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simple_pk.xml
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<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" level="3" version="2" comp:required="true">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Created with <a href="https://github.com/matthiaskoenig/sbmlutils">https://github.com/matthiaskoenig/sbmlutils</a>.
<a href="https://doi.org/10.5281/zenodo.5525390">
<img src="https://zenodo.org/badge/DOI/10.5281/zenodo.5525390.svg" alt="DOI"/></a></p>
</body>
</notes>
<model metaid="meta_simple_pk" id="simple_pk" name="Simple PK model" substanceUnits="mmole" timeUnits="min" volumeUnits="litre" areaUnits="m2" lengthUnits="metre" extentUnits="mmole">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<h1>Model of absorption and distribution of substance y.</h1>
<h2>Terms of use</h2>
<p>The content of this model has been carefully created in a manual research effort.
This file has been created by <a href="https://livermetabolism.com">Matthias König</a>
using <a href="https://github.com/matthiaskoenig/sbmlutils">sbmlutils</a>.
For questions contact <a href="mailto:[email protected]">[email protected]</a>. Copyright © 2024 Matthias König.</p>
<a rel="license" href="http://creativecommons.org/licenses/by/4.0/">
<img alt="Creative Commons License" style="border-width:0" src="https://i.creativecommons.org/l/by/4.0/88x31.png"/>
</a>
<br/>This work is licensed under a <a rel="license" href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution 4.0 International License</a>.
<p>Redistribution and use of any part of this model, with or without modification,
are permitted provided that the following conditions are met:</p>
<ol>
<li>Redistributions of this SBML file must retain the above copyright notice, this
list of conditions and the following disclaimer.</li>
<li>Redistributions in a different form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation and/or
other materials provided with the distribution.</li>
</ol>
<p>This model is distributed in the hope that it will be useful, but WITHOUT ANY
WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
FOR A PARTICULAR PURPOSE.</p></body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#meta_simple_pk">
<dcterms:creator>
<rdf:Bag>
<rdf:li rdf:parseType="Resource">
<vCard4:hasName rdf:parseType="Resource">
<vCard4:family-name>König</vCard4:family-name>
<vCard4:given-name>Matthias</vCard4:given-name>
</vCard4:hasName>
<vCard4:hasEmail>[email protected]</vCard4:hasEmail>
<vCard4:organization-name>Humboldt-University Berlin, Institute for Theoretical Biology</vCard4:organization-name>
</rdf:li>
<rdf:li rdf:parseType="Resource">
<vCard4:hasName rdf:parseType="Resource">
<vCard4:family-name>Alvarez</vCard4:family-name>
<vCard4:given-name>Antonio</vCard4:given-name>
</vCard4:hasName>
<vCard4:hasEmail>[email protected]</vCard4:hasEmail>
<vCard4:organization-name>Humboldt-University Berlin, Institute for Theoretical Biology</vCard4:organization-name>
</rdf:li>
</rdf:Bag>
</dcterms:creator>
<dcterms:created rdf:parseType="Resource">
<dcterms:W3CDTF>1900-01-01T00:00:00Z</dcterms:W3CDTF>
</dcterms:created>
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>1900-01-01T00:00:00Z</dcterms:W3CDTF>
</dcterms:modified>
</rdf:Description>
</rdf:RDF>
</annotation>
<listOfUnitDefinitions>
<unitDefinition id="g_per_mole" name="g/mole">
<listOfUnits>
<unit kind="gram" exponent="1" scale="0" multiplier="1"/>
<unit kind="mole" exponent="-1" scale="0" multiplier="1"/>
</listOfUnits>
</unitDefinition>
<unitDefinition id="l_per_min" name="l/min">
<listOfUnits>
<unit kind="litre" exponent="1" scale="0" multiplier="1"/>
<unit kind="second" exponent="-1" scale="0" multiplier="60"/>
</listOfUnits>
</unitDefinition>
<unitDefinition id="l_per_min_mmole" name="l/min/mmole">
<listOfUnits>
<unit kind="litre" exponent="1" scale="0" multiplier="1"/>
<unit kind="second" exponent="-1" scale="0" multiplier="60"/>
<unit kind="mole" exponent="-1" scale="0" multiplier="0.001"/>
</listOfUnits>
</unitDefinition>
<unitDefinition id="m2" name="meter^2">
<listOfUnits>
<unit kind="metre" exponent="2" scale="0" multiplier="1"/>
</listOfUnits>
</unitDefinition>
<unitDefinition id="mM" name="mmole/liter">
<listOfUnits>
<unit kind="mole" exponent="1" scale="0" multiplier="0.001"/>
<unit kind="litre" exponent="-1" scale="0" multiplier="1"/>
</listOfUnits>
</unitDefinition>
<unitDefinition id="mg" name="mg">
<listOfUnits>
<unit kind="gram" exponent="1" scale="0" multiplier="0.001"/>
</listOfUnits>
</unitDefinition>
<unitDefinition id="min" name="min">
<listOfUnits>
<unit kind="second" exponent="1" scale="0" multiplier="60"/>
</listOfUnits>
</unitDefinition>
<unitDefinition id="mmole" name="mmole">
<listOfUnits>
<unit kind="mole" exponent="1" scale="0" multiplier="0.001"/>
</listOfUnits>
</unitDefinition>
<unitDefinition id="mmole_per_min" name="mmole/min">
<listOfUnits>
<unit kind="mole" exponent="1" scale="0" multiplier="0.001"/>
<unit kind="second" exponent="-1" scale="0" multiplier="60"/>
</listOfUnits>
</unitDefinition>
<unitDefinition id="mmole_per_min_l" name="mmole/min/liter">
<listOfUnits>
<unit kind="mole" exponent="1" scale="0" multiplier="0.001"/>
<unit kind="second" exponent="-1" scale="0" multiplier="60"/>
<unit kind="litre" exponent="-1" scale="0" multiplier="1"/>
</listOfUnits>
</unitDefinition>
<unitDefinition id="per_min" name="1/min">
<listOfUnits>
<unit kind="second" exponent="-1" scale="0" multiplier="60"/>
</listOfUnits>
</unitDefinition>
<unitDefinition id="per_min_l" name="1/min/liter">
<listOfUnits>
<unit kind="second" exponent="-1" scale="0" multiplier="60"/>
<unit kind="litre" exponent="-1" scale="0" multiplier="1"/>
</listOfUnits>
</unitDefinition>
</listOfUnitDefinitions>
<listOfCompartments>
<compartment metaid="meta_Vgut" sboTerm="SBO:0000290" id="Vgut" name="gut compartment" spatialDimensions="3" size="1" units="litre" constant="true">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#meta_Vgut">
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/SBO:0000290"/>
</rdf:Bag>
</bqbiol:is>
</rdf:Description>
</rdf:RDF>
</annotation>
</compartment>
<compartment metaid="meta_Vperi" sboTerm="SBO:0000290" id="Vperi" name="peripheral compartment" spatialDimensions="3" size="1" units="litre" constant="true">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#meta_Vperi">
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/SBO:0000290"/>
</rdf:Bag>
</bqbiol:is>
</rdf:Description>
</rdf:RDF>
</annotation>
</compartment>
<compartment metaid="meta_Vcent" sboTerm="SBO:0000290" id="Vcent" name="central compartment" spatialDimensions="3" size="1" units="litre" constant="true">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#meta_Vcent">
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/SBO:0000290"/>
</rdf:Bag>
</bqbiol:is>
</rdf:Description>
</rdf:RDF>
</annotation>
</compartment>
</listOfCompartments>
<listOfSpecies>
<species metaid="meta_y_gut" sboTerm="SBO:0000247" id="y_gut" name="y gut" compartment="Vgut" initialAmount="1" substanceUnits="mmole" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>handled in amount not concentration</p>
</body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#meta_y_gut">
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/SBO:0000247"/>
</rdf:Bag>
</bqbiol:is>
</rdf:Description>
</rdf:RDF>
</annotation>
</species>
<species metaid="meta_y_cent" sboTerm="SBO:0000247" id="y_cent" name="y central" compartment="Vcent" initialConcentration="0" substanceUnits="mmole" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#meta_y_cent">
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/SBO:0000247"/>
</rdf:Bag>
</bqbiol:is>
</rdf:Description>
</rdf:RDF>
</annotation>
</species>
<species metaid="meta_y_peri" sboTerm="SBO:0000247" id="y_peri" name="y peripheral" compartment="Vperi" initialConcentration="0" substanceUnits="mmole" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#meta_y_peri">
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/SBO:0000247"/>
</rdf:Bag>
</bqbiol:is>
</rdf:Description>
</rdf:RDF>
</annotation>
</species>
</listOfSpecies>
<listOfParameters>
<parameter metaid="meta_k" sboTerm="SBO:0000009" id="k" name="absorption rate" value="1" units="l_per_min" constant="true">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#meta_k">
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/SBO:0000009"/>
</rdf:Bag>
</bqbiol:is>
</rdf:Description>
</rdf:RDF>
</annotation>
</parameter>
<parameter metaid="meta_CL" sboTerm="SBO:0000009" id="CL" name="clearance" value="1" units="l_per_min" constant="true">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#meta_CL">
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/SBO:0000009"/>
</rdf:Bag>
</bqbiol:is>
</rdf:Description>
</rdf:RDF>
</annotation>
</parameter>
<parameter metaid="meta_Q" sboTerm="SBO:0000009" id="Q" name="distribution Q" value="1" units="l_per_min" constant="true">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#meta_Q">
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/SBO:0000009"/>
</rdf:Bag>
</bqbiol:is>
</rdf:Description>
</rdf:RDF>
</annotation>
</parameter>
</listOfParameters>
<listOfReactions>
<reaction metaid="meta_ABSORPTION" sboTerm="SBO:0000176" id="ABSORPTION" name="absorption" reversible="false">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>[mmole/min]
absorption from gut</p>
</body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#meta_ABSORPTION">
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/SBO:0000176"/>
</rdf:Bag>
</bqbiol:is>
</rdf:Description>
</rdf:RDF>
</annotation>
<listOfReactants>
<speciesReference species="y_gut" stoichiometry="1" constant="true"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="y_cent" stoichiometry="1" constant="true"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> k </ci>
<ci> y_gut </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction metaid="meta_CLEARANCE" sboTerm="SBO:0000176" id="CLEARANCE" name="clearance" reversible="false">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>[mmole/min]
clearance from central compartment</p>
</body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#meta_CLEARANCE">
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/SBO:0000176"/>
</rdf:Bag>
</bqbiol:is>
</rdf:Description>
</rdf:RDF>
</annotation>
<listOfReactants>
<speciesReference species="y_cent" stoichiometry="1" constant="true"/>
</listOfReactants>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> CL </ci>
<ci> y_cent </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction metaid="meta_R1" sboTerm="SBO:0000176" id="R1" name="transport peripheral (R1)" reversible="false">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>[mmole/min]
distribution in peripheral compartment</p>
</body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#meta_R1">
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/SBO:0000176"/>
</rdf:Bag>
</bqbiol:is>
</rdf:Description>
</rdf:RDF>
</annotation>
<listOfReactants>
<speciesReference species="y_cent" stoichiometry="1" constant="true"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="y_peri" stoichiometry="1" constant="true"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> Q </ci>
<ci> y_cent </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction metaid="meta_R2" sboTerm="SBO:0000176" id="R2" name="transport central (R2)" reversible="false">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>[mmole/min]
distribution from peripheral compartment</p>
</body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#meta_R2">
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/SBO:0000176"/>
</rdf:Bag>
</bqbiol:is>
</rdf:Description>
</rdf:RDF>
</annotation>
<listOfReactants>
<speciesReference species="y_peri" stoichiometry="1" constant="true"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="y_cent" stoichiometry="1" constant="true"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> Q </ci>
<ci> y_peri </ci>
</apply>
</math>
</kineticLaw>
</reaction>
</listOfReactions>
</model>
</sbml>