- Author:
- WeiweiAi <wai484@aucklanduni.ac.nz>
- Date:
- 2021-04-28 18:15:33+12:00
- Desc:
- Change the unit of T from celsius to kelvin to in line with CellML2.0 spec (but the real temperature unit is still celsius, no need to do conversion when setting the temperature parameter for simulation)
- Permanent Source URI:
- https://models.cellml.org/workspace/64f/rawfile/c56e1d0255183a1d725eec025cbe79eeee2c8087/experiments/voltage_clamp_experiment.cellml
<?xml version='1.0' encoding='UTF-8'?>
<model name="voltage_clamp_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">
<!-- run voltage clamp experiments-->
<import xlink:href="../components/units.cellml">
<units name="ms" units_ref="ms"/>
<units name="uA_per_cmsq" units_ref="uA_per_cmsq"/>
<units name="mV" units_ref="mV"/>
<units name="mS_per_cmsq" units_ref="mS_per_cmsq"/>
</import>
<import xlink:href="../components/clamped_current.cellml">
<component component_ref="membrane_current" name="membrane_current"/>
</import>
<import xlink:href="voltage_clamp_protocol.cellml">
<component component_ref="voltage_clamp_protocol" name="voltage_clamp_protocol"/>
</import>
<import xlink:href="time.cellml">
<component component_ref="time" name="time"/>
</import>
<import xlink:href="../components/default-variable-values.cellml">
<component component_ref="parameters" name="default_parameters_cell"/>
<component component_ref="initial_conditions" name="default_initial_conditions"/>
</import>
<!-- Connect the time source variable to the model and stimulus protocol -->
<connection>
<map_components component_1="membrane_current" component_2="time"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<connection>
<map_components component_1="time" component_2="voltage_clamp_protocol"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<!-- Define the stimulus protocol parameter values -->
<component name="voltage_clamp_protocol_params">
<variable initial_value="0" name="t_start" public_interface="out" units="ms"/>
<variable initial_value="20" name="t_end" public_interface="out" units="ms"/>
<variable initial_value="-20" name="V_clamp" public_interface="out" units="mV"/>
</component>
<!-- and connect the parameters to the protocol definition -->
<connection>
<map_components component_1="voltage_clamp_protocol_params" component_2="voltage_clamp_protocol"/>
<map_variables variable_1="t_start" variable_2="t_start"/>
<map_variables variable_1="t_end" variable_2="t_end"/>
<map_variables variable_1="V_clamp" variable_2="V_clamp"/>
</connection>
<!-- and connect the actual stimulus current to the model -->
<connection>
<map_components component_1="membrane_current" component_2="voltage_clamp_protocol"/>
<map_variables variable_1="V" variable_2="V"/>
</connection>
<!-- Here we could define any parameters that we want to differ from the default -->
<component name="parameters">
<variable initial_value="6.3" name="T" private_interface="out" public_interface="out" units="kelvin" />
</component>
<!-- We connect the default values through to the model -->
<connection>
<map_components component_1="membrane_current" component_2="default_parameters_cell"/>
<map_variables variable_1="Cm" variable_2="Cm"/>
<map_variables variable_1="VNa" variable_2="VNa"/>
<map_variables variable_1="VK" variable_2="VK"/>
<map_variables variable_1="Vleak" variable_2="Vleak"/>
<map_variables variable_1="gNa_max" variable_2="gNa_max"/>
<map_variables variable_1="gK_max" variable_2="gK_max"/>
<map_variables variable_1="gleak_max" variable_2="gleak_max"/>
</connection>
<connection>
<map_components component_1="membrane_current" component_2="parameters"/>
<map_variables variable_1="T" variable_2="T"/>
</connection>
<!-- similarly for the initial conditions -->
<connection>
<map_components component_1="membrane_current" component_2="default_initial_conditions"/>
<map_variables variable_1="m_initial" variable_2="m_initial"/>
<map_variables variable_1="h_initial" variable_2="h_initial"/>
<map_variables variable_1="n_initial" variable_2="n_initial"/>
</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="INa" public_interface="in" units="uA_per_cmsq"/>
<variable name="IK" public_interface="in" units="uA_per_cmsq"/>
<variable name="Ileak" public_interface="in" units="uA_per_cmsq"/>
<variable name="Ii" public_interface="in" units="uA_per_cmsq"/>
<variable name="g" public_interface="in" units="mS_per_cmsq"/>
<variable name="gK" public_interface="in" units="mS_per_cmsq"/>
<variable name="gNa" public_interface="in" units="mS_per_cmsq"/>
<variable name="V" public_interface="in" units="mV"/>
<variable name="minus_V" public_interface="in" units="mV"/>
<variable name="h" public_interface="in" units="dimensionless"/>
<variable name="m" public_interface="in" units="dimensionless"/>
<variable name="n" public_interface="in" units="dimensionless"/>
</component>
<!-- and connect the output variable definitions to their actual source in the model -->
<connection>
<map_components component_1="outputs" component_2="membrane_current"/>
<map_variables variable_1="INa" variable_2="INa"/>
<map_variables variable_1="IK" variable_2="IK"/>
<map_variables variable_1="Ileak" variable_2="Ileak"/>
<map_variables variable_1="Ii" variable_2="Ii"/>
<map_variables variable_1="minus_V" variable_2="minus_V"/>
<map_variables variable_1="h" variable_2="h"/>
<map_variables variable_1="m" variable_2="m"/>
<map_variables variable_1="n" variable_2="n"/>
<map_variables variable_1="g" variable_2="g"/>
<map_variables variable_1="gK" variable_2="gK"/>
<map_variables variable_1="gNa" variable_2="gNa"/>
</connection>
<!-- and connect the time output to the source time variable -->
<connection>
<map_components component_1="outputs" component_2="time"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<connection>
<map_components component_1="outputs" component_2="voltage_clamp_protocol"/>
<map_variables variable_1="V" variable_2="V"/>
</connection>
</model>
