- Author:
- Leyla <lnor300>
- Date:
- 2022-11-02 15:33:57+13:00
- Desc:
- ..
- Permanent Source URI:
- https://models.cellml.org/workspace/763/rawfile/81e638b3f094d00aade965d9e2ca7bd101f33371/Simulation/Figure2/Fig2_Sim.py
# Author : Leyla Noroozbabaee
# Bioengineering Institute
# The University of Auckland
# Date: 2/10/2021
# To reproduce the data needed for Figure 2A 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 Fig2_sim.py
# To Plot: run Fig2_plot.py in the Python console
import opencor as oc
import numpy as np
prefilename = 'Fig2_A'
simfile = 'IP3_Imtiaz_2002.sedml'
simulation = oc.open_simulation(simfile)
data = simulation.data()
# Reset states and parameters
simulation.reset(True)
# Set constant parameter values
start = 0
end = 10
pointInterval = 0.01
data.set_starting_point(start)
data.set_ending_point(end)
data.set_point_interval(pointInterval)
data.constants()['vm/I_clamp1'] = 0
data.constants()['vm/I_clamp2'] = 0
data.constants()['ca/y_init'] = 4.11341208572137
data.constants()['ca/z_init'] = 0.478526130219779
data.constants()['p_ip3/p_ip3_init'] = 0.408438668750528
data.constants()['p_ip3/b_ip3'] = 0.8
# Run simulation
simulation.run()
# Access simulation results
results = simulation.results()
# Grab the selected results
varName = np.array(["time", "Vm", "z", "ip3", "y"])
vars = np.reshape(varName, (1, 5))
rows = end * 100 + 1
print(rows)
r = np.zeros((rows, len(varName)))
r[:, 0] = results.voi().values()
r[:, 1] = results.states()['vm/vm'].values()
r[:, 2] = results.states()['ca/z'].values()
r[:, 3] = results.states()['p_ip3/p_ip3'].values()
r[:, 4] = results.states()['ca/y'].values()
# Save the data
filename = '%s.csv' % prefilename
np.savetxt(filename, vars, fmt='%s', delimiter=",")
with open(filename, "ab") as f:
np.savetxt(f, r, delimiter=",")
f.close
