- Author:
- Weiwei Ai <wai484@aucklanduni.ac.nz>
- Date:
- 2026-05-22 14:34:26+12:00
- Desc:
- update the params
- Permanent Source URI:
- https://staging.physiomeproject.org/workspace/cad/rawfile/464437442fe2529c8751a37cf98977cd34a4135b/models/NKE_BG_6_state_ATPNa_pulseV_pe.sedml
<?xml version="1.0" encoding="UTF-8"?>
<sedML xmlns="http://sed-ml.org/sed-ml/level1/version4" level="1" version="4">
<listOfDataDescriptions>
<dataDescription id="fid_1" name="data_summary" format="csv" source="./simulation/report_task_NKE_BG_15_state_default_0.csv">
<dimensionDescription xmlns="http://www.numl.org/numl/level1/version1">
<compositeDescription xmlns="http://www.numl.org/numl/level1/version1" id="Index" name="Index" indexType="integer">
<compositeDescription xmlns="http://www.numl.org/numl/level1/version1" id="ColumnIds" name="ColumnIds" indexType="string">
<atomicDescription xmlns="http://www.numl.org/numl/level1/version1" valueType="double"/>
</compositeDescription>
</compositeDescription>
</dimensionDescription>
<listOfDataSources>
<dataSource id="fid_1_time">
<listOfSlices>
<slice reference="ColumnIds" value="t" startIndex="0"/>
</listOfSlices>
</dataSource>
<dataSource id="fid_1_i_Vm">
<listOfSlices>
<slice reference="ColumnIds" value="i_Vm"/>
</listOfSlices>
</dataSource>
</listOfDataSources>
</dataDescription>
</listOfDataDescriptions>
<listOfModels>
<model id="NKE_BG_6_state_ATPNa_pulseV" language="urn:sedml:language:cellml" source="NKE_BG_6_state_ATPNa.cellml">
<listOfChanges>
<changeAttribute target="/cellml:model/cellml:component[@name="NKE_BG_Env"]/cellml:variable[@name="c_Nai"]/@initial_value" newValue="10.0"/>
<changeAttribute target="/cellml:model/cellml:component[@name="NKE_BG_Env"]/cellml:variable[@name="c_Nao"]/@initial_value" newValue="140.0"/>
<changeAttribute target="/cellml:model/cellml:component[@name="NKE_BG_Env"]/cellml:variable[@name="c_Ki"]/@initial_value" newValue="145"/>
<changeAttribute target="/cellml:model/cellml:component[@name="NKE_BG_Env"]/cellml:variable[@name="c_Ko"]/@initial_value" newValue="4.5"/>
<changeAttribute target="/cellml:model/cellml:component[@name="NKE_BG_Env"]/cellml:variable[@name="c_ATP"]/@initial_value" newValue="1"/>
<changeAttribute target="/cellml:model/cellml:component[@name="NKE_BG_Env"]/cellml:variable[@name="c_ADP"]/@initial_value" newValue="0.035"/>
<changeAttribute target="/cellml:model/cellml:component[@name="NKE_BG_Env"]/cellml:variable[@name="c_Pi"]/@initial_value" newValue="0.8"/>
<changeAttribute target="/cellml:model/cellml:component[@name="NKE_BG_Env"]/cellml:variable[@name="pH"]/@initial_value" newValue="7.2"/>
</listOfChanges>
</model>
</listOfModels>
<listOfTasks>
<parameterEstimationTask id="pe_task_NKE_BG_6_state_ATPNa_pulseV">
<algorithm name="evolutionary algorithm" kisaoID="KISAO:0000520">
<listOfAlgorithmParameters>
<algorithmParameter name="tol" kisaoID="KISAO:0000597" value="1e-6"/>
<algorithmParameter name="maxiter" kisaoID="KISAO:0000517" value="2000"/>
<algorithmParameter name="popsize" kisaoID="KISAO:0000519" value="100"/>
<algorithmParameter name="workers" kisaoID="KISAO:0000529" value="10"/>
</listOfAlgorithmParameters>
</algorithm>
<leastSquareObjectiveFunction/>
<listOfAdjustableParameters>
<adjustableParameter id="NKE_BG_param_kappa_r1" initialValue="10787" modelReference="NKE_BG_6_state_ATPNa_pulseV" target="/cellml:model/cellml:component[@name="NKE_BG_param"]/cellml:variable[@name="kappa_r1"]/@initial_value">
<bounds lowerBound="0.01" upperBound="100000" scale="linear"/>
<listOfExperimentReferences>
<experimentReference experimentId="fit_1"/>
</listOfExperimentReferences>
</adjustableParameter>
<adjustableParameter id="NKE_BG_param_kappa_r2" initialValue="15" modelReference="NKE_BG_6_state_ATPNa_pulseV" target="/cellml:model/cellml:component[@name="NKE_BG_param"]/cellml:variable[@name="kappa_r2"]/@initial_value">
<bounds lowerBound="0.001" upperBound="1000" scale="linear"/>
<listOfExperimentReferences>
<experimentReference experimentId="fit_1"/>
</listOfExperimentReferences>
</adjustableParameter>
<adjustableParameter id="NKE_BG_param_kappa_r3" initialValue="2.3" modelReference="NKE_BG_6_state_ATPNa_pulseV" target="/cellml:model/cellml:component[@name="NKE_BG_param"]/cellml:variable[@name="kappa_r3"]/@initial_value">
<bounds lowerBound="0.01" upperBound="1000" scale="linear"/>
<listOfExperimentReferences>
<experimentReference experimentId="fit_1"/>
</listOfExperimentReferences>
</adjustableParameter>
<adjustableParameter id="NKE_BG_param_kappa_r4" initialValue="172042" modelReference="NKE_BG_6_state_ATPNa_pulseV" target="/cellml:model/cellml:component[@name="NKE_BG_param"]/cellml:variable[@name="kappa_r4"]/@initial_value">
<bounds lowerBound="0.01" upperBound="1000000" scale="linear"/>
<listOfExperimentReferences>
<experimentReference experimentId="fit_1"/>
</listOfExperimentReferences>
</adjustableParameter>
<adjustableParameter id="NKE_BG_param_kappa_r5" initialValue="597" modelReference="NKE_BG_6_state_ATPNa_pulseV" target="/cellml:model/cellml:component[@name="NKE_BG_param"]/cellml:variable[@name="kappa_r5"]/@initial_value">
<bounds lowerBound="0.001" upperBound="10000" scale="linear"/>
<listOfExperimentReferences>
<experimentReference experimentId="fit_1"/>
</listOfExperimentReferences>
</adjustableParameter>
<adjustableParameter id="NKE_BG_param_kappa_r6" initialValue="300" modelReference="NKE_BG_6_state_ATPNa_pulseV" target="/cellml:model/cellml:component[@name="NKE_BG_param"]/cellml:variable[@name="kappa_r6"]/@initial_value">
<bounds lowerBound="0.001" upperBound="10000" scale="linear"/>
<listOfExperimentReferences>
<experimentReference experimentId="fit_1"/>
</listOfExperimentReferences>
</adjustableParameter>
<adjustableParameter id="NKE_BG_param_K_1" initialValue="0.0124" modelReference="NKE_BG_6_state_ATPNa_pulseV" target="/cellml:model/cellml:component[@name="NKE_BG_param"]/cellml:variable[@name="K_1"]/@initial_value">
<bounds lowerBound="0.0001" upperBound="1" scale="linear"/>
<listOfExperimentReferences>
<experimentReference experimentId="fit_1"/>
</listOfExperimentReferences>
</adjustableParameter>
<adjustableParameter id="NKE_BG_param_K_4" initialValue="100" modelReference="NKE_BG_6_state_ATPNa_pulseV" target="/cellml:model/cellml:component[@name="NKE_BG_param"]/cellml:variable[@name="K_4"]/@initial_value">
<bounds lowerBound="0.01" upperBound="10000" scale="linear"/>
<listOfExperimentReferences>
<experimentReference experimentId="fit_1"/>
</listOfExperimentReferences>
</adjustableParameter>
</listOfAdjustableParameters>
<listOfFitExperiments>
<fitExperiment id="fit_1" type="timeCourse">
<algorithm name="CVODE" kisaoID="KISAO:0000019">
<listOfAlgorithmParameters>
<algorithmParameter name="rtol" kisaoID="KISAO:0000209" value="1e-07"/>
<algorithmParameter name="max_step" kisaoID="KISAO:0000467" value="0.001"/>
<algorithmParameter name="max_step_number" kisaoID="KISAO:0000415" value="5000"/>
<algorithmParameter name="atol" kisaoID="KISAO:0000211" value="1e-09"/>
</listOfAlgorithmParameters>
</algorithm>
<listOfFitMappings>
<fitMapping dataSource="fid_1_time" target="dg_fid_1_time" type="time"/>
<fitMapping dataSource="fid_1_i_Vm" target="dg_fid_1_i_Vm" type="observable" weight="1"/>
</listOfFitMappings>
</fitExperiment>
</listOfFitExperiments>
</parameterEstimationTask>
</listOfTasks>
<listOfDataGenerators>
<dataGenerator id="dg_fid_1_time" name="dataGenerator1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> var_fid_1_time </ci>
</math>
<listOfVariables>
<variable id="var_fid_1_time" target="/cellml:model/cellml:component[@name="NKE_BG_Env"]/cellml:variable[@name="t"]" taskReference="pe_task_NKE_BG_6_state_ATPNa_pulseV" modelReference="NKE_BG_6_state_ATPNa_pulseV"/>
</listOfVariables>
</dataGenerator>
<dataGenerator id="dg_fid_1_i_Vm" name="dataGenerator1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> var_fid_1_i_Vm </ci>
</math>
<listOfVariables>
<variable id="var_fid_1_i_Vm" target="/cellml:model/cellml:component[@name="NKE_BG_6_state_ATPNa"]/cellml:variable[@name="i_Vm"]" taskReference="pe_task_NKE_BG_6_state_ATPNa_pulseV" modelReference="NKE_BG_6_state_ATPNa_pulseV"/>
</listOfVariables>
</dataGenerator>
<dataGenerator id="dg_obj">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> var_obj </ci>
</math>
<listOfVariables>
<variable id="var_obj" symbol="sedml:parameterestimation:objective_value" taskReference="pe_task_NKE_BG_6_state_ATPNa_pulseV"/>
</listOfVariables>
</dataGenerator>
<dataGenerator id="dg_optimal">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> var_optimal </ci>
</math>
<listOfVariables>
<variable id="var_optimal" symbol="sedml:parameterestimation:optimal_adjustableParameters" taskReference="pe_task_NKE_BG_6_state_ATPNa_pulseV"/>
</listOfVariables>
</dataGenerator>
</listOfDataGenerators>
<listOfOutputs>
<report id="report_pe_task_NKE_BG_6_state_ATPNa_pulseV" name="report_pe_task_NKE_BG_6_state_ATPNa_pulseV">
<listOfDataSets>
<dataSet id="dataset_fid_1_i_Vm" label="fid_1_i_Vm" dataReference="dg_fid_1_i_Vm"/>
<dataSet id="dataset_obj" label="OBJ" dataReference="dg_obj"/>
<dataSet id="dataset_optimal" label="ADJ" dataReference="dg_optimal"/>
</listOfDataSets>
</report>
</listOfOutputs>
</sedML>
