- Author:
- Weiwei Ai <wai484@aucklanduni.ac.nz>
- Date:
- 2024-10-21 14:11:01+13:00
- Desc:
- Modify SGLT1_BG_fast.cellml to allow users to modify test_volt and Glco in the simulation tab.
- Permanent Source URI:
- http://models.cellml.org/workspace/b65/rawfile/65898d4880efb52227f2860ddafb4c8cde585d47/src/build_GLUT2.py
import os
import sys
# Get the directory containing the current file
current_dir = os.path.dirname(os.path.abspath(__file__))
sys.path.append(os.path.join(current_dir, '../buildBG/'))
from buildBG import *
from utilities import *
import math
import numpy as np
file_path=os.path.join(current_dir, '../Facilitated transporter/')
fmatrix=file_path+'SLC2_f.csv'
rmatrix=file_path+'SLC2_r.csv'
bg_components_json='../buildBG/BG_components.json'
# build the bond graph model
bg_dict={}
direction = 'e2f'
add_BG_components(bg_dict,bg_components_json, fmatrix)
add_BG_connections(bg_dict, fmatrix, direction)
direction = 'f2e'
add_BG_connections(bg_dict, rmatrix, direction)
# update the equations of the bond graph model
voi={'description': 'Time', 'units': 'second', 'symbol': 't'}
update_BG_eqn(bg_dict,voi)
fmatrix=file_path+'SLC2_f.csv'
rmatrix=file_path+'SLC2_r.csv'
# update the BG parameters for the biochemical reactions
eName, eID, ePort, fName, fID, fPort,N_f=load_matrix(fmatrix)
eName, eID, ePort, fName, fID, fPort,N_r=load_matrix(rmatrix)
V=1
V_o=90
h=0.726;g=12.1;c=1113;d=90.3;a=500000*V_o;b=a*9.5;f=3000*V_o;e=12.8459*f
kf=[h, c, a, e]
kr=[g, d, b, f]
V_i=0.09
V_o=0.09
V_E=1
Ws=[V_i,V_o,V_E,V_E,V_E,V_E]
K_c=[]
N_c=[]
kappa, K, K_eq, diff_, zero_est,k_est= kinetic2BGparams(N_f,N_r,kf,kr,K_c,N_c,Ws)
# print the estimated results
for i in range(len(kappa)):
print(fName[i],kappa[i])
for i in range(len(K)):
print(eName[i],K[i])
k_est_name=['h','c','a','e','g','d','b','f']
for i in range(len(k_est)):
print(k_est_name[i],k_est[i])
print('sum of relative errors',diff_)
update_BioBG_params(bg_dict, kappa, fName, K, eName)
update_BG_params(bg_dict,[('T',293)])
# combine K and kappa to a single array
param_val=np.concatenate((kappa,K))
param_fName=[]
for i in fName:
param_fName.append('$\kappa_{'+i+'}$')
param_eName=[]
for i in eName:
param_eName.append('$K_{'+i+'}$')
param_name=param_fName+param_eName
param_units=['fmol$.s^{-1}$']*len(fName)+['fmol$^{-1}$']*len(eName)
write_params_csv(param_name,param_val,param_units,csv_file=file_path+'SLC2_BG.csv')
# save the bond graph model to a json file
json_file=file_path+'SLC2_BG.json'
save_json(bg_dict, json_file)
