment (fmol)"
legend_states[13] = "q_IBMX in component environment (fmol)"
legend_states[14] = "q_five_AMP in component environment (fmol)"
legend_states[15] = "q_Gia_GTP in component environment (fmol)"
legend_states[16] = "q_ACinh in component environment (fmol)"
legend_states[17] = "q_PPi in component environment (fmol)"
legend_algebraic[18] = "v_1a in component cAMP (fmol_per_sec)"
legend_algebraic[19] = "v_1b in component cAMP (fmol_per_sec)"
legend_algebraic[20] = "v_2a in component cAMP (fmol_per_sec)"
legend_algebraic[21] = "v_2b in component cAMP (fmol_per_sec)"
legend_algebraic[22] = "v_3a in component cAMP (fmol_per_sec)"
legend_algebraic[23] = "v_3b in component cAMP (fmol_per_sec)"
legend_algebraic[24] = "v_4a in component cAMP (fmol_per_sec)"
legend_algebraic[26] = "v_4b in component cAMP (fmol_per_sec)"
legend_algebraic[28] = "v_5 in component cAMP (fmol_per_sec)"
legend_algebraic[25] = "v_6 in component cAMP (fmol_per_sec)"
legend_algebraic[27] = "v_7 in component cAMP (fmol_per_sec)"
legend_algebraic[29] = "v_GiAC in component cAMP (fmol_per_sec)"
legend_constants[0] = "kappa_1a in component cAMP_parameters (fmol_per_sec)"
legend_constants[1] = "kappa_1b in component cAMP_parameters (fmol_per_sec)"
legend_constants[2] = "kappa_2a in component cAMP_parameters (fmol_per_sec)"
legend_constants[3] = "kappa_2b in component cAMP_parameters (fmol_per_sec)"
legend_constants[4] = "kappa_3a in component cAMP_parameters (fmol_per_sec)"
legend_constants[5] = "kappa_3b in component cAMP_parameters (fmol_per_sec)"
legend_constants[6] = "kappa_4a in component cAMP_parameters (fmol_per_sec)"
legend_constants[7] = "kappa_4b in component cAMP_parameters (fmol_per_sec)"
legend_constants[8] = "kappa_5 in component cAMP_parameters (fmol_per_sec)"
legend_constants[9] = "kappa_6 in component cAMP_parameters (fmol_per_sec)"
legend_constants[10] = "kappa_7 in component cAMP_parameters (fmol_per_sec)"
legend_constants[11] = "kappa_GiAC in component cAMP_parameters (fmol_per_sec)"
legend_constants[12] = "K_ATP in component cAMP_parameters (per_fmol)"
legend_constants[13] = "K_cAMP in component cAMP_parameters (per_fmol)"
legend_constants[14] = "K_AC in component cAMP_parameters (per_fmol)"
legend_constants[15] = "K_AC_ATP in component cAMP_parameters (per_fmol)"
legend_constants[16] = "K_Gsa_GTP_AC in component cAMP_parameters (per_fmol)"
legend_constants[17] = "K_Gsa_GTP_AC_ATP in component cAMP_parameters (per_fmol)"
legend_constants[18] = "K_FSK_AC in component cAMP_parameters (per_fmol)"
legend_constants[19] = "K_FSK_AC_ATP in component cAMP_parameters (per_fmol)"
legend_constants[20] = "K_PDE in component cAMP_parameters (per_fmol)"
legend_constants[21] = "K_PDE_cAMP in component cAMP_parameters (per_fmol)"
legend_constants[22] = "K_five_AMP in component cAMP_parameters (per_fmol)"
legend_constants[23] = "K_IBMX in component cAMP_parameters (per_fmol)"
legend_constants[24] = "K_PDEinh in component cAMP_parameters (per_fmol)"
legend_constants[25] = "K_Gsa_GTP in component cAMP_parameters (per_fmol)"
legend_constants[26] = "K_FSK in component cAMP_parameters (per_fmol)"
legend_constants[27] = "K_Gia_GTP in component cAMP_parameters (per_fmol)"
legend_constants[28] = "K_ACinh in component cAMP_parameters (per_fmol)"
legend_constants[29] = "K_PPi in component cAMP_parameters (per_fmol)"
legend_constants[30] = "R in component constants (J_per_K_per_mol)"
legend_constants[31] = "T in component constants (kelvin)"
legend_algebraic[0] = "mu_ATP in component cAMP (J_per_mol)"
legend_algebraic[1] = "mu_cAMP in component cAMP (J_per_mol)"
legend_algebraic[2] = "mu_AC in component cAMP (J_per_mol)"
legend_algebraic[3] = "mu_AC_ATP in component cAMP (J_per_mol)"
legend_algebraic[4] = "mu_Gsa_GTP_AC in component cAMP (J_per_mol)"
legend_algebraic[5] = "mu_Gsa_GTP_AC_ATP in component cAMP (J_per_mol)"
legend_algebraic[6] = "mu_FSK_AC in component cAMP (J_per_mol)"
legend_algebraic[7] = "mu_FSK_AC_ATP in component cAMP (J_per_mol)"
legend_algebraic[8] = "mu_PDE in component cAMP (J_per_mol)"
legend_algebraic[9] = "mu_PDE_cAMP in component cAMP (J_per_mol)"
legend_algebraic[10] = "mu_five_AMP in component cAMP (J_per_mol)"
legend_algebraic[11] = "mu_IBMX in component cAMP (J_per_mol)"
legend_algebraic[12] = "mu_PDEinh in component cAMP (J_per_mol)"
legend_algebraic[13] = "mu_Gsa_GTP in component cAMP (J_per_mol)"
legend_algebraic[14] = "mu_FSK in component cAMP (J_per_mol)"
legend_algebraic[15] = "mu_Gia_GTP in component cAMP (J_per_mol)"
legend_algebraic[16] = "mu_ACinh in component cAMP (J_per_mol)"
legend_algebraic[17] = "mu_PPi in component cAMP (J_per_mol)"
legend_constants[32] = "F in component constants (C_per_mol)"
legend_rates[0] = "d/dt q_ATP in component environment (fmol)"
legend_rates[1] = "d/dt q_AC in component environment (fmol)"
legend_rates[3] = "d/dt q_AC_ATP in component environment (fmol)"
legend_rates[2] = "d/dt q_cAMP in component environment (fmol)"
legend_rates[4] = "d/dt q_FSK in component environment (fmol)"
legend_rates[5] = "d/dt q_FSK_AC in component environment (fmol)"
legend_rates[6] = "d/dt q_FSK_AC_ATP in component environment (fmol)"
legend_rates[7] = "d/dt q_Gsa_GTP in component environment (fmol)"
legend_rates[8] = "d/dt q_Gsa_GTP_AC in component environment (fmol)"
legend_rates[9] = "d/dt q_Gsa_GTP_AC_ATP in component environment (fmol)"
legend_rates[12] = "d/dt q_PDE_cAMP in component environment (fmol)"
legend_rates[10] = "d/dt q_PDE in component environment (fmol)"
legend_rates[13] = "d/dt q_IBMX in component environment (fmol)"
legend_rates[11] = "d/dt q_PDEinh in component environment (fmol)"
legend_rates[14] = "d/dt q_five_AMP in component environment (fmol)"
legend_rates[15] = "d/dt q_Gia_GTP in component environment (fmol)"
legend_rates[16] = "d/dt q_ACinh in component environment (fmol)"
legend_rates[17] = "d/dt q_PPi in component environment (fmol)"
return (legend_states, legend_algebraic, legend_voi, legend_constants)
def initConsts():
constants = [0.0] * sizeConstants; states = [0.0] * sizeStates;
states[0] = 190
states[1] = 1.889E-03
states[2] = 3.212E-02
states[3] = 1e-18
states[4] = 3.8e-5
states[5] = 1e-18
states[6] = 1e-18
states[7] = 9.519E-04
states[8] = 1e-18
states[9] = 1e-18
states[10] = 1.482E-03
states[11] = 1e-18
states[12] = 1e-18
states[13] = 3.80E-06
states[14] = 1e-18
states[15] = 4.81E-04
states[16] = 1e-18
states[17] = 1e-18
constants[0] = 9.47329e+06
constants[1] = 0.00197793
constants[2] = 176000
constants[3] = 0.047492
constants[4] = 5.07667e+08
constants[5] = 5.9031e-17
constants[6] = 36084.5
constants[7] = 0.138787
constants[8] = 751.564
constants[9] = 556.617
constants[10] = 160555
constants[11] = 685.521
constants[12] = 9.19362e-06
constants[13] = 0.0102598
constants[14] = 9.02358
constants[15] = 2.93942
constants[16] = 52.2258
constants[17] = 5.20284
constants[18] = 0.181058
constants[19] = 0.0492449
constants[20] = 2.28256
constants[21] = 1.04728
constants[22] = 0.0102598
constants[23] = 0.01642
constants[24] = 38.679
constants[25] = 0.420618
constants[26] = 1.32565e-05
constants[27] = 0.013661
constants[28] = 42.4053
constants[29] = 2.60488e-05
constants[30] = 8.31
constants[31] = 310
constants[32] = 96485
return (states, constants)
def computeRates(voi, states, constants):
rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic
algebraic[0] = constants[30]*constants[31]*log(constants[12]*states[0])
algebraic[2] = constants[30]*constants[31]*log(constants[14]*states[1])
algebraic[3] = constants[30]*constants[31]*log(constants[15]*states[3])
algebraic[18] = constants[0]*(exp((algebraic[2]+algebraic[0])/(constants[30]*constants[31]))-exp(algebraic[3]/(constants[30]*constants[31])))
algebraic[1] = constants[30]*constants[31]*log(constants[13]*states[2])
algebraic[17] = constants[30]*constants[31]*log(constants[29]*states[17])
algebraic[19] = constants[1]*(exp(algebraic[3]/(constants[30]*constants[31]))-exp((algebraic[2]+algebraic[1]+algebraic[17])/(constants[30]*constants[31])))
rates[3] = algebraic[18]-algebraic[19]
algebraic[4] = constants[30]*constants[31]*log(constants[16]*states[8])
algebraic[5] = constants[30]*constants[31]*log(constants[17]*states[9])
algebraic[20] = constants[2]*(exp((algebraic[4]+algebraic[0])/(constants[30]*constants[31]))-exp(algebraic[5]/(constants[30]*constants[31])))
algebraic[21] = constants[3]*(exp(algebraic[5]/(constants[30]*constants[31]))-exp((algebraic[4]+algebraic[1]+algebraic[17])/(constants[30]*constants[31])))
rates[9] = algebraic[20]-algebraic[21]
algebraic[6] = constants[30]*constants[31]*log(constants[18]*states[5])
algebraic[7] = constants[30]*constants[31]*log(constants[19]*states[6])
algebraic[22] = constants[4]*(exp((algebraic[6]+algebraic[0])/(constants[30]*constants[31]))-exp(algebraic[7]/(constants[30]*constants[31])))
rates[0] = (-algebraic[18]-algebraic[22])-algebraic[20]
algebraic[23] = constants[5]*(exp(algebraic[7]/(constants[30]*constants[31]))-exp((algebraic[6]+algebraic[1]+algebraic[17])/(constants[30]*constants[31])))
rates[6] = algebraic[22]-algebraic[23]
algebraic[8] = constants[30]*constants[31]*log(constants[20]*states[10])
algebraic[9] = constants[30]*constants[31]*log(constants[21]*states[12])
algebraic[24] = constants[6]*(exp((algebraic[8]+algebraic[1])/(constants[30]*constants[31]))-exp(algebraic[9]/(constants[30]*constants[31])))
rates[2] = (algebraic[19]+algebraic[23]+algebraic[21])-algebraic[24]
algebraic[13] = constants[30]*constants[31]*log(constants[25]*states[7])
algebraic[25] = constants[9]*(exp((algebraic[2]+algebraic[13])/(constants[30]*constants[31]))-exp(algebraic[4]/(constants[30]*constants[31])))
rates[7] = -algebraic[25]
rates[8] = (algebraic[25]-algebraic[20])+algebraic[21]
algebraic[14] = constants[30]*constants[31]*log(constants[26]*states[4])
algebraic[27] = constants[10]*(exp((algebraic[14]+algebraic[2])/(constants[30]*constants[31]))-exp(algebraic[6]/(constants[30]*constants[31])))
rates[4] = -algebraic[27]
rates[5] = (algebraic[27]+algebraic[23])-algebraic[22]
algebraic[10] = constants[30]*constants[31]*log(constants[22]*states[14])
algebraic[26] = constants[7]*(exp(algebraic[9]/(constants[30]*constants[31]))-exp((algebraic[8]+algebraic[10])/(constants[30]*constants[31])))
rates[12] = algebraic[24]-algebraic[26]
rates[14] = algebraic[26]
algebraic[15] = constants[30]*constants[31]*log(constants[27]*states[15])
algebraic[16] = constants[30]*constants[31]*log(constants[28]*states[16])
algebraic[29] = constants[11]*(exp((algebraic[2]+algebraic[15])/(constants[30]*constants[31]))-exp(algebraic[16]/(constants[30]*constants[31])))
rates[1] = (((algebraic[19]-algebraic[18])-algebraic[25])-algebraic[27])-algebraic[29]
algebraic[11] = constants[30]*constants[31]*log(constants[23]*states[13])
algebraic[12] = constants[30]*constants[31]*log(constants[24]*states[11])
algebraic[28] = constants[8]*(exp((algebraic[8]+algebraic[11])/(constants[30]*constants[31]))-exp(algebraic[12]/(constants[30]*constants[31])))
rates[10] = (algebraic[26]-algebraic[24])-algebraic[28]
rates[13] = -algebraic[28]
rates[11] = algebraic[28]
rates[15] = -algebraic[29]
rates[16] = algebraic[29]
rates[17] = algebraic[29]
return(rates)
def computeAlgebraic(constants, states, voi):
algebraic = array([[0.0] * len(voi)] * sizeAlgebraic)
states = array(states)
voi = array(voi)
algebraic[0] = constants[30]*constants[31]*log(constants[12]*states[0])
algebraic[2] = constants[30]*constants[31]*log(constants[14]*states[1])
algebraic[3] = constants[30]*constants[31]*log(constants[15]*states[3])
algebraic[18] = constants[0]*(exp((algebraic[2]+algebraic[0])/(constants[30]*constants[31]))-exp(algebraic[3]/(constants[30]*constants[31])))
algebraic[1] = constants[30]*constants[31]*log(constants[13]*states[2])
algebraic[17] = constants[30]*constants[31]*log(constants[29]*states[17])
algebraic[19] = constants[1]*(exp(algebraic[3]/(constants[30]*constants[31]))-exp((algebraic[2]+algebraic[1]+algebraic[17])/(constants[30]*constants[31])))
algebraic[4] = constants[30]*constants[31]*log(constants[16]*states[8])
algebraic[5] = constants[30]*constants[31]*log(constants[17]*states[9])
algebraic[20] = constants[2]*(exp((algebraic[4]+algebraic[0])/(constants[30]*constants[31]))-exp(algebraic[5]/(constants[30]*constants[31])))
algebraic[21] = constants[3]*(exp(algebraic[5]/(constants[30]*constants[31]))-exp((algebraic[4]+algebraic[1]+algebraic[17])/(constants[30]*constants[31])))
algebraic[6] = constants[30]*constants[31]*log(constants[18]*states[5])
algebraic[7] = constants[30]*constants[31]*log(constants[19]*states[6])
algebraic[22] = constants[4]*(exp((algebraic[6]+algebraic[0])/(constants[30]*constants[31]))-exp(algebraic[7]/(constants[30]*constants[31])))
algebraic[23] = constants[5]*(exp(algebraic[7]/(constants[30]*constants[31]))-exp((algebraic[6]+algebraic[1]+algebraic[17])/(constants[30]*constants[31])))
algebraic[8] = constants[30]*constants[31]*log(constants[20]*states[10])
algebraic[9] = constants[30]*constants[31]*log(constants[21]*states[12])
algebraic[24] = constants[6]*(exp((algebraic[8]+algebraic[1])/(constants[30]*constants[31]))-exp(algebraic[9]/(constants[30]*constants[31])))
algebraic[13] = constants[30]*constants[31]*log(constants[25]*states[7])
algebraic[25] = constants[9]*(exp((algebraic[2]+algebraic[13])/(constants[30]*constants[31]))-exp(algebraic[4]/(constants[30]*constants[31])))
algebraic[14] = constants[30]*constants[31]*log(constants[26]*states[4])
algebraic[27] = constants[10]*(exp((algebraic[14]+algebraic[2])/(constants[30]*constants[31]))-exp(algebraic[6]/(constants[30]*constants[31])))
algebraic[10] = constants[30]*constants[31]*log(constants[22]*states[14])
algebraic[26] = constants[7]*(exp(algebraic[9]/(constants[30]*constants[31]))-exp((algebraic[8]+algebraic[10])/(constants[30]*constants[31])))
algebraic[15] = constants[30]*constants[31]*log(constants[27]*states[15])
algebraic[16] = constants[30]*constants[31]*log(constants[28]*states[16])
algebraic[29] = constants[11]*(exp((algebraic[2]+algebraic[15])/(constants[30]*constants[31]))-exp(algebraic[16]/(constants[30]*constants[31])))
algebraic[11] = constants[30]*constants[31]*log(constants[23]*states[13])
algebraic[12] = constants[30]*constants[31]*log(constants[24]*states[11])
algebraic[28] = constants[8]*(exp((algebraic[8]+algebraic[11])/(constants[30]*constants[31]))-exp(algebraic[12]/(constants[30]*constants[31])))
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)