- Author:
- Shelley Fong <sfon036@UoA.auckland.ac.nz>
- Date:
- 2024-09-24 13:57:30+12:00
- Desc:
- Adding new py files and moving pics into folder
- Permanent Source URI:
- https://models.cellml.org/workspace/702/rawfile/c63c733e2057d3e417439cf01363b411899eb53d/fig11_wholecell.py
import os
import math
import numpy as np
import matplotlib
matplotlib.use('agg')
import scipy
import matplotlib.pyplot as plt
from scipy.integrate import solve_ivp
import opencor as opencor
import timeit
start = timeit.default_timer()
def load_sedml(filename):
return opencor.open_simulation(filename)
file = load_sedml("Channels.sedml")
print()
def sim ():
# sedml file
data = file.data()
timespan = [0, 3e3]
data.states()["main/v"] = -75.5966016388547
data.states()["main/ca_SR"] = 0.3350867967323261
data.states()["main/ca_i"] = 0.000219191642424964
data.states()["main/Na_i"] = 7.16928091250999
data.states()["main/Ki"] = 104.748824394112
data.states()["main/ca_ligand"] = 0
data.states()["main/X_ca_act"] = 0.000394925342652924
data.states()["main/X_ca_inact"] = 0.170990105585540
data.states()["main/X_fca_inact"] = 0.877798946134089
data.states()["main/X_kr_act"] = 0.309767485715433
data.states()["main/X_kr_inact"] = 0.450577185148519
data.states()["main/X_ks_act"] = 0.153788281650949
data.states()["main/X_na_h_inact"] = 0.739543607812429
data.states()["main/X_na_j_inact"] = 0.124515982574505
data.states()["main/X_na_m_act"] = 0.0297549962926414
data.states()["main/X_f_act"] = 0.00640338504912616
data.states()["main/X_to_inact"] = 0.746802810614006
data.states()["main/X_to_act"] = 0.000267597833344161
data.states()["main/X_cat_act"] = 0.000270195573471577
data.states()["main/X_cat_inact"] = 0.756032904368393
data.states()["main/C"] = 0.0113120363433751
data.states()["main/O"] = 0.000165045105312396
data.states()["main/I"] = 0.0142153622323012
data.set_starting_point(timespan[0])
data.set_ending_point(timespan[1])
data.set_point_interval(1)
file.run()
ds = file.results().data_store()
v = ds.voi_and_variables()["main/v"].values()
Time_hold = (ds.voi_and_variables()["main/t"].values())
INaCa = ds.voi_and_variables()["main/i_naca"].values()
IpCa = ds.voi_and_variables()["main/i_PCa"].values()
Iup = ds.voi_and_variables()["main/i_up"].values()
cai = ds.voi_and_variables()["main/ca_i"].values()
Cai_buf = ds.voi_and_variables()["main/Cai_buf"].values()
i_leak = ds.voi_and_variables()["main/j_leak"].values()
i_CaL = ds.voi_and_variables()["main/i_CaL"].values()
return v, Time_hold, INaCa, IpCa, Iup, cai, Cai_buf, i_leak, i_CaL
sim()
time = sim()[1]
INaCa = sim()[2]
IpCa = sim()[3]
Iup = sim()[4]
cai = sim()[5]
print()
plt.figure(figsize=(8, 5))
plt.plot(sim()[1], sim()[0], color= 'red', linewidth= 3)
plt.yticks(np.arange(-100, 51, 50))
plt.xticks(np.arange(0, 3001, 1000))
plt.xlim(0, 3000)
plt.ylim(-100, 50)
plt.xlabel('Time (ms)', fontsize= 18)
plt.ylabel('Voltage (mV)', fontsize= 18)
plt.tick_params(axis='both', labelsize='18')
plt.subplots_adjust(left=0.2,
bottom=0.2,
right=0.9,
top=0.9,
wspace=0.3,
hspace=0.3)
stop = timeit.default_timer()
print('Time: ', stop - start)
plt.savefig('figures/Figure11_wholecell.png')
