- Author:
- Leyla <lnor300>
- Date:
- 2022-09-27 19:24:59+13:00
- Desc:
- ..
- Permanent Source URI:
- https://models.physiomeproject.org/workspace/83c/rawfile/881bedcb01f191d01798f0d6266263a935197ee3/Simulations/IAno1.py
# Author : Leyla Noroozbabaee
# Date: 12/09/2021
# To reproduce the data needed for Figure 3 in associated original paper,
# execute this script in the Python console in OpenCOR. This can be done
# with the following commands at the prompt in the OpenCOR Python console:
#
# In [1]: cd path/to/folder_this_file_is_in
# In [2]: run IAno1.py
import opencor as oc
import numpy as np
from pathlib import Path
# The prefix of the saved output file name
prefilename = 'Fig3'
# Load the simulation file
simfile = 'Ano1_Lees_2021.sedml'
simulation = oc.open_simulation(simfile)
# The data object houses all the relevant information
# and pointers to the OpenCOR internal data representations
data = simulation.data()
# Set the experiments
Vm = np.linspace(-100, +100, num=6)
duration = 20
# Define the interval of interest for this simulation experiment
start, end, pointInterval = 0, duration, 0.01
data.set_starting_point(start)
data.set_ending_point(end)
data.set_point_interval(pointInterval)
# Data to save
varName = np.array([ "Time", "IAon1" ])
vars = np.reshape(varName, (1, len(varName)))
rows = duration * 100 + 1
r = np.zeros((rows, len(varName)))
Ca = [0.10, 1, 10, 20]
Ca_local = np.linspace(15, 30, num=6)
c = ['a','b','c','d']
for j, Calocal in enumerate(Ca):
for i, V in enumerate(Vm):
# Reset states and parameters
simulation.reset(True)
# Set constant parameter values
if j == 3 :
data.constants()['ICC_Membrane/I_Ano1/d_Ano1/localCa_clamp'] = Ca_local[i]
data.constants()['ICC_Membrane/I_Ano1/d_Ano1/localCa_bl'] = 0.0
data.constants()['ICC_Membrane/I_Ano1/d_Ano1/localCa_init'] = 0.0
data.constants() ['ICC_Membrane/I_Ano1/d_Ano1/d_Ano1_tscale' ] = 10
data.constants()['ICC_Membrane/V_clamp'] = V
data.constants()['ICC_Membrane/V_bl'] = V
data.constants()['ICC_Membrane/V_init'] = V
else:
data.constants()['ICC_Membrane/I_Ano1/d_Ano1/localCa_clamp'] = Calocal
data.constants()['ICC_Membrane/I_Ano1/d_Ano1/localCa_bl'] = Calocal
data.constants()['ICC_Membrane/I_Ano1/d_Ano1/localCa_init'] = Calocal
data.constants() [ 'ICC_Membrane/I_Ano1/d_Ano1/d_Ano1_tscale' ] = 10
data.constants()['ICC_Membrane/V_clamp'] = V
data.constants()['ICC_Membrane/V_bl'] = -100
data.constants()['ICC_Membrane/V_init'] = 0
data.constants() ['ICC_Membrane/I_Ano1/d_Ano1/Ano1_s'] = 0.0156
simulation.run()
# Access simulation results
results = simulation.results()
# Grab a specific algebraic variable results
r [:, 0] = results.voi().values()
r [ :, 1 ] = results.algebraic()['ICC_Membrane/I_Ano1/I_Ano1'].values()
simulation.clear_results()
# Save the simulation result of the last run
filename = '%s_%d_%s.csv' % (prefilename, i, c[j])
np.savetxt(filename, vars, fmt='%s', delimiter=",")
with open(filename, "ab") as f:
np.savetxt(f, r, delimiter=",")
f.close
