- Author:
- Soroush <ssaf006@aucklanduni.ac.nz>
- Date:
- 2020-05-10 21:27:00+12:00
- Desc:
- added new sedml
- Permanent Source URI:
- https://models.physiomeproject.org/workspace/297/rawfile/5c6d2c520a9faad399fd954401d658362d25ef03/test-stage2.sedml
<?xml version='1.0' encoding='UTF-8'?>
<sedML level="1" version="2" xmlns="http://sed-ml.org/sed-ml/level1/version2" xmlns:cellml="http://www.cellml.org/cellml/1.1#">
<listOfSimulations>
<uniformTimeCourse id="simulation1" initialTime="0" numberOfPoints="10000" outputEndTime="100" outputStartTime="0">
<algorithm kisaoID="KISAO:0000019">
<listOfAlgorithmParameters>
<algorithmParameter kisaoID="KISAO:0000211" value="9.9999999999999995e-08"/>
<algorithmParameter kisaoID="KISAO:0000475" value="BDF"/>
<algorithmParameter kisaoID="KISAO:0000481" value="true"/>
<algorithmParameter kisaoID="KISAO:0000476" value="Newton"/>
<algorithmParameter kisaoID="KISAO:0000477" value="Dense"/>
<algorithmParameter kisaoID="KISAO:0000480" value="0"/>
<algorithmParameter kisaoID="KISAO:0000415" value="500"/>
<algorithmParameter kisaoID="KISAO:0000467" value="0"/>
<algorithmParameter kisaoID="KISAO:0000478" value="Banded"/>
<algorithmParameter kisaoID="KISAO:0000209" value="9.9999999999999995e-08"/>
<algorithmParameter kisaoID="KISAO:0000479" value="0"/>
</listOfAlgorithmParameters>
</algorithm>
</uniformTimeCourse>
</listOfSimulations>
<listOfModels>
<model id="model" language="urn:sedml:language:cellml.1_1" source="acid_base.cellml"/>
</listOfModels>
<listOfTasks>
<repeatedTask id="repeatedTask" range="once" resetModel="true">
<listOfRanges>
<vectorRange id="once">
<value> 1 </value>
</vectorRange>
</listOfRanges>
<listOfSubTasks>
<subTask order="1" task="task1"/>
</listOfSubTasks>
</repeatedTask>
<task id="task1" modelReference="model" simulationReference="simulation1"/>
</listOfTasks>
<listOfDataGenerators>
<dataGenerator id="xDataGenerator1_1">
<listOfVariables>
<variable id="xVariable1_1" target="/cellml:model/cellml:component[@name='environment']/cellml:variable[@name='time']" taskReference="repeatedTask"/>
</listOfVariables>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> xVariable1_1 </ci>
</math>
</dataGenerator>
<dataGenerator id="yDataGenerator1_1">
<listOfVariables>
<variable id="yVariable1_1" target="/cellml:model/cellml:component[@name='renal_proximal_tubule']/cellml:variable[@name='pH_pt']" taskReference="repeatedTask"/>
</listOfVariables>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> yVariable1_1 </ci>
</math>
</dataGenerator>
<dataGenerator id="xDataGenerator1_2">
<listOfVariables>
<variable id="xVariable1_2" target="/cellml:model/cellml:component[@name='environment']/cellml:variable[@name='time']" taskReference="repeatedTask"/>
</listOfVariables>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> xVariable1_2 </ci>
</math>
</dataGenerator>
<dataGenerator id="yDataGenerator1_2">
<listOfVariables>
<variable id="yVariable1_2" target="/cellml:model/cellml:component[@name='renal_epithelial_cell']/cellml:variable[@name='pH_ec']" taskReference="repeatedTask"/>
</listOfVariables>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> yVariable1_2 </ci>
</math>
</dataGenerator>
<dataGenerator id="xDataGenerator1_3">
<listOfVariables>
<variable id="xVariable1_3" target="/cellml:model/cellml:component[@name='environment']/cellml:variable[@name='time']" taskReference="repeatedTask"/>
</listOfVariables>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> xVariable1_3 </ci>
</math>
</dataGenerator>
<dataGenerator id="yDataGenerator1_3">
<listOfVariables>
<variable id="yVariable1_3" target="/cellml:model/cellml:component[@name='renal_interstitial_fluid']/cellml:variable[@name='pH_if']" taskReference="repeatedTask"/>
</listOfVariables>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> yVariable1_3 </ci>
</math>
</dataGenerator>
<dataGenerator id="xDataGenerator1_4">
<listOfVariables>
<variable id="xVariable1_4" target="/cellml:model/cellml:component[@name='environment']/cellml:variable[@name='time']" taskReference="repeatedTask"/>
</listOfVariables>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> xVariable1_4 </ci>
</math>
</dataGenerator>
<dataGenerator id="yDataGenerator1_4">
<listOfVariables>
<variable id="yVariable1_4" target="/cellml:model/cellml:component[@name='peritubular_capillary_blood']/cellml:variable[@name='pH_cb']" taskReference="repeatedTask"/>
</listOfVariables>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> yVariable1_4 </ci>
</math>
</dataGenerator>
<dataGenerator id="xDataGenerator2_1">
<listOfVariables>
<variable id="xVariable2_1" target="/cellml:model/cellml:component[@name='environment']/cellml:variable[@name='time']" taskReference="repeatedTask"/>
</listOfVariables>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> xVariable2_1 </ci>
</math>
</dataGenerator>
<dataGenerator id="yDataGenerator2_1">
<listOfVariables>
<variable id="yVariable2_1" target="/cellml:model/cellml:component[@name='renal_proximal_tubule']/cellml:variable[@name='CO2_pt']" taskReference="repeatedTask"/>
</listOfVariables>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> yVariable2_1 </ci>
</math>
</dataGenerator>
<dataGenerator id="xDataGenerator2_2">
<listOfVariables>
<variable id="xVariable2_2" target="/cellml:model/cellml:component[@name='environment']/cellml:variable[@name='time']" taskReference="repeatedTask"/>
</listOfVariables>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> xVariable2_2 </ci>
</math>
</dataGenerator>
<dataGenerator id="yDataGenerator2_2">
<listOfVariables>
<variable id="yVariable2_2" target="/cellml:model/cellml:component[@name='renal_epithelial_cell']/cellml:variable[@name='CO2_ec']" taskReference="repeatedTask"/>
</listOfVariables>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> yVariable2_2 </ci>
</math>
</dataGenerator>
<dataGenerator id="xDataGenerator2_3">
<listOfVariables>
<variable id="xVariable2_3" target="/cellml:model/cellml:component[@name='environment']/cellml:variable[@name='time']" taskReference="repeatedTask"/>
</listOfVariables>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> xVariable2_3 </ci>
</math>
</dataGenerator>
<dataGenerator id="yDataGenerator2_3">
<listOfVariables>
<variable id="yVariable2_3" target="/cellml:model/cellml:component[@name='renal_interstitial_fluid']/cellml:variable[@name='CO2_if']" taskReference="repeatedTask"/>
</listOfVariables>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> yVariable2_3 </ci>
</math>
</dataGenerator>
<dataGenerator id="xDataGenerator2_4">
<listOfVariables>
<variable id="xVariable2_4" target="/cellml:model/cellml:component[@name='environment']/cellml:variable[@name='time']" taskReference="repeatedTask"/>
</listOfVariables>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> xVariable2_4 </ci>
</math>
</dataGenerator>
<dataGenerator id="yDataGenerator2_4">
<listOfVariables>
<variable id="yVariable2_4" target="/cellml:model/cellml:component[@name='peritubular_capillary_blood']/cellml:variable[@name='CO2_cb']" taskReference="repeatedTask"/>
</listOfVariables>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> yVariable2_4 </ci>
</math>
</dataGenerator>
<dataGenerator id="xDataGenerator3_1">
<listOfVariables>
<variable id="xVariable3_1" target="/cellml:model/cellml:component[@name='environment']/cellml:variable[@name='time']" taskReference="repeatedTask"/>
</listOfVariables>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> xVariable3_1 </ci>
</math>
</dataGenerator>
<dataGenerator id="yDataGenerator3_1">
<listOfVariables>
<variable id="yVariable3_1" target="/cellml:model/cellml:component[@name='renal_proximal_tubule']/cellml:variable[@name='J_hyd_pt']" taskReference="repeatedTask"/>
</listOfVariables>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> yVariable3_1 </ci>
</math>
</dataGenerator>
<dataGenerator id="xDataGenerator3_2">
<listOfVariables>
<variable id="xVariable3_2" target="/cellml:model/cellml:component[@name='environment']/cellml:variable[@name='time']" taskReference="repeatedTask"/>
</listOfVariables>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> xVariable3_2 </ci>
</math>
</dataGenerator>
<dataGenerator id="yDataGenerator3_2">
<listOfVariables>
<variable id="yVariable3_2" target="/cellml:model/cellml:component[@name='renal_epithelial_cell']/cellml:variable[@name='J_hyd_ec']" taskReference="repeatedTask"/>
</listOfVariables>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> yVariable3_2 </ci>
</math>
</dataGenerator>
<dataGenerator id="xDataGenerator3_3">
<listOfVariables>
<variable id="xVariable3_3" target="/cellml:model/cellml:component[@name='environment']/cellml:variable[@name='time']" taskReference="repeatedTask"/>
</listOfVariables>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> xVariable3_3 </ci>
</math>
</dataGenerator>
<dataGenerator id="yDataGenerator3_3">
<listOfVariables>
<variable id="yVariable3_3" target="/cellml:model/cellml:component[@name='peritubular_capillary_blood']/cellml:variable[@name='J_hyd_cb']" taskReference="repeatedTask"/>
</listOfVariables>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> yVariable3_3 </ci>
</math>
</dataGenerator>
<dataGenerator id="xDataGenerator4_1">
<listOfVariables>
<variable id="xVariable4_1" target="/cellml:model/cellml:component[@name='environment']/cellml:variable[@name='time']" taskReference="repeatedTask"/>
</listOfVariables>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> xVariable4_1 </ci>
</math>
</dataGenerator>
<dataGenerator id="yDataGenerator4_1">
<listOfVariables>
<variable id="yVariable4_1" target="/cellml:model/cellml:component[@name='renal_proximal_tubule']/cellml:variable[@name='HCO3_pt']" taskReference="repeatedTask"/>
</listOfVariables>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> yVariable4_1 </ci>
</math>
</dataGenerator>
<dataGenerator id="xDataGenerator4_2">
<listOfVariables>
<variable id="xVariable4_2" target="/cellml:model/cellml:component[@name='environment']/cellml:variable[@name='time']" taskReference="repeatedTask"/>
</listOfVariables>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> xVariable4_2 </ci>
</math>
</dataGenerator>
<dataGenerator id="yDataGenerator4_2">
<listOfVariables>
<variable id="yVariable4_2" target="/cellml:model/cellml:component[@name='renal_epithelial_cell']/cellml:variable[@name='HCO3_ec']" taskReference="repeatedTask"/>
</listOfVariables>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> yVariable4_2 </ci>
</math>
</dataGenerator>
<dataGenerator id="xDataGenerator4_3">
<listOfVariables>
<variable id="xVariable4_3" target="/cellml:model/cellml:component[@name='environment']/cellml:variable[@name='time']" taskReference="repeatedTask"/>
</listOfVariables>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> xVariable4_3 </ci>
</math>
</dataGenerator>
<dataGenerator id="yDataGenerator4_3">
<listOfVariables>
<variable id="yVariable4_3" target="/cellml:model/cellml:component[@name='renal_interstitial_fluid']/cellml:variable[@name='HCO3_if']" taskReference="repeatedTask"/>
</listOfVariables>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> yVariable4_3 </ci>
</math>
</dataGenerator>
<dataGenerator id="xDataGenerator4_4">
<listOfVariables>
<variable id="xVariable4_4" target="/cellml:model/cellml:component[@name='environment']/cellml:variable[@name='time']" taskReference="repeatedTask"/>
</listOfVariables>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> xVariable4_4 </ci>
</math>
</dataGenerator>
<dataGenerator id="yDataGenerator4_4">
<listOfVariables>
<variable id="yVariable4_4" target="/cellml:model/cellml:component[@name='peritubular_capillary_blood']/cellml:variable[@name='HCO3_cb']" taskReference="repeatedTask"/>
</listOfVariables>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> yVariable4_4 </ci>
</math>
</dataGenerator>
</listOfDataGenerators>
<listOfOutputs>
<plot2D id="plot1">
<listOfCurves>
<curve id="curve1_1" logX="false" logY="false" xDataReference="xDataGenerator1_1" yDataReference="yDataGenerator1_1"/>
<curve id="curve1_2" logX="false" logY="false" xDataReference="xDataGenerator1_2" yDataReference="yDataGenerator1_2"/>
<curve id="curve1_3" logX="false" logY="false" xDataReference="xDataGenerator1_3" yDataReference="yDataGenerator1_3"/>
<curve id="curve1_4" logX="false" logY="false" xDataReference="xDataGenerator1_4" yDataReference="yDataGenerator1_4"/>
</listOfCurves>
</plot2D>
<plot2D id="plot2">
<listOfCurves>
<curve id="curve2_1" logX="false" logY="false" xDataReference="xDataGenerator2_1" yDataReference="yDataGenerator2_1"/>
<curve id="curve2_2" logX="false" logY="false" xDataReference="xDataGenerator2_2" yDataReference="yDataGenerator2_2"/>
<curve id="curve2_3" logX="false" logY="false" xDataReference="xDataGenerator2_3" yDataReference="yDataGenerator2_3"/>
<curve id="curve2_4" logX="false" logY="false" xDataReference="xDataGenerator2_4" yDataReference="yDataGenerator2_4"/>
</listOfCurves>
</plot2D>
<plot2D id="plot3">
<listOfCurves>
<curve id="curve3_1" logX="false" logY="false" xDataReference="xDataGenerator3_1" yDataReference="yDataGenerator3_1"/>
<curve id="curve3_2" logX="false" logY="false" xDataReference="xDataGenerator3_2" yDataReference="yDataGenerator3_2"/>
<curve id="curve3_3" logX="false" logY="false" xDataReference="xDataGenerator3_3" yDataReference="yDataGenerator3_3"/>
</listOfCurves>
</plot2D>
<plot2D id="plot4">
<listOfCurves>
<curve id="curve4_1" logX="false" logY="false" xDataReference="xDataGenerator4_1" yDataReference="yDataGenerator4_1"/>
<curve id="curve4_2" logX="false" logY="false" xDataReference="xDataGenerator4_2" yDataReference="yDataGenerator4_2"/>
<curve id="curve4_3" logX="false" logY="false" xDataReference="xDataGenerator4_3" yDataReference="yDataGenerator4_3"/>
<curve id="curve4_4" logX="false" logY="false" xDataReference="xDataGenerator4_4" yDataReference="yDataGenerator4_4"/>
</listOfCurves>
</plot2D>
</listOfOutputs>
</sedML>
