- Author:
- David Nickerson <david.nickerson@gmail.com>
- Date:
- 2021-09-15 23:47:07+12:00
- Desc:
- Updating BR model with SED-ML for the default periodic stimulus simulation experinment
- Permanent Source URI:
- https://models.fieldml.org/workspace/a1/rawfile/faec014e4ba6524541fe8093d6bf343861caacfd/sed-ml/BR-INa-variants.xml
<?xml version="1.0" encoding="utf-8"?>
<sedML xmlns="http://www.biomodels.net/sed-ml">
<listOfSimulations>
<uniformTimeCourse id="simulation"
algorithm="KISAO:0000019"
initialTime="0"
outputStartTime="0"
outputEndTime="1500"
numberOfPoints="1500" />
<!--
FIXME: need to reference IVOI - can't go here though...
-->
</listOfSimulations>
<listOfModels>
<model id="BR"
type="CellML"
source="../models/1977_beeler/experiments/periodic_stimulus.xml" />
<model id="BREJ"
type="CellML"
source="../models/1977_beeler/experiments/1980_ebihara_johnson.xml" />
<model id="BRDR"
type="CellML"
source="../models/1977_beeler/experiments/1987_drouhard_roberge.xml" />
</listOfModels>
<listOfTasks>
<task id="BR-task" modelReference="BR" simulationReference="simulation" />
<task id="BREJ-task" modelReference="BREJ" simulationReference="simulation" />
<task id="BRDR-task" modelReference="BRDR" simulationReference="simulation" />
</listOfTasks>
<listOfDataGenerators>
<dataGenerator id="BR-time" name="BR time">
<listOfVariables>
<variable id="BR-time" taskReference="BR-task" target="/cellml:model/cellml:component[@name='time']/cellml:variable[@name='time']" />
</listOfVariables>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> BR-time </ci>
</math>
</dataGenerator>
<dataGenerator id="BR-Vm" name="BR Vm">
<listOfVariables>
<variable id="BR-Vm" taskReference="BR-task"
target="/cellml:model/cellml:component[@name='exposed_variables']/cellml:variable[@name='Vm']" />
</listOfVariables>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> BR-Vm </ci>
</math>
</dataGenerator>
<dataGenerator id="BREJ-time" name="BREJ time">
<listOfVariables>
<variable id="BREJ-time" taskReference="BREJ-task" target="/cellml:model/cellml:component[@name='time']/cellml:variable[@name='time']" />
</listOfVariables>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> BREJ-time </ci>
</math>
</dataGenerator>
<dataGenerator id="BREJ-Vm" name="BREJ Vm">
<listOfVariables>
<variable id="BREJ-Vm" taskReference="BREJ-task"
target="/cellml:model/cellml:component[@name='fast_sodium_current']/cellml:variable[@name='V']" />
</listOfVariables>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> BREJ-Vm </ci>
</math>
</dataGenerator>
<dataGenerator id="BRDR-time" name="BRDR time">
<listOfVariables>
<variable id="BRDR-time" taskReference="BRDR-task" target="/cellml:model/cellml:component[@name='time']/cellml:variable[@name='time']" />
</listOfVariables>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> BRDR-time </ci>
</math>
</dataGenerator>
<dataGenerator id="BRDR-Vm" name="BRDR Vm">
<listOfVariables>
<variable id="BRDR-Vm" taskReference="BRDR-task"
target="/cellml:model/cellml:component[@name='fast_sodium_current']/cellml:variable[@name='V']" />
</listOfVariables>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> BRDR-Vm </ci>
</math>
</dataGenerator>
</listOfDataGenerators>
<listOfOutputs>
<plot2D id="plot1" name="Action Potentials" logX="false" logY="false">
<listOfCurves>
<curve xDataReference="BR-time" yDataReference="BR-Vm" />
<curve xDataReference="BREJ-time" yDataReference="BREJ-Vm" />
<curve xDataReference="BRDR-time" yDataReference="BRDR-Vm" />
</listOfCurves>
</plot2D>
</listOfOutputs>
</sedML>
