# 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 Fig1_sim.py import opencor as oc import matplotlib.pyplot as plt import numpy as np # The prefix of the saved output file name cai_var = 1; cai_var_ka = 0; sub =['a', 'b'] V_hold = 0; if cai_var: prefilename = 'Fig8' # Load the simulation file simfile = 'CaVAR_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 = 2000 pointInterval = 1 data.set_starting_point(start) data.set_ending_point(end) data.set_point_interval(pointInterval) # data.constants() ['interface/parameters/kmca'] = 0.001 # data.constants() [ 'interface/I_h/a_correction' ] = 1 ca_i = [0.00001, 0.00005, 0.0001, 0.0005, 0.001, 0.005, 0.01, 0.05, 0.1, 0.5, 0.8, 1.0, 5.0, 10, 50, 100] for j in range(len(ca_i)): simulation.reset(True) data.constants()['interface/membrane_potential/v_init'] = 280#-200 data.constants() [ 'interface/Ca_Concentrations/cai' ] = ca_i [ j ] simulation.run() # Access simulation results results = simulation.results() # Data to save if cai_var_ka: varName = np.array(["Time", "xass_z", "xass_vh", "xatc", "xass", "iBKa","xa", "v"]) vars = np.reshape(varName, (1,8)) rows = end * 1 + 1 print(rows) # Grab a some algebraic variable results r = np.zeros((rows, len(varName))) r [ :, 0 ] = results.voi().values() r [ :, 1 ] = results.constants()['interface/I_BKa/xass_z'].values() r [ :, 2 ] = results.constants()['interface/I_BKa/xass_vh'].values() r [ :, 3 ] = results.algebraic() [ 'interface/I_BKa/xatc'].values() r [ :, 4 ] = results.algebraic() [ 'interface/I_BKa/xass' ].values() r [ :, 5 ] = results.algebraic() [ 'interface/I_BKa/iBKa'].values() r [ :, 6 ] = results.states() [ 'interface/I_BKa/xa' ].values() r [ :, 7] = results.states() [ 'interface/membrane_potential/v' ].values() filename = '%s_%s_%s.csv' % (prefilename, sub[0],j) np.savetxt(filename, vars, fmt='%s', delimiter=",") with open(filename, "ab") as f: np.savetxt(f, r, delimiter=",") f.close else: varName = np.array([ "Time", "xabss_z", "xabss_vh", "xabtc", "xabss", "iBKab","xab", "v" ]) vars = np.reshape(varName, (1, 8)) rows = end * 1 + 1 print(rows) # Grab a some algebraic variable results r = np.zeros((rows, len(varName))) r [ :, 0 ] = results.voi().values() r [ :, 1 ] = results.constants() [ 'interface/I_BKab/xabss_z' ].values() r [ :, 2 ] = results.constants() [ 'interface/I_BKab/xabss_vh' ].values() r [ :, 3 ] = results.algebraic() [ 'interface/I_BKab/xabtc' ].values() r [ :, 4 ] = results.algebraic() [ 'interface/I_BKab/xabss' ].values() r [ :, 5 ] = results.algebraic() [ 'interface/I_BKab/iBKab' ].values() r [ :, 6 ] = results.states() [ 'interface/I_BKab/xab' ].values() r [ :, 7 ] = results.states() [ 'interface/membrane_potential/v' ].values() filename = '%s_%s_%s.csv' % (prefilename, sub[1],j) np.savetxt(filename, vars, fmt='%s', delimiter=",") with open(filename, "ab") as f: np.savetxt(f, r, delimiter=",") f.close elif V_hold: # Load the simulation file simfile = 'VoltageVAR_Tong_2011.sedml' simulation = oc.open_simulation(simfile) data = simulation.data() simulation.reset(True) # Reset states variables and parameters #simulation.reset(True) # Set constant values start = 0 end = 1000 pointInterval = 1 data.set_starting_point(start) data.set_ending_point(end) data.set_point_interval(pointInterval) time_clamp = 40 v_clamp = [ -200,-180,-160,-140,-120,-100,-80,-60,-40,-30, -20, -10, 0, 10, 20, 30, 40,60] v_hold = [-80, -40] 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)): prefilename = 'Fig8_c' data.constants() [ 'interface/membrane_potential/v_clamp' ] = v_clamp [ i ] print(i,j) data.constants() [ 'interface/membrane_potential/time_clamp' ] = time_clamp data.constants() [ 'interface/parameters/ki' ] = 110 data.constants() [ 'interface/parameters/ko' ] = 5 #data.constants() [ 'interface/membrane_potential/v_clamp' ] = v[ i ] simulation.run() # Access simulation results results = simulation.results() # Data to save # Data to save varName = np.array([ "Time", "ik2", "v","max" ]) vars = np.reshape(varName, (1, 4)) rows = end * 1 + 1 # Grab a some algebraic variable results r = np.zeros((rows, len(varName))) r [ :, 0 ] = results.voi().values() r [ :, 1 ] = results.algebraic() [ 'interface/I_BKa/ik2' ].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 else: prefilename = 'Fig8_5' # Load the simulation file simfile = 'VoltageVAR_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 = 10000 pointInterval = 0.5 data.set_starting_point(start) data.set_ending_point(end) data.set_point_interval(pointInterval) time_clamp = 60 v_clamp = [-40,-30,-20,-10,0, 10 ] for i in range(len(v_clamp)): data.constants() [ 'interface/membrane_potential/v_hold' ] = -80 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' ] = time_clamp simulation.run() # Access simulation results results = simulation.results() # Data to save # Data to save varName = np.array([ "Time", "ik2", "v" ]) vars = np.reshape(varName, (1, 3)) rows = end * 2 + 1 # Grab a some algebraic variable results r = np.zeros((rows, len(varName))) r [ :, 0 ] = results.voi().values() r [ :, 1 ] = results.algebraic() ['interface/I_BKa/ik2'].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