- Author:
- leyla <noroozbabaee@gmail.com>
- Date:
- 2022-06-20 15:25:51+12:00
- Desc:
- A Computational Model of the Ionic Currents, Ca Dynamics and Action Potentials Underlying Contraction of Isolated Uterine Smooth Muscle
- Permanent Source URI:
- https://staging.physiomeproject.org/workspace/8aa/rawfile/539364647a9050858e906191c88d1552b6711c57/Experiments/Figure_7/Fig7_sim.py
# To reproduce the data needed for Figure 7 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 Fig7_sim.py
import opencor as oc
import numpy as np
Fig_A = 1
Fig_BCD = 1
if Fig_A:
prefilename = 'Fig7'
# Load the simulation file
simfile = 'C:/Users/lnor300/Documents/CellML/12_Labors/Tong_2011_V1/Simulations/Tong_2011.sedml'
simulation = oc.open_simulation(simfile)
data = simulation.data()
# Reset states variables and parameters
simulation.reset(True)
# Set constant values
start = 0
end = 20000
pointInterval = 0.5
data.set_starting_point(start)
data.set_ending_point(end)
data.set_point_interval(pointInterval)
data.constants()['interface/membrane_potential/v_init'] = -90
simulation.run()
# Access simulation results
results = simulation.results()
# Data to save
varName = np.array(["Time", "sss", "xss", "stc", "xtc","ika", "v"])
vars = np.reshape(varName, (1,7))
rows = end * 2 + 1
# Grab some variable results
r = np.zeros((rows, len(varName)))
r [ :, 0 ] = results.voi().values()
r [ :, 1 ] = results.algebraic()['interface/I_Ka/sss'].values()
r [ :, 2 ] = results.algebraic()['interface/I_Ka/xss'].values()
r [ :, 3 ] = results.algebraic() ['interface/I_Ka/stc'].values()
r [ :, 4 ] = results.algebraic() ['interface/I_Ka/xtc'].values()
r [ :, 5 ] = results.algebraic() ['interface/I_Ka/ika'].values()
r [ :, 6 ] = results.states() ['interface/membrane_potential/v'].values()
filename = '%s.csv' % (prefilename)
np.savetxt(filename, vars, fmt='%s', delimiter=",")
with open(filename, "ab") as f:
np.savetxt(f, r, delimiter=",")
f.close
if Fig_BCD:
prefilename = 'Fig7_BCD'
# Load the simulation file
simfile = 'C:/Users/lnor300/Documents/CellML/12_Labors/Tong_2011_V1/Simulations/VoltageVAR_Tong_2011.sedml'
simulation = oc.open_simulation(simfile)
data = simulation.data()
# Set constant values
start = 0
end = 10000
pointInterval = 0.5
data.set_starting_point(start)
data.set_ending_point(end)
data.set_point_interval(pointInterval)
v_clamp = [-40,-30,-20,-10, 0, 10,20,30, 40,50 ]
for i in range(len(v_clamp)):
data.constants() [ 'interface/membrane_potential/v_hold' ] = -80
# Reset states variables and parameters
simulation.reset(True)
data.constants() [ 'interface/parameters/kmca' ] = 0.001
data.constants() [ 'interface/membrane_potential/v_clamp' ] = v_clamp [ i ]
data.constants() [ 'interface/membrane_potential/time_clamp_end' ] = end
data.constants() [ 'interface/membrane_potential/time_clamp_sta' ] = 10
simulation.run()
# Access simulation results
results = simulation.results()
# Data to save
varName = np.array(["Time", "ika", "v", " stc"])
vars = np.reshape(varName, (1, 4))
rows = end * 2 + 1
# Grab some algebraic results
r = np.zeros((rows, len(varName)))
r [ :, 0 ] = results.voi().values()
r [ :, 1 ] = results.algebraic() ['interface/I_Ka/ika'].values()
r [ :, 2 ] = results.algebraic() [ 'interface/membrane_potential/v'].values()
r [ :, 3 ] = results.algebraic() [ 'interface/I_Ka/stc' ].values()
# Save the simulation result of the last run
filename = '%s_%s.csv' % (prefilename, i)
np.savetxt(filename, vars, fmt='%s', delimiter=",")
with open(filename, "ab") as f:
np.savetxt(f, r, delimiter=",")
f.close
