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 = 16
sizeStates = 6
sizeConstants = 23
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_algebraic[0] = "q_L_B1_init in component environment (fmol)"
legend_constants[0] = "q_R_B1_init in component environment (fmol)"
legend_constants[1] = "q_Gs_init in component environment (fmol)"
legend_constants[2] = "q_LR_B1_init in component environment (fmol)"
legend_constants[3] = "q_R_B1Gs_init in component environment (fmol)"
legend_constants[4] = "q_LR_B1Gs_init in component environment (fmol)"
legend_constants[5] = "stimSt in component environment (second)"
legend_constants[6] = "stimDur in component environment (second)"
legend_constants[7] = "tR in component environment (second)"
legend_constants[8] = "stimMag in component environment (fmol)"
legend_constants[9] = "stimHolding in component environment (fmol)"
legend_constants[22] = "m in component environment (fmol_per_sec)"
legend_algebraic[1] = "q_L_B1 in component environment (fmol)"
legend_algebraic[2] = "q_R_B1 in component environment (fmol)"
legend_algebraic[3] = "q_Gs in component environment (fmol)"
legend_algebraic[4] = "q_LR_B1 in component environment (fmol)"
legend_algebraic[5] = "q_R_B1Gs in component environment (fmol)"
legend_algebraic[6] = "q_LR_B1Gs in component environment (fmol)"
legend_states[0] = "q_L_B1 in component LRGbinding_B1AR (fmol)"
legend_states[1] = "q_R_B1 in component LRGbinding_B1AR (fmol)"
legend_states[2] = "q_Gs in component LRGbinding_B1AR (fmol)"
legend_states[3] = "q_LR_B1 in component LRGbinding_B1AR (fmol)"
legend_states[4] = "q_R_B1Gs in component LRGbinding_B1AR (fmol)"
legend_states[5] = "q_LR_B1Gs in component LRGbinding_B1AR (fmol)"
legend_constants[10] = "kappa_R_C_B1 in component LRGbinding_B1AR_parameters (fmol_per_sec)"
legend_constants[11] = "kappa_R_R_B1 in component LRGbinding_B1AR_parameters (fmol_per_sec)"
legend_constants[12] = "kappa_R_L_B1 in component LRGbinding_B1AR_parameters (fmol_per_sec)"
legend_constants[13] = "K_L_B1 in component LRGbinding_B1AR_parameters (per_fmol)"
legend_constants[14] = "K_R_B1 in component LRGbinding_B1AR_parameters (per_fmol)"
legend_constants[15] = "K_Gs in component LRGbinding_B1AR_parameters (per_fmol)"
legend_constants[16] = "K_LR_B1 in component LRGbinding_B1AR_parameters (per_fmol)"
legend_constants[17] = "K_R_B1Gs in component LRGbinding_B1AR_parameters (per_fmol)"
legend_constants[18] = "K_LR_B1Gs in component LRGbinding_B1AR_parameters (per_fmol)"
legend_constants[19] = "R in component constants (J_per_K_per_mol)"
legend_constants[20] = "T in component constants (kelvin)"
legend_algebraic[7] = "mu_L_B1 in component LRGbinding_B1AR (J_per_mol)"
legend_algebraic[8] = "mu_R_B1 in component LRGbinding_B1AR (J_per_mol)"
legend_algebraic[9] = "mu_Gs in component LRGbinding_B1AR (J_per_mol)"
legend_algebraic[10] = "mu_LR_B1 in component LRGbinding_B1AR (J_per_mol)"
legend_algebraic[11] = "mu_R_B1Gs in component LRGbinding_B1AR (J_per_mol)"
legend_algebraic[12] = "mu_LR_B1Gs in component LRGbinding_B1AR (J_per_mol)"
legend_algebraic[13] = "v_R_C_B1 in component LRGbinding_B1AR (fmol_per_sec)"
legend_algebraic[14] = "v_R_R_B1 in component LRGbinding_B1AR (fmol_per_sec)"
legend_algebraic[15] = "v_R_L_B1 in component LRGbinding_B1AR (fmol_per_sec)"
legend_constants[21] = "F in component constants (C_per_mol)"
legend_rates[0] = "d/dt q_L_B1 in component LRGbinding_B1AR (fmol)"
legend_rates[1] = "d/dt q_R_B1 in component LRGbinding_B1AR (fmol)"
legend_rates[2] = "d/dt q_Gs in component LRGbinding_B1AR (fmol)"
legend_rates[3] = "d/dt q_LR_B1 in component LRGbinding_B1AR (fmol)"
legend_rates[4] = "d/dt q_R_B1Gs in component LRGbinding_B1AR (fmol)"
legend_rates[5] = "d/dt q_LR_B1Gs in component LRGbinding_B1AR (fmol)"
return (legend_states, legend_algebraic, legend_voi, legend_constants)
def initConsts():
constants = [0.0] * sizeConstants; states = [0.0] * sizeStates;
constants[0] = 0.0004579000
constants[1] = 0.1455400000
constants[2] = 0
constants[3] = 0
constants[4] = 0
constants[5] = 3.1
constants[6] = 0.5e1
constants[7] = 0.3e1
constants[8] = 1e-7
constants[9] = 1e-8
states[0] = 1e-16
states[1] = 1e-16
states[2] = 1e-16
states[3] = 1e-16
states[4] = 1e-16
states[5] = 1e-16
constants[10] = 5573.84
constants[11] = 641.71
constants[12] = 1143.57
constants[13] = 0.885956
constants[14] = 0.834078
constants[15] = 0.18177
constants[16] = 7.24472
constants[17] = 172.108
constants[18] = 2.80863
constants[19] = 8.31
constants[20] = 310
constants[21] = 96485
constants[22] = constants[8]/constants[7]
return (states, constants)
def computeRates(voi, states, constants):
rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic
algebraic[2] = states[1]+constants[0]
algebraic[8] = constants[19]*constants[20]*log(constants[14]*algebraic[2])
algebraic[3] = states[2]+constants[1]
algebraic[9] = constants[19]*constants[20]*log(constants[15]*algebraic[3])
algebraic[5] = states[4]+constants[3]
algebraic[11] = constants[19]*constants[20]*log(constants[17]*algebraic[5])
algebraic[13] = constants[10]*exp((algebraic[8]+algebraic[9])/(constants[19]*constants[20]))-exp(algebraic[11]/(constants[19]*constants[20]))
rates[4] = algebraic[13]
algebraic[4] = states[3]+constants[2]
algebraic[10] = constants[19]*constants[20]*log(constants[16]*algebraic[4])
algebraic[6] = states[5]+constants[4]
algebraic[12] = constants[19]*constants[20]*log(constants[18]*algebraic[6])
algebraic[14] = constants[11]*exp((algebraic[10]+algebraic[9])/(constants[19]*constants[20]))-exp(algebraic[12]/(constants[19]*constants[20]))
rates[2] = -algebraic[13]-algebraic[14]
rates[5] = algebraic[14]
algebraic[0] = custom_piecewise([less(voi , constants[5]) & greater(voi , constants[5]-constants[7]), constants[9]+constants[22]*((voi-constants[5])+constants[7]) , greater_equal(voi , constants[5]) & less(voi , constants[5]+constants[6]), constants[8]+constants[9] , less(voi , constants[5]+constants[7]+constants[6]) & greater_equal(voi , constants[5]+constants[6]), constants[9]+-constants[22]*(((voi-constants[5])-constants[7])-constants[6]) , True, constants[9]])
algebraic[1] = states[0]+algebraic[0]
algebraic[7] = constants[19]*constants[20]*log(constants[13]*algebraic[1])
algebraic[15] = constants[12]*exp((algebraic[8]+algebraic[7])/(constants[19]*constants[20]))-exp(algebraic[10]/(constants[19]*constants[20]))
rates[0] = -algebraic[15]
rates[1] = -algebraic[13]-algebraic[15]
rates[3] = -algebraic[14]+algebraic[15]
return(rates)
def computeAlgebraic(constants, states, voi):
algebraic = array([[0.0] * len(voi)] * sizeAlgebraic)
states = array(states)
voi = array(voi)
algebraic[2] = states[1]+constants[0]
algebraic[8] = constants[19]*constants[20]*log(constants[14]*algebraic[2])
algebraic[3] = states[2]+constants[1]
algebraic[9] = constants[19]*constants[20]*log(constants[15]*algebraic[3])
algebraic[5] = states[4]+constants[3]
algebraic[11] = constants[19]*constants[20]*log(constants[17]*algebraic[5])
algebraic[13] = constants[10]*exp((algebraic[8]+algebraic[9])/(constants[19]*constants[20]))-exp(algebraic[11]/(constants[19]*constants[20]))
algebraic[4] = states[3]+constants[2]
algebraic[10] = constants[19]*constants[20]*log(constants[16]*algebraic[4])
algebraic[6] = states[5]+constants[4]
algebraic[12] = constants[19]*constants[20]*log(constants[18]*algebraic[6])
algebraic[14] = constants[11]*exp((algebraic[10]+algebraic[9])/(constants[19]*constants[20]))-exp(algebraic[12]/(constants[19]*constants[20]))
algebraic[0] = custom_piecewise([less(voi , constants[5]) & greater(voi , constants[5]-constants[7]), constants[9]+constants[22]*((voi-constants[5])+constants[7]) , greater_equal(voi , constants[5]) & less(voi , constants[5]+constants[6]), constants[8]+constants[9] , less(voi , constants[5]+constants[7]+constants[6]) & greater_equal(voi , constants[5]+constants[6]), constants[9]+-constants[22]*(((voi-constants[5])-constants[7])-constants[6]) , True, constants[9]])
algebraic[1] = states[0]+algebraic[0]
algebraic[7] = constants[19]*constants[20]*log(constants[13]*algebraic[1])
algebraic[15] = constants[12]*exp((algebraic[8]+algebraic[7])/(constants[19]*constants[20]))-exp(algebraic[10]/(constants[19]*constants[20]))
return algebraic
def custom_piecewise(cases):
"""Compute result of a piecewise function"""
return select(cases[0::2],cases[1::2])
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)