- Author:
- AnandR <a.rampadarath@auckland.ac.nz>
- Date:
- 2019-04-05 14:25:01+13:00
- Desc:
- Added some semgen annotated models (AnandR)
- Permanent Source URI:
- https://staging.physiomeproject.org/workspace/584/rawfile/ade7933153a72bb89e0b02d75db92d6e4be285f5/semgen_annotated_models/friel_1995.cellml
<?xml version="1.0" encoding="UTF-8"?>
<model xmlns="http://www.cellml.org/cellml/1.1#" xmlns:cmeta="http://www.cellml.org/metadata/1.0#" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqs="http://www.cellml.org/bqs/1.0#" xmlns:semsim="http://www.bhi.washington.edu/SemSim#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" name="friel_1995" cmeta:id="friel_1995">
<units name="picolitre">
<unit prefix="pico" units="litre" />
</units>
<units name="nanomolar">
<unit exponent="-1.0" units="litre" />
<unit prefix="nano" units="mole" />
</units>
<units name="micromolar">
<unit exponent="-1.0" units="litre" />
<unit prefix="micro" units="mole" />
</units>
<units name="nanomolar_per_second">
<unit units="nanomolar" />
<unit exponent="-1.0" units="second" />
</units>
<units name="picolitre_nanomolar_per_second">
<unit units="nanomolar" />
<unit exponent="-1.0" units="second" />
<unit units="picolitre" />
</units>
<units name="picolitre_per_second">
<unit exponent="-1.0" units="second" />
<unit units="picolitre" />
</units>
<units name="per_second">
<unit exponent="-1.0" units="second" />
</units>
<component name="environment">
<variable cmeta:id="environment_time" name="time" public_interface="out" units="second" />
</component>
<component name="rate_constants" cmeta:id="id_00011">
<variable cmeta:id="rate_constants.kappa_L1" name="kappa_L1" public_interface="out" units="per_second" />
<variable cmeta:id="rate_constants.kappa_P1" initial_value="0.132" name="kappa_P1" public_interface="out" units="per_second" />
<variable cmeta:id="rate_constants.kappa_L2" name="kappa_L2" public_interface="out" units="per_second" />
<variable cmeta:id="rate_constants.kappa_P2" initial_value="3.78" name="kappa_P2" public_interface="out" units="per_second" />
<variable cmeta:id="rate_constants.kappa_L2_0" initial_value="0.054" name="kappa_L2_0" units="per_second" />
<variable cmeta:id="rate_constants.kappa_L2_1" initial_value="2.4" name="kappa_L2_1" units="per_second" />
<variable cmeta:id="id_00010" name="Kd_Ca" units="nanomolar" />
<variable cmeta:id="rate_constants.n" initial_value="3" name="n" units="dimensionless" />
<variable cmeta:id="rate_constants.time" name="time" public_interface="in" units="second" />
<variable cmeta:id="id_00009" name="Ca_i" public_interface="in" units="nanomolar" />
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply id="kappa_L1_calculation">
<eq />
<ci>kappa_L1</ci>
<piecewise>
<piece>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="per_second">0.000005</cn>
<apply>
<and />
<apply>
<geq />
<ci>time</ci>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="second">0</cn>
</apply>
<apply>
<lt />
<ci>time</ci>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="second">40</cn>
</apply>
</apply>
</piece>
<otherwise>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="per_second">0.00002</cn>
</otherwise>
</piecewise>
</apply>
<apply id="kappa_L2_calculation">
<eq />
<ci>kappa_L2</ci>
<apply>
<plus />
<ci>kappa_L2_0</ci>
<apply>
<divide />
<ci>kappa_L2_1</ci>
<apply>
<plus />
<cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">1</cn>
<apply>
<power />
<apply>
<divide />
<ci>Kd_Ca</ci>
<ci>Ca_i</ci>
</apply>
<ci>n</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply id="Kd_Ca_calculation">
<eq />
<ci>Kd_Ca</ci>
<piecewise>
<piece>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="nanomolar">1000</cn>
<apply>
<and />
<apply>
<geq />
<ci>time</ci>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="second">0</cn>
</apply>
<apply>
<lt />
<ci>time</ci>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="second">80</cn>
</apply>
</apply>
</piece>
<otherwise>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="nanomolar">500</cn>
</otherwise>
</piecewise>
</apply>
</math>
</component>
<component name="cytosolic_calcium" cmeta:id="id_00001">
<variable cmeta:id="cytosolic_calcium_Ca_i" initial_value="75" name="Ca_i" public_interface="out" units="nanomolar" />
<variable cmeta:id="id_00002" initial_value="2000000.0" name="Ca_o" public_interface="out" units="nanomolar" />
<variable cmeta:id="id_00003" name="Ca_i_ss" public_interface="out" units="nanomolar" />
<variable cmeta:id="cytosolic_calcium.gamma" initial_value="0.24" name="gamma" public_interface="out" units="dimensionless" />
<variable cmeta:id="cytosolic_calcium.kappa_L1" name="kappa_L1" public_interface="in" units="per_second" />
<variable cmeta:id="cytosolic_calcium.kappa_P1" name="kappa_P1" public_interface="in" units="per_second" />
<variable cmeta:id="cytosolic_calcium.kappa_L2" name="kappa_L2" public_interface="in" units="per_second" />
<variable cmeta:id="cytosolic_calcium.kappa_P2" name="kappa_P2" public_interface="in" units="per_second" />
<variable cmeta:id="id_00004" name="Ca_s" public_interface="in" units="nanomolar" />
<variable cmeta:id="cytosolic_calcium.time" name="time" public_interface="in" units="second" />
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply id="Ca_i_diff_eq">
<eq />
<apply>
<diff />
<bvar>
<ci>time</ci>
</bvar>
<ci>Ca_i</ci>
</apply>
<apply>
<plus />
<apply>
<times />
<apply>
<minus />
<apply>
<plus />
<ci>kappa_L1</ci>
<ci>kappa_P1</ci>
<apply>
<times />
<ci>gamma</ci>
<apply>
<plus />
<ci>kappa_L2</ci>
<ci>kappa_P2</ci>
</apply>
</apply>
</apply>
</apply>
<ci>Ca_i</ci>
</apply>
<apply>
<times />
<ci>gamma</ci>
<ci>kappa_L2</ci>
<ci>Ca_s</ci>
</apply>
<apply>
<times />
<ci>kappa_L1</ci>
<ci>Ca_o</ci>
</apply>
</apply>
</apply>
<apply id="Ca_i_ss_calculation">
<eq />
<ci>Ca_i_ss</ci>
<apply>
<divide />
<ci>Ca_o</ci>
<apply>
<plus />
<cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">1.0</cn>
<apply>
<divide />
<ci>kappa_P1</ci>
<ci>kappa_L1</ci>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<component name="subspace_calcium" cmeta:id="id_00005">
<variable cmeta:id="subspace_calcium_Ca_s" initial_value="5300.0" name="Ca_s" public_interface="out" units="nanomolar" />
<variable cmeta:id="id_00006" name="Ca_s_ss" public_interface="out" units="nanomolar" />
<variable cmeta:id="id_00007" name="Ca_i" public_interface="in" units="nanomolar" />
<variable cmeta:id="id_00008" name="Ca_i_ss" public_interface="in" units="nanomolar" />
<variable cmeta:id="subspace_calcium.kappa_L2" name="kappa_L2" public_interface="in" units="per_second" />
<variable cmeta:id="subspace_calcium.kappa_P2" name="kappa_P2" public_interface="in" units="per_second" />
<variable cmeta:id="subspace_calcium.time" name="time" public_interface="in" units="second" />
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply id="Ca_s_diff_eq">
<eq />
<apply>
<diff />
<bvar>
<ci>time</ci>
</bvar>
<ci>Ca_s</ci>
</apply>
<apply>
<minus />
<apply>
<times />
<apply>
<plus />
<ci>kappa_L2</ci>
<ci>kappa_P2</ci>
</apply>
<ci>Ca_i</ci>
</apply>
<apply>
<times />
<ci>kappa_L2</ci>
<ci>Ca_s</ci>
</apply>
</apply>
</apply>
<apply id="Ca_s_ss_calculation">
<eq />
<ci>Ca_s_ss</ci>
<apply>
<times />
<ci>Ca_i_ss</ci>
<apply>
<plus />
<cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">1.0</cn>
<apply>
<divide />
<ci>kappa_P2</ci>
<ci>kappa_L2</ci>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<connection>
<map_components component_1="rate_constants" component_2="subspace_calcium" />
<map_variables variable_1="kappa_L2" variable_2="kappa_L2" />
<map_variables variable_1="kappa_P2" variable_2="kappa_P2" />
</connection>
<connection>
<map_components component_1="environment" component_2="cytosolic_calcium" />
<map_variables variable_1="time" variable_2="time" />
</connection>
<connection>
<map_components component_1="environment" component_2="subspace_calcium" />
<map_variables variable_1="time" variable_2="time" />
</connection>
<connection>
<map_components component_1="cytosolic_calcium" component_2="rate_constants" />
<map_variables variable_1="Ca_i" variable_2="Ca_i" />
</connection>
<connection>
<map_components component_1="rate_constants" component_2="cytosolic_calcium" />
<map_variables variable_1="kappa_L2" variable_2="kappa_L2" />
<map_variables variable_1="kappa_P1" variable_2="kappa_P1" />
<map_variables variable_1="kappa_L1" variable_2="kappa_L1" />
<map_variables variable_1="kappa_P2" variable_2="kappa_P2" />
</connection>
<connection>
<map_components component_1="cytosolic_calcium" component_2="subspace_calcium" />
<map_variables variable_1="Ca_i" variable_2="Ca_i" />
<map_variables variable_1="Ca_i_ss" variable_2="Ca_i_ss" />
</connection>
<connection>
<map_components component_1="subspace_calcium" component_2="cytosolic_calcium" />
<map_variables variable_1="Ca_s" variable_2="Ca_s" />
</connection>
<connection>
<map_components component_1="environment" component_2="rate_constants" />
<map_variables variable_1="time" variable_2="time" />
</connection>
<rdf:RDF xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:ro="http://www.obofoundry.org/ro/ro.owl#" xmlns:opb="http://bhi.washington.edu/OPB#">
<rdf:Description rdf:about="#cytosolic_calcium.kappa_L1">
<dcterms:description>calcium leak through the plasma membrane rate constant</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#id_00004">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_4">
<semsim:physicalPropertyOf>
<rdf:Description rdf:about="#entity_7">
<ro:part_of>
<rdf:Description rdf:about="#entity_8" dcterms:description="">
<semsim:name>Neuronal calicum store</semsim:name>
<bqbiol:isVersionOf rdf:resource="http://identifiers.org/fma/FMA:226054" />
</rdf:Description>
</ro:part_of>
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/chebi/CHEBI:29108" />
</rdf:Description>
</semsim:physicalPropertyOf>
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>Concentration of calcium in the store of the cytosol of the neuron</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#environment_time">
<bqbiol:is rdf:resource="http://identifiers.org/opb/OPB_01023" />
</rdf:Description>
<rdf:Description rdf:about="#subspace_calcium.kappa_L2">
<dcterms:description>calcium leak through the store membrane rate constant</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#rate_constants.kappa_P1">
<dcterms:description>calcium pump through the plasma membrane rate constant</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#id_00002">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_2">
<semsim:physicalPropertyOf>
<rdf:Description rdf:about="#entity_3">
<ro:part_of>
<rdf:Description rdf:about="#entity_4">
<ro:part_of>
<rdf:Description rdf:about="#entity_5">
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/fma/FMA:54527" />
</rdf:Description>
</ro:part_of>
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/fma/FMA:70022" />
</rdf:Description>
</ro:part_of>
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/chebi/CHEBI:29108" />
</rdf:Description>
</semsim:physicalPropertyOf>
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>Extracellular calcium concentration in sympathetic neurons</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#id_00008">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_8">
<semsim:physicalPropertyOf>
<rdf:Description rdf:about="#entity_6" dcterms:description="">
<semsim:name>Steady state Intracellular calcium</semsim:name>
<ro:has_part rdf:resource="http://identifiers.org/fma/FMA:226054" />
<ro:has_part rdf:resource="http://identifiers.org/fma/FMA:9906" />
<bqbiol:isVersionOf rdf:resource="http://identifiers.org/chebi/CHEBI:29108" />
</rdf:Description>
</semsim:physicalPropertyOf>
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>Concentration of steady state intracellular calcium in sympathetic neurons</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#id_00006">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_6">
<semsim:physicalPropertyOf>
<rdf:Description rdf:about="#entity_9">
<ro:part_of rdf:resource="#entity_6" />
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/chebi/CHEBI:29108" />
</rdf:Description>
</semsim:physicalPropertyOf>
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>Steady state calcium concentration in the neuronal calcium store.</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#subspace_calcium.kappa_P2">
<dcterms:description>calcium pump through the store membrane rate constant</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#rate_constants.kappa_L1">
<dcterms:description>calcium leak through the plasma membrane rate constant</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#subspace_calcium_Ca_s">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_5">
<semsim:physicalPropertyOf rdf:resource="#entity_7" />
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>Concentration of calcium in the store of the cytosol of the neuron</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#cytosolic_calcium.kappa_P2">
<dcterms:description>calcium pump through the store membrane rate constant</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#cytosolic_calcium_Ca_i">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_1">
<semsim:physicalPropertyOf>
<rdf:Description rdf:about="#entity_0">
<ro:part_of>
<rdf:Description rdf:about="#entity_1">
<ro:part_of>
<rdf:Description rdf:about="#entity_2">
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/fma/FMA:9906" />
</rdf:Description>
</ro:part_of>
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/fma/FMA:226054" />
</rdf:Description>
</ro:part_of>
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/chebi/CHEBI:29108" />
</rdf:Description>
</semsim:physicalPropertyOf>
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>Concentration of intracellular calcium in sympathetic neurons</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#cytosolic_calcium.kappa_L2">
<dcterms:description>calcium leak through the store membrane rate constant</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#id_00003">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_3">
<semsim:physicalPropertyOf rdf:resource="#entity_6" />
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>Concentration of steady state intracellular calcium in sympathetic neurons</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#id_00009">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_0">
<semsim:physicalPropertyOf rdf:resource="#entity_0" />
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>Concentration of intracellular calcium in sympathetic neurons</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#friel_1995" semsim:modelName="friel_1995" />
<rdf:Description rdf:about="#id_00007">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_7">
<semsim:physicalPropertyOf rdf:resource="#entity_0" />
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>Concentration of intracellular calcium in sympathetic neurons</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#subspace_calcium.time">
<bqbiol:is rdf:resource="http://identifiers.org/opb/OPB_01023" />
</rdf:Description>
<rdf:Description rdf:about="#cytosolic_calcium.time">
<bqbiol:is rdf:resource="http://identifiers.org/opb/OPB_01023" />
</rdf:Description>
<rdf:Description rdf:about="#rate_constants.kappa_L2">
<dcterms:description>calcium leak through the store membrane rate constant</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#rate_constants.time">
<bqbiol:is rdf:resource="http://identifiers.org/opb/OPB_01023" />
</rdf:Description>
<rdf:Description rdf:about="#rate_constants.kappa_P2">
<dcterms:description>calcium pump through the store membrane rate constant</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#cytosolic_calcium.kappa_P1">
<dcterms:description>calcium pump through the plasma membrane rate constant</dcterms:description>
</rdf:Description>
</rdf:RDF>
</model>
