Location: BG_Ca_leak @ 9e42555de571 / BG_Ca_leak.cellml

Author:
Shelley Fong <s.fong@auckland.ac.nz>
Date:
2022-03-03 13:59:42+13:00
Desc:
Changing Xi to X_i, and adding python param finder code
Permanent Source URI:
https://models.physiomeproject.org/workspace/835/rawfile/9e42555de571e0ea1b4cad67686a66dfba8cfcd8/BG_Ca_leak.cellml

<?xml version='1.0' encoding='UTF-8'?>
<!--Simple mass action reaction for this flux-->
<model name="Ca_leak_model" xmlns="http://www.cellml.org/cellml/1.1#" xmlns:cellml="http://www.cellml.org/cellml/1.1#" xmlns:xlink="http://www.w3.org/1999/xlink">
    <import xlink:href="units_and_constants/units_BG.cellml">
        <units name="mM" units_ref="mM"/>
        <units name="per_mol" units_ref="per_mol"/>
        <units name="J_per_mol" units_ref="J_per_mol"/>
        <units name="J_per_C" units_ref="J_per_C"/>
        <units name="mol_per_s" units_ref="mol_per_s"/>
        <units name="C_per_mol" units_ref="C_per_mol"/>
        <units name="microm3" units_ref="microm3"/>
        <units name="fF" units_ref="fF"/>
        <units name="fC" units_ref="fC"/>
        <units name="fA" units_ref="fA"/>
        <units name="fmol" units_ref="fmol"/>
        <units name="fmol_per_sec" units_ref="fmol_per_sec"/>
        <units name="per_fmol" units_ref="per_fmol"/>
        <units name="pL" units_ref="pL"/>
        <units name="mA_per_mM" units_ref="mA_per_mM"/>
    </import>
    <component name="environment">
        <variable name="t" public_interface="out" units="second"/>
        <variable initial_value="25.8" name="w_i" public_interface="out" units="pL"/>
        <variable name="w_SR" public_interface="out" units="pL"/>
        <variable initial_value="2494.34" name="RT" public_interface="out" units="J_per_mol"/>
        <variable name="v_leak" public_interface="in" units="fmol_per_sec"/>
        <variable initial_value="0.00456" name="q_Ca_i" public_interface="out" units="fmol"/>
        <variable initial_value="6.41e-1" name="q_Ca_SR" public_interface="out" units="fmol"/>
        <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
                <eq/>
                <ci>w_SR</ci>
                <apply>
                    <times/>
                    <ci>w_i</ci>
                    <cn cellml:units="dimensionless">0.088235</cn>
                </apply>
            </apply>
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>t</ci>
                    </bvar>
                    <ci>q_Ca_SR</ci>
                </apply>
                <apply>
                    <minus/>
                    <ci>v_leak</ci>
                </apply>
            </apply>
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>t</ci>
                    </bvar>
                    <ci>q_Ca_i</ci>
                </apply>
                <ci>v_leak</ci>
            </apply>
        </math>
    </component>
    <component name="Ca_leak_parameters">
        <variable initial_value="0.698143" name="kappa_leak" public_interface="out" units="fmol_per_sec"/>
        <variable initial_value="0.367039" name="K_Ca_SR" public_interface="out" units="per_fmol"/>
        <variable initial_value="0.0323856" name="K_Ca_i" public_interface="out" units="per_fmol"/>
    </component>
    <component name="Ca_leak">
        <variable name="t" public_interface="in" units="second"/>
        <variable name="RT" public_interface="in" units="J_per_mol"/>
        <variable name="K_Ca_SR" public_interface="in" units="per_fmol"/>
        <variable name="K_Ca_i" public_interface="in" units="per_fmol"/>
        <variable name="kappa_leak" public_interface="in" units="fmol_per_sec"/>
        <variable name="q_Ca_SR" public_interface="in" units="fmol"/>
        <variable name="q_Ca_i" public_interface="in" units="fmol"/>
        <variable name="mu_Ca_SR" units="J_per_mol"/>
        <variable name="mu_Ca_i" units="J_per_mol"/>
        <variable name="v_leak" public_interface="out" units="fmol_per_sec"/>
        <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
                <eq/>
                <ci>mu_Ca_SR</ci>
                <apply>
                    <times/>
                    <ci>RT</ci>
                    <apply>
                        <ln/>
                        <apply>
                            <times/>
                            <ci>K_Ca_SR</ci>
                            <ci>q_Ca_SR</ci>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>mu_Ca_i</ci>
                <apply>
                    <times/>
                    <ci>RT</ci>
                    <apply>
                        <ln/>
                        <apply>
                            <times/>
                            <ci>K_Ca_i</ci>
                            <ci>q_Ca_i</ci>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>v_leak</ci>
                <apply>
                    <times/>
                    <ci>kappa_leak</ci>
                    <apply>
                        <minus/>
                        <apply>
                            <exp/>
                            <apply>
                                <divide/>
                                <ci>mu_Ca_SR</ci>
                                <ci>RT</ci>
                            </apply>
                        </apply>
                        <apply>
                            <exp/>
                            <apply>
                                <divide/>
                                <ci>mu_Ca_i</ci>
                                <ci>RT</ci>
                            </apply>
                        </apply>
                    </apply>
                </apply>
            </apply>
        </math>
    </component>
    <connection>
        <map_components component_1="environment" component_2="Ca_leak"/>
        <map_variables variable_1="t" variable_2="t"/>
        <map_variables variable_1="RT" variable_2="RT"/>
        <map_variables variable_1="v_leak" variable_2="v_leak"/>
        <map_variables variable_1="q_Ca_SR" variable_2="q_Ca_SR"/>
        <map_variables variable_1="q_Ca_i" variable_2="q_Ca_i"/>
    </connection>
    <connection>
        <map_components component_1="Ca_leak" component_2="Ca_leak_parameters"/>
        <map_variables variable_1="K_Ca_SR" variable_2="K_Ca_SR"/>
        <map_variables variable_1="K_Ca_i" variable_2="K_Ca_i"/>
        <map_variables variable_1="kappa_leak" variable_2="kappa_leak"/>
    </connection>
</model>