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 = 22
sizeStates = 11
sizeConstants = 25
from math import *
from numpy import *
def createLegends():
legend_states = [""] * sizeStates
legend_rates = [""] * sizeStates
legend_algebraic = [""] * sizeAlgebraic
legend_voi = ""
legend_constants = [""] * sizeConstants
legend_constants[0] = "kappa_R_1a_cGMP in component BG_parameters (fmol_per_sec)"
legend_constants[1] = "kappa_R_1b_cGMP in component BG_parameters (fmol_per_sec)"
legend_constants[2] = "kappa_R_2a_cGMP in component BG_parameters (fmol_per_sec)"
legend_constants[3] = "kappa_R_2b_cGMP in component BG_parameters (fmol_per_sec)"
legend_constants[4] = "kappa_R_1_sGC in component BG_parameters (fmol_per_sec)"
legend_constants[5] = "kappa_R_2_sGC in component BG_parameters (fmol_per_sec)"
legend_constants[6] = "kappa_R_3_sGC in component BG_parameters (fmol_per_sec)"
legend_constants[7] = "kappa_R_4_sGC in component BG_parameters (fmol_per_sec)"
legend_constants[8] = "kappa_R_DNO_sGC in component BG_parameters (fmol_per_sec)"
legend_constants[9] = "K_GTP in component BG_parameters (per_fmol)"
legend_constants[10] = "K_E5c in component BG_parameters (per_fmol)"
legend_constants[11] = "K_cGMP in component BG_parameters (per_fmol)"
legend_constants[12] = "K_PDE in component BG_parameters (per_fmol)"
legend_constants[13] = "K_GTP_E5c in component BG_parameters (per_fmol)"
legend_constants[14] = "K_cGMP_PDE in component BG_parameters (per_fmol)"
legend_constants[15] = "K_GMP in component BG_parameters (per_fmol)"
legend_constants[16] = "K_Eb in component BG_parameters (per_fmol)"
legend_constants[17] = "K_NO in component BG_parameters (per_fmol)"
legend_constants[18] = "K_E6c in component BG_parameters (per_fmol)"
legend_constants[19] = "K_NO_product in component BG_parameters (per_fmol)"
legend_voi = "t in component environment (second)"
legend_constants[20] = "vol_myo in component environment (pL)"
legend_states[0] = "q_cGMP in component environment (fmol)"
legend_states[1] = "q_GTP in component environment (fmol)"
legend_states[2] = "q_E5c in component environment (fmol)"
legend_states[3] = "q_PDE in component environment (fmol)"
legend_states[4] = "q_GTP_E5c in component environment (fmol)"
legend_states[5] = "q_cGMP_PDE in component environment (fmol)"
legend_states[6] = "q_GMP in component environment (fmol)"
legend_states[7] = "q_Eb in component environment (fmol)"
legend_states[8] = "q_NO in component environment (fmol)"
legend_states[9] = "q_E6c in component environment (fmol)"
legend_states[10] = "q_NO_product in component environment (fmol)"
legend_algebraic[7] = "v_R_1a_cGMP in component cGMP (fmol_per_sec)"
legend_algebraic[8] = "v_R_1b_cGMP in component cGMP (fmol_per_sec)"
legend_algebraic[9] = "v_R_2a_cGMP in component cGMP (fmol_per_sec)"
legend_algebraic[10] = "v_R_2b_cGMP in component cGMP (fmol_per_sec)"
legend_algebraic[17] = "v_R_1_sGC in component sGC (fmol_per_sec)"
legend_algebraic[18] = "v_R_2_sGC in component sGC (fmol_per_sec)"
legend_algebraic[19] = "v_R_3_sGC in component sGC (fmol_per_sec)"
legend_algebraic[20] = "v_R_4_sGC in component sGC (fmol_per_sec)"
legend_algebraic[21] = "v_R_DNO_sGC in component sGC (fmol_per_sec)"
legend_constants[21] = "v_NO_generation in component environment (fmol_per_sec)"
legend_constants[22] = "R in component constants (J_per_K_per_mol)"
legend_constants[23] = "T in component constants (kelvin)"
legend_constants[24] = "F in component constants (C_per_mol)"
legend_algebraic[0] = "mu_GTP in component cGMP (J_per_mol)"
legend_algebraic[1] = "mu_E5c in component cGMP (J_per_mol)"
legend_algebraic[2] = "mu_cGMP in component cGMP (J_per_mol)"
legend_algebraic[3] = "mu_PDE in component cGMP (J_per_mol)"
legend_algebraic[4] = "mu_GTP_E5c in component cGMP (J_per_mol)"
legend_algebraic[5] = "mu_cGMP_PDE in component cGMP (J_per_mol)"
legend_algebraic[6] = "mu_GMP in component cGMP (J_per_mol)"
legend_algebraic[11] = "mu_Eb in component sGC (J_per_mol)"
legend_algebraic[12] = "mu_NO in component sGC (J_per_mol)"
legend_algebraic[13] = "mu_E6c in component sGC (J_per_mol)"
legend_algebraic[14] = "mu_E5c in component sGC (J_per_mol)"
legend_algebraic[15] = "mu_cGMP in component sGC (J_per_mol)"
legend_algebraic[16] = "mu_NO_product in component sGC (J_per_mol)"
legend_rates[0] = "d/dt q_cGMP in component environment (fmol)"
legend_rates[1] = "d/dt q_GTP in component environment (fmol)"
legend_rates[2] = "d/dt q_E5c in component environment (fmol)"
legend_rates[3] = "d/dt q_PDE in component environment (fmol)"
legend_rates[4] = "d/dt q_GTP_E5c in component environment (fmol)"
legend_rates[5] = "d/dt q_cGMP_PDE in component environment (fmol)"
legend_rates[6] = "d/dt q_GMP in component environment (fmol)"
legend_rates[7] = "d/dt q_Eb in component environment (fmol)"
legend_rates[8] = "d/dt q_NO in component environment (fmol)"
legend_rates[9] = "d/dt q_E6c in component environment (fmol)"
legend_rates[10] = "d/dt q_NO_product in component environment (fmol)"
return (legend_states, legend_algebraic, legend_voi, legend_constants)
def initConsts():
constants = [0.0] * sizeConstants; states = [0.0] * sizeStates;
constants[0] = 192.663
constants[1] = 0.00328297
constants[2] = 56591.2
constants[3] = 0.0110353
constants[4] = 3.61127e+06
constants[5] = 0.00328297
constants[6] = 4.92446
constants[7] = 0.0361127
constants[8] = 0.01
constants[9] = 17040
constants[10] = 0.304602
constants[11] = 1
constants[12] = 17.6706
constants[13] = 5190.42
constants[14] = 35.3412
constants[15] = 0.0051282
constants[16] = 0.0276911
constants[17] = 1
constants[18] = 30.4602
constants[19] = 0.1
constants[20] = 1
states[0] = 1e-6
states[1] = 0.0005
states[2] = 1e-16
states[3] = 1e-10
states[4] = 1e-16
states[5] = 1e-16
states[6] = 1e-16
states[7] = 1e-6
states[8] = 0.00836
states[9] = 1e-16
states[10] = 1e-16
constants[21] = 0.000114
constants[22] = 8.31
constants[23] = 310
constants[24] = 96485
return (states, constants)
def computeRates(voi, states, constants):
rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic
algebraic[0] = constants[22]*constants[23]*log(constants[9]*states[1])
algebraic[1] = constants[22]*constants[23]*log(constants[10]*states[2])
algebraic[4] = constants[22]*constants[23]*log(constants[13]*states[4])
algebraic[7] = constants[0]*(exp((algebraic[0]+algebraic[1])/(constants[22]*constants[23]))-exp(algebraic[4]/(constants[22]*constants[23])))
rates[1] = -algebraic[7]
algebraic[2] = constants[22]*constants[23]*log(constants[11]*states[0])
algebraic[8] = constants[1]*(exp(algebraic[4]/(constants[22]*constants[23]))-exp((algebraic[2]+algebraic[1])/(constants[22]*constants[23])))
rates[4] = algebraic[7]-algebraic[8]
algebraic[3] = constants[22]*constants[23]*log(constants[12]*states[3])
algebraic[5] = constants[22]*constants[23]*log(constants[14]*states[5])
algebraic[9] = constants[2]*(exp((algebraic[2]+algebraic[3])/(constants[22]*constants[23]))-exp(algebraic[5]/(constants[22]*constants[23])))
algebraic[6] = constants[22]*constants[23]*log(constants[15]*states[6])
algebraic[10] = constants[3]*(exp((algebraic[5]+algebraic[2])/(constants[22]*constants[23]))-exp((algebraic[6]+algebraic[3])/(constants[22]*constants[23])))
rates[3] = -algebraic[9]+algebraic[10]
rates[5] = algebraic[9]-algebraic[10]
rates[6] = algebraic[10]
algebraic[11] = constants[22]*constants[23]*log(constants[16]*states[7])
algebraic[12] = constants[22]*constants[23]*log(constants[17]*states[8])
algebraic[13] = constants[22]*constants[23]*log(constants[18]*states[9])
algebraic[17] = constants[4]*(exp((algebraic[11]+algebraic[12])/(constants[22]*constants[23]))-exp(algebraic[13]/(constants[22]*constants[23])))
algebraic[14] = constants[22]*constants[23]*log(constants[10]*states[2])
algebraic[18] = constants[5]*(exp(algebraic[13]/(constants[22]*constants[23]))-exp(algebraic[14]/(constants[22]*constants[23])))
algebraic[19] = constants[6]*(exp((algebraic[13]+algebraic[12])/(constants[22]*constants[23]))-exp((algebraic[14]+algebraic[12])/(constants[22]*constants[23])))
rates[9] = (algebraic[17]-algebraic[18])-algebraic[19]
algebraic[15] = constants[22]*constants[23]*log(constants[11]*states[0])
algebraic[20] = constants[7]*(exp((algebraic[14]+algebraic[15]*2.00000)/(constants[22]*constants[23]))-exp((algebraic[11]+algebraic[12])/(constants[22]*constants[23])))
rates[0] = ((algebraic[8]-algebraic[9])-algebraic[10])-2.00000*algebraic[20]
rates[2] = (-algebraic[7]+algebraic[8]+algebraic[18]+algebraic[19])-algebraic[20]
rates[7] = -algebraic[17]+algebraic[20]
algebraic[16] = constants[22]*constants[23]*log(constants[19]*states[10])
algebraic[21] = constants[8]*(exp(algebraic[12]/(constants[22]*constants[23]))-exp(algebraic[16]/(constants[22]*constants[23])))
rates[8] = ((-algebraic[17]+algebraic[20])-algebraic[21])+constants[21]
rates[10] = algebraic[21]
return(rates)
def computeAlgebraic(constants, states, voi):
algebraic = array([[0.0] * len(voi)] * sizeAlgebraic)
states = array(states)
voi = array(voi)
algebraic[0] = constants[22]*constants[23]*log(constants[9]*states[1])
algebraic[1] = constants[22]*constants[23]*log(constants[10]*states[2])
algebraic[4] = constants[22]*constants[23]*log(constants[13]*states[4])
algebraic[7] = constants[0]*(exp((algebraic[0]+algebraic[1])/(constants[22]*constants[23]))-exp(algebraic[4]/(constants[22]*constants[23])))
algebraic[2] = constants[22]*constants[23]*log(constants[11]*states[0])
algebraic[8] = constants[1]*(exp(algebraic[4]/(constants[22]*constants[23]))-exp((algebraic[2]+algebraic[1])/(constants[22]*constants[23])))
algebraic[3] = constants[22]*constants[23]*log(constants[12]*states[3])
algebraic[5] = constants[22]*constants[23]*log(constants[14]*states[5])
algebraic[9] = constants[2]*(exp((algebraic[2]+algebraic[3])/(constants[22]*constants[23]))-exp(algebraic[5]/(constants[22]*constants[23])))
algebraic[6] = constants[22]*constants[23]*log(constants[15]*states[6])
algebraic[10] = constants[3]*(exp((algebraic[5]+algebraic[2])/(constants[22]*constants[23]))-exp((algebraic[6]+algebraic[3])/(constants[22]*constants[23])))
algebraic[11] = constants[22]*constants[23]*log(constants[16]*states[7])
algebraic[12] = constants[22]*constants[23]*log(constants[17]*states[8])
algebraic[13] = constants[22]*constants[23]*log(constants[18]*states[9])
algebraic[17] = constants[4]*(exp((algebraic[11]+algebraic[12])/(constants[22]*constants[23]))-exp(algebraic[13]/(constants[22]*constants[23])))
algebraic[14] = constants[22]*constants[23]*log(constants[10]*states[2])
algebraic[18] = constants[5]*(exp(algebraic[13]/(constants[22]*constants[23]))-exp(algebraic[14]/(constants[22]*constants[23])))
algebraic[19] = constants[6]*(exp((algebraic[13]+algebraic[12])/(constants[22]*constants[23]))-exp((algebraic[14]+algebraic[12])/(constants[22]*constants[23])))
algebraic[15] = constants[22]*constants[23]*log(constants[11]*states[0])
algebraic[20] = constants[7]*(exp((algebraic[14]+algebraic[15]*2.00000)/(constants[22]*constants[23]))-exp((algebraic[11]+algebraic[12])/(constants[22]*constants[23])))
algebraic[16] = constants[22]*constants[23]*log(constants[19]*states[10])
algebraic[21] = constants[8]*(exp(algebraic[12]/(constants[22]*constants[23]))-exp(algebraic[16]/(constants[22]*constants[23])))
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)