- 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/Multi_stim_experiment.cellml
<?xml version='1.0' encoding='UTF-8'?>
<model name="Multi_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="../cellLib/Components/units.cellml">
<units name="mV" units_ref="mV"/>
<units name="mM" units_ref="mM"/>
<units name="mM_per_s" units_ref="mM_per_s"/>
</import>
<import xlink:href="../Components/EC_uSMC.cellml">
<component component_ref="EC_uSMC" name="EC_uSMC"/>
</import>
<import xlink:href="../cellLib/Protocols/Patch_clamp_protocol.cellml">
<component component_ref="mPulse_protocol_s" name="mPulse_protocol_s"/>
</import>
<import xlink:href="../cellLib/Components/time.cellml">
<component component_ref="time_s" name="time_s"/>
</import>
<import xlink:href="../Components/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 -->
<connection>
<map_components component_1="time_s" component_2="mPulse_protocol_s"/>
<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>
<!-- Connect the parameters to the protocol definition -->
<component name="Vstim_para">
<variable initial_value="0" name="t_ss" public_interface="out" units="second"/>
<variable initial_value="-80" name="V_actHolding" public_interface="out" units="mV"/>
<variable initial_value="0.1" name="t_act" public_interface="out" units="second"/>
<variable initial_value="0" name="V_actTest" public_interface="out" units="mV"/>
<variable initial_value="0.33" name="t_intp" public_interface="out" units="second"/>
<variable initial_value="10" name="np" public_interface="out" units="dimensionless"/>
</component>
<connection>
<map_components component_1="Vstim_para" component_2="mPulse_protocol_s"/>
<map_variables variable_1="t_ss" variable_2="t_ss"/>
<map_variables variable_1="V_actHolding" variable_2="V_actHolding"/>
<map_variables variable_1="t_act" variable_2="t_act"/>
<map_variables variable_1="V_actTest" variable_2="V_actTest"/>
<map_variables variable_1="t_intp" variable_2="t_intp"/>
<map_variables variable_1="np" variable_2="np"/>
</connection>
<component name="control_para">
<variable initial_value="16.55" name="Nai" public_interface="out" units="mM"/>
<variable initial_value="0.1e-3" name="Cai_init" public_interface="out" units="mM"/>
<variable initial_value="1" name="inhPump" public_interface="out" units="dimensionless"/>
</component>
<connection>
<map_components component_1="control_para" component_2="EC_uSMC"/>
<map_variables variable_1="Nai" variable_2="Nai"/>
<map_variables variable_1="Cai_init" variable_2="Cai_init"/>
<map_variables variable_1="inhPump" variable_2="inhPump"/>
</connection>
<!-- and connect the actual stimulus current to the model -->
<connection>
<map_components component_1="mPulse_protocol_s" 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="stress" public_interface="in" units="dimensionless"/>
<variable name="phosphorylation" public_interface="in" units="dimensionless"/>
</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"/>
<map_variables variable_1="stress" variable_2="stress"/>
<map_variables variable_1="phosphorylation" variable_2="phosphorylation"/>
</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="mPulse_protocol_s" 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="K_Cahalf" variable_2="K_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"/>
<map_variables variable_1="K_7" variable_2="K_7"/>
<map_variables variable_1="K_2" variable_2="K_2"/>
<map_variables variable_1="K_3" variable_2="K_3"/>
<map_variables variable_1="K_4" variable_2="K_4"/>
<map_variables variable_1="K_5" variable_2="K_5"/>
</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"/>
<map_variables variable_1="M_init" variable_2="M_init"/>
<map_variables variable_1="Mp_init" variable_2="Mp_init"/>
<map_variables variable_1="AM_init" variable_2="AM_init"/>
<map_variables variable_1="AMp_init" variable_2="AMp_init"/>
</connection>
</model>
