- Author:
- David Nickerson <david.nickerson@gmail.com>
- Date:
- 2019-11-04 22:25:48+09:00
- Desc:
- adding CellML 2.0 version of this model generated using the CellML1to2 XSL
- Permanent Source URI:
- https://models.physiomeproject.org/w/andre/VPH-MIP/rawfile/bd1651a373bbed124d4bd763a86c32c2bf2f3ff0/experiments/periodic-stimulus.xml
<?xml version="1.0" encoding="iso-8859-1"?>
<model 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" name="periodic_stimulus">
<!-- this block of XML is used by CSim to execute a simulation (https://code.google.com/p/cellml-simulator/) -->
<simulation xmlns="http://cellml.sourceforge.net/csim/simulation/0.1#" id="simulation1">
<boundVariable start="0.0" end="220.0" maxStep="0.05" tabulationStep="0.1"/>
<outputVariable component="outputs" variable="time" column="1"/>
<outputVariable component="outputs" variable="INa" column="2"/>
<outputVariable component="outputs" variable="IK" column="3"/>
<outputVariable component="outputs" variable="Ileak" column="4"/>
<outputVariable component="outputs" variable="V" column="5"/>
<outputVariable component="outputs" variable="minus_V" column="6"/>
<outputVariable component="outputs" variable="h" column="7"/>
<outputVariable component="outputs" variable="m" column="8"/>
<outputVariable component="outputs" variable="n" column="9"/>
</simulation>
<import xlink:href="../components/units.xml">
<units name="ms" units_ref="ms"/>
<units name="uA_per_cmsq" units_ref="uA_per_cmsq"/>
</import>
<import xlink:href="../components/stimulated.xml">
<component name="model" component_ref="action_potential"/>
</import>
<import xlink:href="periodic-IStim-protocol.xml">
<component name="stimulus_protocol" component_ref="stimulus_protocol"/>
</import>
<import xlink:href="time.xml">
<component name="time" component_ref="time"/>
</import>
<import xlink:href="../components/default-variable-values.xml">
<component name="default_parameters" component_ref="parameters"/>
<component name="default_initial_conditions" component_ref="initial_conditions"/>
</import>
<!-- Connect the time source variable to the model and stimulus protocol -->
<connection>
<map_components component_1="model" 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 name="stimPeriod" initial_value="50" public_interface="out" units="ms"/>
<variable name="stimDuration" initial_value="0.5" public_interface="out" units="ms"/>
<variable name="stimCurrent" initial_value="-10.0" 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="model" 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">
</component>
<!-- but since we want all default parameters we just connect the default values through to the model -->
<connection>
<map_components component_1="model" component_2="default_parameters"/>
<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>
<!-- similarly for the initial conditions -->
<component name="initial_conditions">
</component>
<connection>
<map_components component_1="model" component_2="default_initial_conditions"/>
<map_variables variable_1="V_initial" variable_2="V_initial"/>
<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="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="model"/>
<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="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"/>
</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>
