- 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>
