- Author:
- WeiweiAi <wai484@aucklanduni.ac.nz>
- Date:
- 2022-10-19 10:24:37+13:00
- Desc:
- Add readme to link the documentation on overleaf.
- Permanent Source URI:
- https://models.physiomeproject.org/workspace/701/rawfile/6741283829975cd4f084159e7734dcbece29f7b1/Experiments/Patch_clamp_INa.cellml
<?xml version='1.0' encoding='UTF-8'?>
<model name="Patch_clamp_INa" 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="ms" units_ref="ms"/>
<units name="pA" units_ref="pA"/>
<units name="mV" units_ref="mV"/>
<units name="mM" units_ref="mM"/>
<units name="pA_per_pF" units_ref="pA_per_pF"/>
</import>
<import xlink:href="../Components/INa.cellml">
<component component_ref="INa" name="INa"/>
</import>
<import xlink:href="../cellLib/Protocols/Patch_clamp_protocol.cellml">
<component component_ref="sPulse_protocol_ms" name="Patch_clamp_protocol"/>
</import>
<import xlink:href="../cellLib/Components/time.cellml">
<component component_ref="time_ms" name="time"/>
</import>
<import xlink:href="../Components/default_values.cellml">
<component component_ref="constants" name="constants"/>
<component component_ref="model_parameters" name="model_parameters"/>
<component component_ref="initial_conditions" name="initial_conditions"/>
</import>
<!-- Connect the time source variable to the model and stimulus protocol -->
<connection>
<map_components component_1="time" component_2="Patch_clamp_protocol"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<connection>
<map_components component_1="time" component_2="INa"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<!-- Connect the parameters to the protocol definition -->
<component name="Clamp_parameters">
<variable initial_value="50" name="t_ss" public_interface="out" units="ms"/>
<variable initial_value="-90" name="V_actHolding" public_interface="out" units="mV"/>
<variable initial_value="50" name="t_act" public_interface="out" units="ms"/>
<variable initial_value="-50" name="V_actTest" public_interface="out" units="mV"/>
<variable initial_value="4" name="Nai" public_interface="out" units="mM"/>
</component>
<connection>
<map_components component_1="Clamp_parameters" component_2="INa"/>
<map_variables variable_1="Nai" variable_2="Nai"/>
</connection>
<connection>
<map_components component_1="Clamp_parameters" component_2="Patch_clamp_protocol"/>
<map_variables variable_1="t_ss" variable_2="t_ss"/>
<map_variables variable_1="t_act" variable_2="t_act"/>
<map_variables variable_1="V_actHolding" variable_2="V_actHolding"/>
<map_variables variable_1="V_actTest" variable_2="V_actTest"/>
</connection>
<!-- and connect the actual stimulus current to the model -->
<connection>
<map_components component_1="Patch_clamp_protocol" component_2="INa"/>
<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="ms"/>
<variable name="V" public_interface="in" units="mV"/>
<variable name="I_Na" public_interface="in" units="pA_per_pF"/>
<variable name="P_Nai" public_interface="in" units="dimensionless"/>
<variable name="m" public_interface="in" units="dimensionless"/>
<variable name="h" public_interface="in" units="dimensionless"/>
</component>
<!-- and connect the output variable definitions to their actual source in the model -->
<connection>
<map_components component_1="INa" component_2="outputs"/>
<map_variables variable_1="I_Na" variable_2="I_Na"/>
<map_variables variable_1="P_Na" variable_2="P_Nai"/>
<map_variables variable_1="m" variable_2="m"/>
<map_variables variable_1="h" variable_2="h"/>
</connection>
<connection>
<map_components component_1="outputs" component_2="time"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<!-- and connect the time output to the source time variable -->
<connection>
<map_components component_1="Patch_clamp_protocol" 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_parameters" component_2="INa"/>
<map_variables variable_1="T" variable_2="T"/>
<map_variables variable_1="Cm" variable_2="Cm"/>
<map_variables variable_1="Ac" variable_2="Ac"/>
<map_variables variable_1="g_Na" variable_2="g_Na"/>
<map_variables variable_1="T0Na" variable_2="T0Na"/>
<map_variables variable_1="Q10Na" variable_2="Q10Na"/>
<map_variables variable_1="Nao" variable_2="Nao"/>
</connection>
<connection>
<map_components component_1="constants" component_2="INa"/>
<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="initial_conditions" component_2="INa"/>
<map_variables variable_1="m_init" variable_2="m_init"/>
<map_variables variable_1="h_init" variable_2="h_init"/>
</connection>
</model>
