- Author:
- nima <nafs080@aucklanduni.ac.nz>
- Date:
- 2021-06-19 09:23:55+12:00
- Desc:
- 1 script instead of 2
- Permanent Source URI:
- https://staging.physiomeproject.org/workspace/648/rawfile/7cb8a9d44ad7e22d7ee5ee37d836a6f97e05758f/Figure7.py
# To reproduce the data needed for Figure 7 in associated
# Physiome 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/the/folder/this/file/is/in
# In [2]: %run Figure7.py
import opencor as opencor
import numpy as np
# load the reference model
simulation = opencor.open_simulation("HumanSAN_Fabbri_Fantini_Wilders_Severi_2017.sedml")
data = simulation.data()
data.set_ending_point(2.5)
data.set_point_interval(0.001)
simulation.reset(True)
results = np.zeros((25, 2501))
for i in range(0, 1):
simulation.run()
ds = simulation.results().data_store()
results[0] = ds.voi_and_variables()["environment/time"].values()
for i in range(0, 25):
simulation.run()
simulation.clear_results()
simulation.run()
ds = simulation.results().data_store()
results[1] = ds.voi_and_variables()["Membrane/V"].values()
results[4] = ds.voi_and_variables()["i_NaK/i_NaK"].values()
results[7] = ds.voi_and_variables()["Membrane/i_tot"].values()
results[10] = ds.voi_and_variables()["i_Ks/i_Ks"].values()
results[13] = ds.voi_and_variables()["i_f/i_f"].values()
results[16] = ds.voi_and_variables()["i_KACh/i_KACh"].values()
results[19] = ds.voi_and_variables()["i_CaL/i_CaL"].values()
results[22] = ds.voi_and_variables()["Ca_intracellular_fluxes/j_up"].values()
simulation.reset(True)
for i in range(0, 14):
data.constants()["Rate_modulation_experiments/ACh"] = 1e-5
simulation.run()
simulation.clear_results()
simulation.run()
ds = simulation.results().data_store()
results[2] = ds.voi_and_variables()["Membrane/V"].values()
results[5] = ds.voi_and_variables()["i_NaK/i_NaK"].values()
results[8] = ds.voi_and_variables()["Membrane/i_tot"].values()
results[11] = ds.voi_and_variables()["i_Ks/i_Ks"].values()
results[14] = ds.voi_and_variables()["i_f/i_f"].values()
results[17] = ds.voi_and_variables()["i_KACh/i_KACh"].values()
results[20] = ds.voi_and_variables()["i_CaL/i_CaL"].values()
results[23] = ds.voi_and_variables()["Ca_intracellular_fluxes/j_up"].values()
simulation.reset(True)
for i in range(0, 13):
data.constants()["Rate_modulation_experiments/Iso_1_uM"] = 1
simulation.run()
simulation.clear_results()
simulation.run()
ds = simulation.results().data_store()
results[3] = ds.voi_and_variables()["Membrane/V"].values()
results[6] = ds.voi_and_variables()["i_NaK/i_NaK"].values()
results[9] = ds.voi_and_variables()["Membrane/i_tot"].values()
results[12] = ds.voi_and_variables()["i_Ks/i_Ks"].values()
results[15] = ds.voi_and_variables()["i_f/i_f"].values()
results[18] = ds.voi_and_variables()["i_KACh/i_KACh"].values()
results[21] = ds.voi_and_variables()["i_CaL/i_CaL"].values()
results[24] = ds.voi_and_variables()["Ca_intracellular_fluxes/j_up"].values()
np.savetxt("Figure7.csv", results[:25].T, fmt='%.4e', delimiter=',')
