Location: Reproducibility of the computational model of induced pluripotent stem-cell derived cardiomyocytes @ 430939c5c1b8 / Experiments / fig9-new.py

Author:
David Nickerson <david.nickerson@gmail.com>
Date:
2021-11-25 11:13:34+13:00
Desc:
making internal links in overview relative instead of absolute
Permanent Source URI:
https://staging.physiomeproject.org/workspace/702/rawfile/430939c5c1b887fcf0d899b0dd11370b77bf495f/Experiments/fig9-new.py
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import os

import matplotlib
matplotlib.use('agg')

import numpy as np
import matplotlib.pyplot as plt

import opencor as opencor


# root = "C:/Nima/ABI/Physiome Journal/pluripotent stem cell/src/cellml/Channels/"


def load_sedml(filename):
    return opencor.open_simulation(filename)

def get_data(filename):
    data = filename.data()
    data.set_ending_point(10)
    data.set_point_interval(1)
    return data


def run_sim(data, filename, protocol):
    ik1_list = []


    voltage = np.arange(-150, 51, 1)

    var1_list = [0.0229, 0.0841, 0.1338, 0.3745, 0.185]
    var2_list = [0.0012, 0.0861, 0.4780, 0.1815, 1.6433]
    var3_list = [1.2173, 93.9391, 27.2428, 10.5111, 0.3036]
    var4_list = [8.5590, 9.5527, 4.9250, 0.0448, 1.5436]
    var5_list = [0.1162, 23.0096, 8.7222, 0.0203, 0.1132]
    var6_list = [77.5571, 5.8902, 56.6362, 89.1151, 53.9824]
    key_ids = ["one", "two", "three", "four", "five"]
    results1 = {}
    file = load_sedml(filename)
    for var1, var2, var3, var4, var5, var6, index in zip(var1_list, var2_list, var3_list, var4_list, var5_list, var6_list, key_ids):
        file.reset(True)
        file.clear_results()
        data.constants()["main/var_1"] = var1
        data.constants()["main/var_2"] = var2
        data.constants()["main/var_3"] = var3
        data.constants()["main/var_4"] = var4
        data.constants()["main/var_5"] = var5
        data.constants()["main/var_6"] = var6
        results1[index] = []

        for v in voltage:
            data.constants()["main/protocol"] = protocol
            data.constants()["main/v"] = v
            file.run()
            ds = file.results().data_store()
            value1 = ds.voi_and_variables()["main/i_k1"].values()[-1]
            results1[index].append(value1)

    return results1


if __name__ == '__main__':
    Channel_file = "Channels.sedml"


    Channel = load_sedml(Channel_file)



    data = get_data(Channel)



    Ik1_kurokawa_list = run_sim(data, Channel_file, 3)
    Ik1_ma_list = run_sim(data, Channel_file, 1)
    Ik1_baseline_list = run_sim(data, Channel_file, 2)
    Jalife_Mature_IK1_list = run_sim(data, Channel_file, 2)
    Jalife_Immature_IK1_list = run_sim(data, Channel_file, 2)

    voltage = np.arange(-150, 51, 1)

    plt.figure(figsize=(7, 7))
    plt.plot(voltage, Jalife_Mature_IK1_list["four"], color='green', linewidth= 3, label='Jalife Mature')
    plt.plot(voltage, Jalife_Immature_IK1_list["five"], color='purple', linewidth= 3, label='Jalife Immature')
    plt.plot(voltage, Ik1_ma_list['two'], color='blue', linewidth=3, label='Ma et al.')
    plt.plot(voltage, Ik1_kurokawa_list['one'], color='orange', linewidth=3, label='Kurokawa Lab')
    plt.plot(voltage, Ik1_baseline_list["three"], color='black', linewidth=3, label='Baseline Model')

    plt.xlabel('Voltage (mV)', fontsize=14)
    plt.ylabel('I$_{K1}$ (pA/pF)', fontsize=14)
    plt.xlim(-150, 50, 50)
    plt.ylim(-20, 5, 5)
    plt.legend(fontsize='14')

    # plt.show()
    plt.savefig('Figure09.png')