- 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_10/Fig10_sim.py
# 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 Fig10_sim.py
import opencor as oc
import numpy as np
# The prefix of the saved output file name
prefilename = 'Fig10'
# Load the simulation file
Fig_AC = 1
Fig_B = 1
Fig_DE = 0
Fig_FG = 0
sub =['A_C', 'B', 'D_E', 'F_G']
if Fig_AC:
varName = np.array([ "Time", "css", "ctc", "icl", "c", "v", "cai" ])
simfile = 'C:/Users/lnor300/Documents/CellML/12_Labors/Tong_2011_V1/Simulations/Tong_2011_newVersion.sedml'
simulation = oc.open_simulation(simfile)
data = simulation.data()
# Set constant values
start = 0
end = 10000
pointInterval = 0.1
# Reset states variables
data.set_starting_point(start)
data.set_ending_point(end)
data.set_point_interval(pointInterval)
cai = [ 100e-6, 250e-6, 500e-6]
for i in range(len(cai)):
# Reset states variables and parameters
simulation.reset(True)
data.constants()['interface/membrane_potential/v_init'] = 190
data.constants() [ 'interface/Ca_Concentrations/ca_var' ] = 0
data.constants() [ 'interface/membrane_potential/v_var' ] = 1
data.constants() [ 'interface/Ca_Concentrations/time_clamp_sta' ] = 0
data.constants() [ 'interface/Ca_Concentrations/time_clamp_end' ] = end
data.constants()['interface/Ca_Concentrations/cai_init'] = cai[i]
data.constants()['interface/Ca_Concentrations/cai_hold'] = cai[i]
simulation.run()
# Access simulation results
results = simulation.results()
# Data to save
rows = end * 10 + 1
vars = np.reshape(varName, (1, 7))
# Grab some algebraic (state variable) results
r = np.zeros((rows, len(varName)))
r [ :, 0 ] = results.voi().values()
r [ :, 1 ] = results.algebraic()['interface/I_Cl/css'].values()
r [ :, 2 ] = results.algebraic()['interface/I_Cl/ctc'].values()
r [ :, 3 ] = results.algebraic() [ 'interface/I_Cl/icl'].values()
r [ :, 4 ] = results.states() [ 'interface/I_Cl/c'].values()
r [ :, 5 ] = results.algebraic() [ 'interface/membrane_potential/v'].values()
r [ :, 6 ] = results.algebraic() [ 'interface/Ca_Concentrations/cai'].values()
filename = '%s_%s_%s.csv' % (prefilename,sub[0],i)
np.savetxt(filename, vars, fmt='%s', delimiter=",")
with open(filename, "ab") as f:
np.savetxt(f, r, delimiter=",")
f.close
if Fig_B :
simfile = 'C:/Users/lnor300/Documents/CellML/12_Labors/Tong_2011_V1/Simulations/Tong_2011_newVersion.sedml'
simulation = oc.open_simulation(simfile)
data = simulation.data()
# Set constant values
start = 0
end = 50000
pointInterval = 0.1
data.set_starting_point(start)
data.set_ending_point(end)
data.set_point_interval(pointInterval)
v_cons = [-60, -30, 0, 30]
varName = np.array([ "Time", "css", "cai","v" ])
for i in range(len(v_cons)):
# Reset states variables and parameters
simulation.reset(True)
data.constants()['interface/membrane_potential/v_init'] = 100
data.constants() [ 'interface/Ca_Concentrations/cai_init' ] = 0.000116
data.constants() [ 'interface/Ca_Concentrations/ca_var' ] = 1
data.constants() [ 'interface/membrane_potential/v_var' ] = 0
data.constants() [ 'interface/membrane_potential/time_clamp_sta' ] = 0
data.constants() [ 'interface/membrane_potential/time_clamp_end' ] = end
data.constants() [ 'interface/membrane_potential/v_hold1'] = v_cons[i]
data.constants() [ 'interface/membrane_potential/v_clamp' ] = v_cons[i]
data.constants() [ 'interface/membrane_potential/v_hold2' ] = v_cons[i]
simulation.run()
# Access simulation results
results = simulation.results()
# Data to save
rows = end * 10 + 1
vars = np.reshape(varName, (1,4))
# Grab a some algebraic variable results
r = np.zeros((rows, len(varName)))
r [ :, 0 ] = results.voi().values()
r [ :, 1 ] = results.algebraic()['interface/I_Cl/css'].values()
r [ :, 2 ] = results.algebraic() [ 'interface/Ca_Concentrations/cai'].values()
r [ :, 3 ] = results.algebraic() [ 'interface/membrane_potential/v' ].values()
filename = '%s_%s_%s.csv' % (prefilename,sub[1],i)
np.savetxt(filename, vars, fmt='%s', delimiter=",")
with open(filename, "ab") as f:
np.savetxt(f, r, delimiter=",")
f.close
if Fig_DE:
simfile = 'C:/Users/lnor300/Documents/CellML/12_Labors/Tong_2011_V1/Simulations/Tong_2011_newVersion.sedml'
simulation = oc.open_simulation(simfile)
data = simulation.data()
# Set constant values
start = 0
end = 400
pointInterval = 0.1
data.set_starting_point(start)
data.set_ending_point(end)
data.set_point_interval(pointInterval)
varName = np.array([ "Time", "css", "ctc", "icl", "c", "v", "ical" ])
vars = np.reshape(varName, (1,7))
rows = end * 10 + 1
v_clamp = [ 50, 40, 30, 20, 10, 0, -10, -20, -30, -40, -50 ]
for i in range(len(v_clamp)):
# Reset states variables and parameters
simulation.reset(True)
data.constants() [ 'interface/membrane_potential/v_var' ] = 0
data.constants() [ 'interface/membrane_potential/time_clamp_sta' ] = 100
data.constants() [ 'interface/membrane_potential/time_clamp_end' ] = 200
data.constants() [ 'interface/membrane_potential/a_correction' ] = 0
data.constants() [ 'interface/Ca_Concentrations/cai_init' ] = 0.000116
data.constants() [ 'interface/membrane_potential/v_hold1' ] = -60
data.constants() [ 'interface/membrane_potential/v_clamp' ] = v_clamp [ i ]
data.constants() [ 'interface/membrane_potential/v_hold2' ] = -60
simulation.run()
# Access simulation results
results = simulation.results()
# Grab some algebraic results
r = np.zeros((rows, len(varName)))
r [ :, 0 ] = results.voi().values()
r [ :, 1 ] = results.algebraic() [ 'interface/I_Cl/css' ].values()
r [ :, 2 ] = results.algebraic() [ 'interface/I_Cl/ctc' ].values()
r [ :, 3 ] = results.algebraic() [ 'interface/I_Cl/icl' ].values()
r [ :, 4 ] = results.states() [ 'interface/I_Cl/c' ].values()
r [ :, 5 ] = results.algebraic() [ 'interface/membrane_potential/v' ].values()
r [ :, 6 ] = results.algebraic() [ 'interface/I_CaL/ical' ].values()
filename = '%s_%s_%s.csv' % (prefilename, sub[2], i)
np.savetxt(filename, vars, fmt='%s', delimiter=",")
with open(filename, "ab") as f:
np.savetxt(f, r, delimiter=",")
f.close
if Fig_FG:
simfile = 'C:/Users/lnor300/Documents/CellML/12_Labors/Tong_2011_V1/Simulations/Tong_2011_newVersion.sedml'
simulation = oc.open_simulation(simfile)
data = simulation.data()
# Set constant values
start = 0
end = 400
pointInterval = 0.1
data.set_starting_point(start)
data.set_ending_point(end)
data.set_point_interval(pointInterval)
varName = np.array([ "Time", "css", "ctc", "icl", "c", "v", "ical" ])
vars = np.reshape(varName, (1,7))
rows = end * 10 + 1
v_clamp = [ 40, 20, 0, -20, -40, -60, -80, -100 ]
for i in range(len(v_clamp)):
# Reset states variables and parameters
simulation.reset(True)
data.constants() [ 'interface/membrane_potential/v_var' ] = 0
data.constants() [ 'interface/membrane_potential/time_clamp_sta' ] = 100
data.constants() [ 'interface/membrane_potential/time_clamp_end' ] = 200
data.constants() [ 'interface/membrane_potential/a_correction' ] = 0
data.constants() [ 'interface/Ca_Concentrations/cai_init' ] = 0.000116
data.constants() [ 'interface/membrane_potential/v_hold1' ] = -60
data.constants() [ 'interface/membrane_potential/v_clamp' ] = 0
data.constants() [ 'interface/membrane_potential/v_hold2' ] = v_clamp[i]
simulation.run()
# Access simulation results
results = simulation.results()
# Grab a some algebraic variable results
r = np.zeros((rows, len(varName)))
r [ :, 0 ] = results.voi().values()
r [ :, 1 ] = results.algebraic() [ 'interface/I_Cl/css' ].values()
r [ :, 2 ] = results.algebraic() [ 'interface/I_Cl/ctc' ].values()
r [ :, 3 ] = results.algebraic() [ 'interface/I_Cl/icl' ].values()
r [ :, 4 ] = results.states() [ 'interface/I_Cl/c' ].values()
r [ :, 5 ] = results.algebraic() [ 'interface/membrane_potential/v' ].values()
r [ :, 6 ] = results.algebraic() [ 'interface/I_CaL/ical' ].values()
filename = '%s_%s_%s.csv' % (prefilename, sub[3], i)
np.savetxt(filename, vars, fmt='%s', delimiter=",")
with open(filename, "ab") as f:
np.savetxt(f, r, delimiter=",")
f.close
