Location: 12 L Platform 1 model codes @ 7863a08ae436 / USMC / Vm_stim_experiment.cellml
- Author:
- aram148 <a.rampadarath@auckland.ac.nz>
- Date:
- 2021-09-01 13:35:00+12:00
- Desc:
- Added coupled USMC model maggio + Bursztyn model
- Permanent Source URI:
- https://models.physiomeproject.org/workspace/6b0/rawfile/7863a08ae43627665fd6f9513f1e4e67dc175b34/USMC/Vm_stim_experiment.cellml
<?xml version='1.0' encoding='UTF-8'?>
<model name="Vm_stim_experiment" 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="mV" units_ref="mV"/>
<units name="mM" units_ref="mM"/>
<units name="mM_per_s_mV" units_ref="mM_per_s_mV"/>
<units name="mV_per_s" units_ref="mV_per_s"/>
</import>
<import xlink:href="EC_uSMC.cellml">
<component component_ref="EC_uSMC" name="EC_uSMC"/>
<component component_ref="K_1" name="K_1"/>
</import>
<import xlink:href="time.cellml">
<component component_ref="time_s" name="time_s"/>
</import>
<import xlink:href="default_values.cellml">
<component component_ref="model_para" name="model_para"/>
<component component_ref="initials" name="initials"/>
<component component_ref="constants" name="constants"/>
</import>
<!-- Connect the time source variable to the model and stimulus protocol -->
<component name="Vm">
<variable name="time" public_interface="in" units="second"/>
<variable name="V" public_interface="out" units="mV"/>
<variable name="p1" units="mV_per_s"/>
<variable name="p2" units="mV"/>
<variable name="t0" units="second"/>
<variable initial_value="0" name="tss" units="second"/>
<!-- V = -60{mV}*(time <= 50{second})+-30{mV}*((time >= 50{second}) and (time <= 400{second}))+-60{mV}*(time >= 400{second});-->
<!-- V = -60{mV}*1{dimensionless}/(1{dimensionless}+exp(time-25{mV}))*(time < 50{second})+-60{mV}*1{dimensionless}/(1{dimensionless}+exp(-(time-50{mV})))*(time >= 50{second});-->
<!--+-60{mV}*1{dimensionless}/(1{dimensionless}+exp(time-40{mV}))*(time < 40{second})+-60{mV}*1{dimensionless}/(1{dimensionless}+exp(-(time-80{mV})))*(time >= 80{second});-->
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
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<apply>
<plus/>
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<ci>t0</ci>
</apply>
<ci>tss</ci>
</apply>
</apply>
<ci>p2</ci>
</apply>
</apply>
<apply>
<eq/>
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</math>
</component>
<connection>
<map_components component_1="time_s" component_2="Vm"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<connection>
<map_components component_1="time_s" component_2="EC_uSMC"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<component name="control_para">
<variable initial_value="2.9836" name="Nai" public_interface="out" units="mM"/>
<variable initial_value="1" name="inhPump" public_interface="out" units="dimensionless"/>
<variable initial_value="11" name="K_Cahalf" public_interface="out" units="mV"/>
</component>
<connection>
<map_components component_1="control_para" component_2="EC_uSMC"/>
<map_variables variable_1="Nai" variable_2="Nai"/>
<map_variables variable_1="inhPump" variable_2="inhPump"/>
<map_variables variable_1="K_Cahalf" variable_2="K_Cahalf"/>
</connection>
<!-- and connect the actual stimulus current to the model -->
<connection>
<map_components component_1="Vm" component_2="EC_uSMC"/>
<map_variables variable_1="V" variable_2="V"/>
</connection>
<!-- SED-ML (and CSim simulation description above) is only able to address variables at the top level of the model hierarchy, so we need to define the variables we want SED-ML to be able to address here. -->
<component name="outputs">
<variable name="time" public_interface="in" units="second"/>
<variable name="V" public_interface="in" units="mV"/>
<variable name="Cai" public_interface="in" units="mM"/>
<variable name="J_VOCC" public_interface="in" units="mM_per_s"/>
<variable name="J_CaPump" public_interface="in" units="mM_per_s"/>
<variable name="J_NaCa" public_interface="in" units="mM_per_s"/>
<variable name="K_1" public_interface="in" units="per_s"/>
<!-- var stress: dimensionless {pub: in};
var phosphorylation: dimensionless {pub: in};-->
</component>
<!-- and connect the output variable definitions to their actual source in the model -->
<connection>
<map_components component_1="EC_uSMC" component_2="outputs"/>
<map_variables variable_1="Cai" variable_2="Cai"/>
<map_variables variable_1="J_VOCC" variable_2="J_VOCC"/>
<map_variables variable_1="J_CaPump" variable_2="J_CaPump"/>
<map_variables variable_1="J_NaCa" variable_2="J_NaCa"/>
<!-- vars stress and stress;
vars phosphorylation and phosphorylation;-->
</connection>
<connection>
<map_components component_1="outputs" component_2="K_1"/>
<map_variables variable_1="K_1" variable_2="K_1"/>
</connection>
<connection>
<map_components component_1="outputs" component_2="time_s"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<!-- and connect the time output to the source time variable -->
<connection>
<map_components component_1="Vm" component_2="outputs"/>
<map_variables variable_1="V" variable_2="V"/>
</connection>
<!-- We connect the default parameters through to the model-->
<connection>
<map_components component_1="model_para" component_2="EC_uSMC"/>
<map_variables variable_1="T" variable_2="T"/>
<map_variables variable_1="Nao" variable_2="Nao"/>
<map_variables variable_1="Cao" variable_2="Cao"/>
<map_variables variable_1="V_cell" variable_2="V_cell"/>
<map_variables variable_1="V_Cahalf" variable_2="V_Cahalf"/>
<map_variables variable_1="g_mCa" variable_2="g_mCa"/>
<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="K_NaCa" variable_2="K_NaCa"/>
<map_variables variable_1="G_NaCa" variable_2="G_NaCa"/>
<map_variables variable_1="n_M" variable_2="n_M"/>
<map_variables variable_1="Ca_halfMLCK" variable_2="Ca_halfMLCK"/>
<!-- vars K_7 and K_7;
vars K_2 and K_2;
vars K_3 and K_3;-->
</connection>
<connection>
<map_components component_1="constants" component_2="EC_uSMC"/>
<map_variables variable_1="R" variable_2="R"/>
<map_variables variable_1="F" variable_2="F"/>
</connection>
<!-- We connect the initial conditions through to the model-->
<connection>
<map_components component_1="initials" component_2="EC_uSMC"/>
<!-- vars M_init and M_init;
vars Mp_init and Mp_init;
vars AM_init and AM_init;
vars AMp_init and AMp_init;-->
<map_variables variable_1="Cai_init" variable_2="Cai_init"/>
</connection>
</model>