Location: Intracellular pH regulation @ 920a714dbe07 / models / CellMLV2 / Boron_acid.sedml

Author:
Weiwei Ai <wai484@aucklanduni.ac.nz>
Date:
2024-02-27 17:21:53+13:00
Desc:
Add H buffering in the acid BG model
Permanent Source URI:
https://staging.physiomeproject.org/workspace/b61/rawfile/920a714dbe070a8ab1215d82e465d4aaa7216a0a/models/CellMLV2/Boron_acid.sedml
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<?xml version="1.0" encoding="UTF-8"?>
<sedML xmlns="http://sed-ml.org/sed-ml/level1/version4" level="1" version="4">
  <listOfModels>
    <model id="Boron_acid" language="urn:sedml:language:cellml" source="Boron_acid.cellml"/>
  </listOfModels>
  <listOfSimulations>
    <uniformTimeCourse id="sim_Boron_acid" initialTime="0" outputStartTime="0" outputEndTime="5000" numberOfSteps="5000">
      <algorithm name="VODE" kisaoID="KISAO:0000535">
        <listOfAlgorithmParameters>
          <algorithmParameter name="max_step" kisaoID="KISAO:0000467" value="1"/>
        </listOfAlgorithmParameters>
      </algorithm>
    </uniformTimeCourse>
  </listOfSimulations>
  <listOfTasks>
    <task id="task_Boron_acid" modelReference="Boron_acid" simulationReference="sim_Boron_acid"/>
  </listOfTasks>
  <listOfDataGenerators>
    <dataGenerator id="dg_Boron_acid_CO2_o" name="dg_Boron_acid_CO2_o">
      <math xmlns="http://www.w3.org/1998/Math/MathML">
        <ci> Boron_acid_CO2_o </ci>
      </math>
      <listOfVariables>
        <variable id="Boron_acid_CO2_o" target="/cellml:model/cellml:component[@name=&quot;main&quot;]/cellml:variable[@name=&quot;CO2_o&quot;]" taskReference="task_Boron_acid" modelReference="Boron_acid"/>
      </listOfVariables>
    </dataGenerator>
    <dataGenerator id="dg_Boron_acid_CO2_i" name="dg_Boron_acid_CO2_i">
      <math xmlns="http://www.w3.org/1998/Math/MathML">
        <ci> Boron_acid_CO2_i </ci>
      </math>
      <listOfVariables>
        <variable id="Boron_acid_CO2_i" target="/cellml:model/cellml:component[@name=&quot;main&quot;]/cellml:variable[@name=&quot;CO2_i&quot;]" taskReference="task_Boron_acid" modelReference="Boron_acid"/>
      </listOfVariables>
    </dataGenerator>
    <dataGenerator id="dg_Boron_acid_HCO3_o" name="dg_Boron_acid_HCO3_o">
      <math xmlns="http://www.w3.org/1998/Math/MathML">
        <ci> Boron_acid_HCO3_o </ci>
      </math>
      <listOfVariables>
        <variable id="Boron_acid_HCO3_o" target="/cellml:model/cellml:component[@name=&quot;main&quot;]/cellml:variable[@name=&quot;HCO3_o&quot;]" taskReference="task_Boron_acid" modelReference="Boron_acid"/>
      </listOfVariables>
    </dataGenerator>
    <dataGenerator id="dg_Boron_acid_HCO3_i" name="dg_Boron_acid_HCO3_i">
      <math xmlns="http://www.w3.org/1998/Math/MathML">
        <ci> Boron_acid_HCO3_i </ci>
      </math>
      <listOfVariables>
        <variable id="Boron_acid_HCO3_i" target="/cellml:model/cellml:component[@name=&quot;main&quot;]/cellml:variable[@name=&quot;HCO3_i&quot;]" taskReference="task_Boron_acid" modelReference="Boron_acid"/>
      </listOfVariables>
    </dataGenerator>
    <dataGenerator id="dg_Boron_acid_H_i" name="dg_Boron_acid_H_i">
      <math xmlns="http://www.w3.org/1998/Math/MathML">
        <ci> Boron_acid_H_i </ci>
      </math>
      <listOfVariables>
        <variable id="Boron_acid_H_i" target="/cellml:model/cellml:component[@name=&quot;main&quot;]/cellml:variable[@name=&quot;H_i&quot;]" taskReference="task_Boron_acid" modelReference="Boron_acid"/>
      </listOfVariables>
    </dataGenerator>
    <dataGenerator id="dg_Boron_acid_pH_o" name="dg_Boron_acid_pH_o">
      <math xmlns="http://www.w3.org/1998/Math/MathML">
        <ci> Boron_acid_pH_o </ci>
      </math>
      <listOfVariables>
        <variable id="Boron_acid_pH_o" target="/cellml:model/cellml:component[@name=&quot;main&quot;]/cellml:variable[@name=&quot;pH_o&quot;]" taskReference="task_Boron_acid" modelReference="Boron_acid"/>
      </listOfVariables>
    </dataGenerator>
    <dataGenerator id="dg_Boron_acid_pH_i" name="dg_Boron_acid_pH_i">
      <math xmlns="http://www.w3.org/1998/Math/MathML">
        <ci> Boron_acid_pH_i </ci>
      </math>
      <listOfVariables>
        <variable id="Boron_acid_pH_i" target="/cellml:model/cellml:component[@name=&quot;main&quot;]/cellml:variable[@name=&quot;pH_i&quot;]" taskReference="task_Boron_acid" modelReference="Boron_acid"/>
      </listOfVariables>
    </dataGenerator>
    <dataGenerator id="dg_Boron_acid_J_CO2" name="dg_Boron_acid_J_CO2">
      <math xmlns="http://www.w3.org/1998/Math/MathML">
        <apply>
          <times/>
          <ci> Boron_acid_J_CO2 </ci>
          <ci> scale </ci>
        </apply>
      </math>
      <listOfVariables>
        <variable id="Boron_acid_J_CO2" target="/cellml:model/cellml:component[@name=&quot;main&quot;]/cellml:variable[@name=&quot;J_CO2&quot;]" taskReference="task_Boron_acid" modelReference="Boron_acid"/>
      </listOfVariables>
      <listOfParameters>
        <parameter id="scale" value="8000"/>
      </listOfParameters>
    </dataGenerator>
    <dataGenerator id="dg_Boron_acid_J_HCO3" name="dg_Boron_acid_J_HCO3">
      <math xmlns="http://www.w3.org/1998/Math/MathML">
        <apply>
          <times/>
          <ci> Boron_acid_J_HCO3 </ci>
          <ci> scale </ci>
        </apply>
      </math>
      <listOfVariables>
        <variable id="Boron_acid_J_HCO3" target="/cellml:model/cellml:component[@name=&quot;main&quot;]/cellml:variable[@name=&quot;J_HCO3&quot;]" taskReference="task_Boron_acid" modelReference="Boron_acid"/>
      </listOfVariables>
      <listOfParameters>
        <parameter id="scale" value="8000"/>
      </listOfParameters>
    </dataGenerator>
    <dataGenerator id="dg_Boron_acid_J_H" name="dg_Boron_acid_J_H">
      <math xmlns="http://www.w3.org/1998/Math/MathML">
        <apply>
          <times/>
          <ci> Boron_acid_J_H </ci>
          <ci> scale </ci>
        </apply>
      </math>
      <listOfVariables>
        <variable id="Boron_acid_J_H" target="/cellml:model/cellml:component[@name=&quot;main&quot;]/cellml:variable[@name=&quot;J_H&quot;]" taskReference="task_Boron_acid" modelReference="Boron_acid"/>
      </listOfVariables>
      <listOfParameters>
        <parameter id="scale" value="8000"/>
      </listOfParameters>
    </dataGenerator>
    <dataGenerator id="dg_Boron_acid_t" name="dg_Boron_acid_t">
      <math xmlns="http://www.w3.org/1998/Math/MathML">
        <ci> Boron_acid_t </ci>
      </math>
      <listOfVariables>
        <variable id="Boron_acid_t" target="/cellml:model/cellml:component[@name=&quot;main&quot;]/cellml:variable[@name=&quot;t&quot;]" taskReference="task_Boron_acid" modelReference="Boron_acid"/>
      </listOfVariables>
    </dataGenerator>
  </listOfDataGenerators>
  <listOfOutputs>
    <report id="report_task_Boron_acid" name="report_task_Boron_acid">
      <listOfDataSets>
        <dataSet id="dataset_Boron_acid_CO2_o" label="CO2_o" dataReference="dg_Boron_acid_CO2_o"/>
        <dataSet id="dataset_Boron_acid_CO2_i" label="CO2_i" dataReference="dg_Boron_acid_CO2_i"/>
        <dataSet id="dataset_Boron_acid_HCO3_o" label="HCO3_o" dataReference="dg_Boron_acid_HCO3_o"/>
        <dataSet id="dataset_Boron_acid_HCO3_i" label="HCO3_i" dataReference="dg_Boron_acid_HCO3_i"/>
        <dataSet id="dataset_Boron_acid_H_i" label="H_i" dataReference="dg_Boron_acid_H_i"/>
        <dataSet id="dataset_Boron_acid_pH_o" label="pH_o" dataReference="dg_Boron_acid_pH_o"/>
        <dataSet id="dataset_Boron_acid_pH_i" label="pH_i" dataReference="dg_Boron_acid_pH_i"/>
        <dataSet id="dataset_Boron_acid_J_CO2" label="J_CO2" dataReference="dg_Boron_acid_J_CO2"/>
        <dataSet id="dataset_Boron_acid_J_HCO3" label="J_HCO3" dataReference="dg_Boron_acid_J_HCO3"/>
        <dataSet id="dataset_Boron_acid_J_H" label="J_H" dataReference="dg_Boron_acid_J_H"/>
        <dataSet id="dataset_Boron_acid_t" label="t" dataReference="dg_Boron_acid_t"/>
      </listOfDataSets>
    </report>
  </listOfOutputs>
</sedML>