- 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_5/Fig5_sim.py
# Author : Leyla Noroozbabaee
# Date: 12/04/2022
# FOR the case of time dependent state variable such as membrane potential the following definition is applied.
# var v: mV {init: v_init, pub: out};
# ode(v, time) = - I_tot;
#
# FOR the case of step-wise changes in state variable such as membrane potential the following definition is applied
# var v: mV {pub: out};
# v = sel
# case (time <= time_clamp_sta) and (v_var == 0{dimensionless}):
# v_hold;
# case (time > time_clamp_sta) and (time <= time_clamp_end) and (v_var == 0{dimensionless}):
# v_clamp;
# otherwise:
# v_hold;
# endsel;
# To reproduce the data needed for Figure 5 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 Fig5_sim.py
import opencor as oc
import numpy as np
Fig_D = 1
Fig_ABC = 1
Fig_EF = 1
if Fig_ABC:
prefilename = 'Fig5'
# 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 = 1000
pointInterval = 0.1
data.set_starting_point(start)
data.set_ending_point(end)
data.set_point_interval(pointInterval)
# simulation.reset(True)
data.constants()['interface/membrane_potential/v_init'] = -80
data.constants() ['interface/parameters/kmca'] = 0.001
data.constants() [ 'interface/I_h/a_correction' ] = 1
simulation.run()
# Access simulation results
results = simulation.results()
# Data to save
varName = np.array(["Time", "qss", "rss", "qtc", "r1tc","r2tc", "ik1", "v"])
vars = np.reshape(varName, (1,8))
rows = end * 10 + 1
# Grab some algebraic results
r = np.zeros((rows, len(varName)))
r [ :, 0 ] = results.voi().values()
r [ :, 1 ] = results.algebraic()['interface/I_K1/qss'].values()
r [ :, 2 ] = results.algebraic()['interface/I_K1/rss'].values()
r [ :, 3 ] = results.algebraic() [ 'interface/I_K1/qtc'].values()
r [ :, 4 ] = results.algebraic() [ 'interface/I_K1/r1tc'].values()
r [ :, 5 ] = results.algebraic() [ 'interface/I_K1/r2tc'].values()
r [ :, 6 ] = results.algebraic() [ 'interface/I_K1/ik1'].values()
r [ :, 7 ] = 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_EF:
prefilename = 'Fig5_4'
# 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 = 1
data.set_starting_point(start)
data.set_ending_point(end)
data.set_point_interval(pointInterval)
v_clamp = [-30, -20, -10, 0, 10, 20, 30, 40,45]
v_hold = [-380, -40]
# Reset states variables and parameters
simulation.reset(True)
for j in range(len(v_hold)):
data.constants()['interface/membrane_potential/v_hold'] = v_hold[j]
for i in range(len(v_clamp)):
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' ] = 40
data.constants() [ 'interface/parameters/ki' ] = 110
data.constants() [ 'interface/parameters/ko' ] = 4
simulation.run()
# Access simulation results
results = simulation.results()
# Data to save
varName = np.array([ "Time", "ik1", "v","max" ])
vars = np.reshape(varName, (1, 4))
rows = end * 1 + 1
# Grab some algebraic results
r = np.zeros((rows, len(varName)))
r [ :, 0 ] = results.voi().values()
r [ :, 1 ] = results.algebraic() [ 'interface/I_K1/ik1' ].values()
r [ :, 2 ] = results.algebraic() [ 'interface/membrane_potential/v' ].values()
r [ :, 3 ] = max(r [ :, 1 ])
# Save the simulation result of the last run
filename = '%s_%s_%s.csv' % (prefilename, j,i)
np.savetxt(filename, vars, fmt='%s', delimiter=",")
with open(filename, "ab") as f:
np.savetxt(f, r, delimiter=",")
f.close
if Fig_D:
prefilename = 'Fig5_5'
# 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)
time_clamp = 40
v_clamp = [-40,-30,-20,-10,0, 10 ]
for i in range(len(v_clamp)):
# Reset states variables and parameters
simulation.reset(True)
data.constants() [ 'interface/membrane_potential/v_hold' ] = -80
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' ] = 40
simulation.run()
# Access simulation results
results = simulation.results()
# Data to save
varName = np.array([ "Time", "ik1", "v" ])
vars = np.reshape(varName, (1, 3))
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_K1/ik1'].values()
r [ :, 2 ] = results.algebraic() [ 'interface/membrane_potential/v'].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
