- Author:
- WeiweiAi <wai484@aucklanduni.ac.nz>
- Date:
- 2022-03-31 10:48:40+13:00
- Desc:
- Add open channel IV of HH models; Add simulation and plot python scripts
- Permanent Source URI:
- http://models.cellml.org/workspace/64f/rawfile/ab2962b8796666ad9938a2577611c954f006b5fd/experiments/periodic-stimulus.cellml
<?xml version='1.0' encoding='UTF-8'?>
<model name="periodic_stimulus" 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">
<!-- this block of XML is used by CSim to execute a simulation (https://code.google.com/p/cellml-simulator/) -->
<import xlink:href="../cellLib/Components/units.cellml">
<units name="ms" units_ref="ms"/>
<units name="mV" units_ref="mV"/>
<units name="uA_per_cmsq" units_ref="uA_per_cmsq"/>
<units name="mS_per_cmsq" units_ref="mS_per_cmsq"/>
</import>
<import xlink:href="../cellLib/Components/time.cellml">
<component component_ref="time_ms" name="time"/>
</import>
<import xlink:href="../components/stimulated.cellml">
<component component_ref="action_potential" name="periodic_stimulus"/>
</import>
<import xlink:href="../cellLib/Protocols/periodic-IStim-protocol.cellml">
<component component_ref="stimulus_protocol" name="stimulus_protocol"/>
</import>
<import xlink:href="../components/default-variable-values.cellml">
<component component_ref="parameters" name="default_parameters_cell"/>
</import>
<import xlink:href="../components/gate_initials.cellml">
<component component_ref="gate_initials" name="gate_initials"/>
</import>
<!-- Connect the time source variable to the model and stimulus protocol -->
<connection>
<map_components component_1="periodic_stimulus" component_2="time"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<connection>
<map_components component_1="time" component_2="stimulus_protocol"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<!-- Define the stimulus protocol parameter values -->
<component name="stimulus_protocol_params">
<variable initial_value="50" name="stimPeriod" public_interface="out" units="ms"/>
<variable initial_value="1" name="stimDuration" public_interface="out" units="ms"/>
<variable initial_value="0.0" name="stimCurrent" public_interface="out" units="uA_per_cmsq"/>
</component>
<!-- and connect the parameters to the protocol definition -->
<connection>
<map_components component_1="stimulus_protocol_params" component_2="stimulus_protocol"/>
<map_variables variable_1="stimPeriod" variable_2="stimPeriod"/>
<map_variables variable_1="stimDuration" variable_2="stimDuration"/>
<map_variables variable_1="stimCurrent" variable_2="stimCurrent"/>
</connection>
<!-- and connect the actual stimulus current to the model -->
<connection>
<map_components component_1="periodic_stimulus" component_2="stimulus_protocol"/>
<map_variables variable_1="Istim" variable_2="IStim"/>
</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>
<component name="initial_conditions">
<variable initial_value="-15.0" name="V_initial" private_interface="out" public_interface="out" units="mV"/>
</component>
<component name="boundary_conditions">
<variable initial_value="0" name="V_b" private_interface="out" public_interface="out" units="mV"/>
</component>
<!-- We connect the default values through to the model -->
<connection>
<map_components component_1="periodic_stimulus" 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"/>
<map_variables variable_1="T0Na" variable_2="T0Na"/>
<map_variables variable_1="Q10Na" variable_2="Q10Na"/>
<map_variables variable_1="T0K" variable_2="T0K"/>
<map_variables variable_1="Q10K" variable_2="Q10K"/>
</connection>
<connection>
<map_components component_1="periodic_stimulus" component_2="parameters"/>
<map_variables variable_1="T" variable_2="T"/>
</connection>
<!-- similarly for the initial conditions -->
<connection>
<map_components component_1="periodic_stimulus" component_2="gate_initials"/>
<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>
<connection>
<map_components component_1="boundary_conditions" component_2="gate_initials"/>
<map_variables variable_1="V_b" variable_2="V_b"/>
</connection>
<connection>
<map_components component_1="periodic_stimulus" component_2="initial_conditions"/>
<map_variables variable_1="V_initial" variable_2="V_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="Istim" public_interface="in" units="uA_per_cmsq"/>
<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="periodic_stimulus"/>
<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="V" variable_2="V"/>
<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>
<connection>
<map_components component_1="outputs" component_2="stimulus_protocol"/>
<map_variables variable_1="Istim" variable_2="IStim"/>
</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>
</model>
