Location: 12 L Platform 1 model codes @ a8a92308e217 / USMC / EC_uSMC.cellml

Author:
aram148 <42922407+aram148@users.noreply.github.com>
Date:
2022-07-22 15:47:05+12:00
Desc:
Added documentation for VSM model
Permanent Source URI:
https://models.physiomeproject.org/workspace/6b0/rawfile/a8a92308e217ac5626809237dd90a31240b22834/USMC/EC_uSMC.cellml

<?xml version='1.0' encoding='UTF-8'?>
<model name="EC_uSMC" 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.cellml">
        <units name="J_per_K_mol" units_ref="J_per_K_mol"/>
        <units name="mV" units_ref="mV"/>
        <units name="mM" units_ref="mM"/>
        <units name="nS" units_ref="nS"/>
        <units name="mM_per_s" units_ref="mM_per_s"/>
        <units name="C_per_mmol" units_ref="C_per_mmol"/>
        <units name="fm3" units_ref="fm3"/>
        <units name="mM_per_s_mV" units_ref="mM_per_s_mV"/>
        <units name="per_s" units_ref="per_s"/>
    </import>
    <import xlink:href="E_Nernst.cellml">
        <component component_ref="E_Ca" name="E_Ca"/>
        <component component_ref="E_Na" name="E_Na"/>
    </import>
    <!--    def import using "../cellLib/Components/CB4HM.cellml" for
        comp CB4HM using comp CB4HM;
    enddef;-->
    <import xlink:href="J_Ca.cellml">
        <component component_ref="J_VOCC" name="J_VOCC"/>
        <component component_ref="J_CaPump" name="J_CaPump"/>
        <component component_ref="J_NaCa" name="J_NaCa"/>
        <component component_ref="Cai" name="Cai"/>
    </import>
    <component name="EC_uSMC">
        <!-- Parameters-->
        <variable name="R" private_interface="out" public_interface="in" units="J_per_K_mol"/>
        <variable name="F" private_interface="out" public_interface="in" units="C_per_mmol"/>
        <variable name="T" private_interface="out" public_interface="in" units="kelvin"/>
        <variable name="Nai" private_interface="out" public_interface="in" units="mM"/>
        <variable name="Nao" private_interface="out" public_interface="in" units="mM"/>
        <variable name="Cao" private_interface="out" public_interface="in" units="mM"/>
        <variable name="V_cell" private_interface="out" public_interface="in" units="fm3"/>
        <variable name="V_Cahalf" private_interface="out" public_interface="in" units="mV"/>
        <variable name="K_Cahalf" private_interface="out" public_interface="in" units="mV"/>
        <variable name="g_mCa" private_interface="out" public_interface="in" units="nS"/>
        <variable name="V_pmax" private_interface="out" public_interface="in" units="mM_per_s"/>
        <variable name="n" private_interface="out" public_interface="in" units="dimensionless"/>
        <variable name="K_ph" private_interface="out" public_interface="in" units="mM"/>
        <variable name="K_NaCa" private_interface="out" public_interface="in" units="mM"/>
        <variable name="G_NaCa" private_interface="out" public_interface="in" units="mM_per_s_mV"/>
        <variable name="Cai_init" private_interface="out" public_interface="in" units="mM"/>
        <variable name="n_M" private_interface="out" public_interface="in" units="dimensionless"/>
        <variable name="Ca_halfMLCK" private_interface="out" public_interface="in" units="mM"/>
        <variable name="inhPump" private_interface="out" public_interface="in" units="dimensionless"/>
        <!--        var M_init: dimensionless {pub: in, priv: out};
        var Mp_init: dimensionless {pub: in, priv: out};
        var AM_init: dimensionless {pub: in, priv: out};
        var AMp_init: dimensionless {pub: in, priv: out};
        var K_7: per_s {pub: in, priv: out};
        var K_2: per_s {pub: in, priv: out};
        var K_3: per_s {pub: in, priv: out};-->
        <!-- Inputs-->
        <variable name="time" private_interface="out" public_interface="in" units="second"/>
        <variable name="V" private_interface="out" public_interface="in" units="mV"/>
        <!-- Outputs              -->
        <variable name="Cai" private_interface="in" public_interface="out" units="mM"/>
        <variable name="J_VOCC" private_interface="in" public_interface="out" units="mM_per_s"/>
        <variable name="J_CaPump" private_interface="in" public_interface="out" units="mM_per_s"/>
        <variable name="J_NaCa" private_interface="in" public_interface="out" units="mM_per_s"/>
        <variable name="rho_vCa" private_interface="in" public_interface="out" units="dimensionless"/>
        <!--        var stress: dimensionless {pub: out, priv: in};
        var phosphorylation: dimensionless {pub: out, priv: in};-->
    </component>
    <component name="K_1">
        <variable name="n_M" public_interface="in" units="dimensionless"/>
        <variable name="Ca_halfMLCK" public_interface="in" units="mM"/>
        <variable name="Cai" public_interface="in" units="mM"/>
        <variable name="K_1" public_interface="out" units="per_s"/>
        <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
                <eq/>
                <ci>K_1</ci>
                <apply>
                    <times/>
                    <apply>
                        <divide/>
                        <apply>
                            <power/>
                            <ci>Cai</ci>
                            <ci>n_M</ci>
                        </apply>
                        <apply>
                            <plus/>
                            <apply>
                                <power/>
                                <ci>Ca_halfMLCK</ci>
                                <ci>n_M</ci>
                            </apply>
                            <apply>
                                <power/>
                                <ci>Cai</ci>
                                <ci>n_M</ci>
                            </apply>
                        </apply>
                    </apply>
                    <cn cellml:units="per_s">1</cn>
                </apply>
            </apply>
        </math>
    </component>
    <group>
        <relationship_ref relationship="encapsulation"/>
        <component_ref component="EC_uSMC">
            <component_ref component="E_Ca"/>
            <component_ref component="E_Na"/>
            <component_ref component="J_VOCC"/>
            <component_ref component="J_CaPump"/>
            <component_ref component="J_NaCa"/>
            <component_ref component="Cai"/>
            <!--            comp CB4HM;-->
            <component_ref component="K_1"/>
        </component_ref>
    </group>
    <connection>
        <map_components component_1="EC_uSMC" component_2="E_Na"/>
        <map_variables variable_1="R" variable_2="R"/>
        <map_variables variable_1="F" variable_2="F"/>
        <map_variables variable_1="T" variable_2="T"/>
        <map_variables variable_1="Nai" variable_2="Nai"/>
        <map_variables variable_1="Nao" variable_2="Nao"/>
    </connection>
    <connection>
        <map_components component_1="EC_uSMC" component_2="E_Ca"/>
        <map_variables variable_1="R" variable_2="R"/>
        <map_variables variable_1="F" variable_2="F"/>
        <map_variables variable_1="T" variable_2="T"/>
        <map_variables variable_1="Cao" variable_2="Cao"/>
    </connection>
    <connection>
        <map_components component_1="EC_uSMC" component_2="K_1"/>
        <map_variables variable_1="n_M" variable_2="n_M"/>
        <map_variables variable_1="Ca_halfMLCK" variable_2="Ca_halfMLCK"/>
    </connection>
    <connection>
        <map_components component_1="EC_uSMC" component_2="J_VOCC"/>
        <map_variables variable_1="F" variable_2="F"/>
        <map_variables variable_1="V_cell" variable_2="V_cell"/>
        <map_variables variable_1="V_Cahalf" variable_2="V_Cahalf"/>
        <map_variables variable_1="K_Cahalf" variable_2="K_Cahalf"/>
        <map_variables variable_1="g_mCa" variable_2="g_mCa"/>
        <map_variables variable_1="V" variable_2="V"/>
        <map_variables variable_1="J_VOCC" variable_2="J_VOCC"/>
        <map_variables variable_1="rho_vCa" variable_2="rho_vCa"/>
    </connection>
    <connection>
        <map_components component_1="EC_uSMC" component_2="J_CaPump"/>
        <map_variables variable_1="V_pmax" variable_2="V_pmax"/>
        <map_variables variable_1="n" variable_2="n"/>
        <map_variables variable_1="K_ph" variable_2="K_ph"/>
        <map_variables variable_1="J_CaPump" variable_2="J_CaPump"/>
    </connection>
    <connection>
        <map_components component_1="EC_uSMC" component_2="J_NaCa"/>
        <map_variables variable_1="K_NaCa" variable_2="K_NaCa"/>
        <map_variables variable_1="G_NaCa" variable_2="G_NaCa"/>
        <map_variables variable_1="V" variable_2="V"/>
        <map_variables variable_1="J_NaCa" variable_2="J_NaCa"/>
    </connection>
    <connection>
        <map_components component_1="EC_uSMC" component_2="Cai"/>
        <map_variables variable_1="Cai_init" variable_2="Cai_init"/>
        <map_variables variable_1="time" variable_2="time"/>
        <map_variables variable_1="Cai" variable_2="Cai"/>
        <map_variables variable_1="inhPump" variable_2="inhPump"/>
    </connection>
    <!--    def map between EC_uSMC and CB4HM for
        vars time and time;
        vars M_init and M_init;
        vars Mp_init and Mp_init;
        vars AM_init and AM_init;
        vars AMp_init and AMp_init;
        vars K_2 and K_2;
        vars K_3 and K_3;
        vars K_7 and K_7;
        vars stress and stress;
        vars phosphorylation and phosphorylation;
    enddef;-->
    <connection>
        <map_components component_1="Cai" component_2="E_Ca"/>
        <map_variables variable_1="Cai" variable_2="Cai"/>
    </connection>
    <connection>
        <map_components component_1="J_VOCC" component_2="E_Ca"/>
        <map_variables variable_1="E_Ca" variable_2="E_Ca"/>
    </connection>
    <connection>
        <map_components component_1="J_NaCa" component_2="E_Ca"/>
        <map_variables variable_1="E_Ca" variable_2="E_Ca"/>
    </connection>
    <connection>
        <map_components component_1="J_NaCa" component_2="E_Na"/>
        <map_variables variable_1="E_Na" variable_2="E_Na"/>
    </connection>
    <connection>
        <map_components component_1="Cai" component_2="K_1"/>
        <map_variables variable_1="Cai" variable_2="Cai"/>
    </connection>
    <connection>
        <map_components component_1="Cai" component_2="J_CaPump"/>
        <map_variables variable_1="Cai" variable_2="Cai"/>
        <map_variables variable_1="J_CaPump" variable_2="J_CaPump"/>
    </connection>
    <connection>
        <map_components component_1="Cai" component_2="J_VOCC"/>
        <map_variables variable_1="J_VOCC" variable_2="J_VOCC"/>
    </connection>
    <connection>
        <map_components component_1="Cai" component_2="J_NaCa"/>
        <map_variables variable_1="Cai" variable_2="Cai"/>
        <map_variables variable_1="J_NaCa" variable_2="J_NaCa"/>
    </connection>
    <!--    def map between CB4HM and K_1 for
        vars K_1 and K_1;
    enddef;-->
</model>