<?xml version="1.0"?>
<!-- FILE : PGM_1999.xml
CREATED : 5th March 2002
LAST MODIFIED : 20th April 2005
AUTHOR : Catherine Lloyd
Department of Engineering Science
The University of Auckland
MODEL STATUS : This model conforms to the CellML 1.0 Specification released on
10th August 2001, and the 16/01/2002 CellML Metadata 1.0 Specification.
DESCRIPTION : This file contains a CellML description of the 1999 Mulquiney,
Bubb and Kuchel mathematical model of the 2,3-bisphosphoglycerate shunt in
erythrocytes.
CHANGES:
18/07/2002 - CML - Added more metadata
09/04/2003 - AAC - Added publication date information.
20/04/2005 - PJV - Updated syntax to conform with cellml 1.1 specs
-->
<model name="PGM_1999" cmeta:id="PGM_1999" pathway_editor:rendering_config_file="PGM_1999_cellmlrender.xml" xmlns="http://www.cellml.org/cellml/1.0#" xmlns:cellml="http://www.cellml.org/cellml/1.0#" xmlns:cmeta="http://www.cellml.org/metadata/1.0#" xmlns:pathway_editor="http://www.physiome.com/pathway_editor/1.0#">
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqs="http://www.cellml.org/bqs/1.0#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#">
<!--
The following RDF block contains metadata that applies to this document
as a whole, as indicated by the empty about attribute on the
<rdf:Description> element.
-->
<rdf:Description rdf:about="">
<!--
The Model Builder Metadata. The Dublin Core "creator" element is used
to indicate the person who translated the model into CellML.
-->
<dc:creator rdf:parseType="Resource">
<vCard:N rdf:parseType="Resource">
<vCard:Family>Lloyd</vCard:Family>
<vCard:Given>Catherine</vCard:Given>
<vCard:Other>May</vCard:Other>
</vCard:N>
<vCard:EMAIL rdf:parseType="Resource">
<rdf:value>c.lloyd@auckland.ac.nz</rdf:value>
<rdf:type rdf:resource="http://imc.org/vCard/3.0#internet" />
</vCard:EMAIL>
<vCard:ORG rdf:parseType="Resource">
<vCard:Orgname>The University of Auckland</vCard:Orgname>
<vCard:Orgunit>The Bioengineering Institute</vCard:Orgunit>
</vCard:ORG>
</dc:creator>
<!--
The Creation Date metadata. This is the date on which the model
was translated into CellML.
-->
<dcterms:created rdf:parseType="Resource">
<dcterms:W3CDTF>2002-03-05</dcterms:W3CDTF>
</dcterms:created>
<!--
The Modification History metadata. This lists the changes that have been
made to the document, who made the changes, and when they were made.
-->
<cmeta:modification rdf:parseType="Resource">
<rdf:value>
Updated syntax to conform with cellml1.1 specs
</rdf:value>
<cmeta:modifier rdf:parseType="Resource">
<vCard:N rdf:parseType="Resource">
<vCard:Family>Villiger</vCard:Family>
<vCard:Given>Peter</vCard:Given>
<vCard:Other>J</vCard:Other>
</vCard:N>
</cmeta:modifier>
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2005-04-20</dcterms:W3CDTF>
</dcterms:modified>
</cmeta:modification>
<cmeta:modification rdf:parseType="Resource">
<rdf:value>
Added publication date information.
</rdf:value>
<cmeta:modifier rdf:parseType="Resource">
<vCard:N rdf:parseType="Resource">
<vCard:Family>Cuellar</vCard:Family>
<vCard:Given>Autumn</vCard:Given>
<vCard:Other>A</vCard:Other>
</vCard:N>
</cmeta:modifier>
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2003-04-09</dcterms:W3CDTF>
</dcterms:modified>
</cmeta:modification>
<cmeta:modification rdf:parseType="Resource">
<rdf:value>
Added more metadata.
</rdf:value>
<cmeta:modifier rdf:parseType="Resource">
<vCard:N rdf:parseType="Resource">
<vCard:Family>Lloyd</vCard:Family>
<vCard:Given>Catherine</vCard:Given>
<vCard:Other>May</vCard:Other>
</vCard:N>
</cmeta:modifier>
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2002-07-18</dcterms:W3CDTF>
</dcterms:modified>
</cmeta:modification>
<!-- The Publisher metadata. -->
<dc:publisher>
The University of Auckland, Bioengineering Research Group
</dc:publisher>
</rdf:Description>
<!--
The following metadata refers to the model itself, as indicated by the
reference to the ID "PGM_1999", which is declared on
the <model> element.
-->
<rdf:Description rdf:about="#PGM_1999">
<!-- A human readable name for the model. -->
<dc:title>
A model of the 2,3-BPG shunt in human erythrocytes.
</dc:title>
<!-- A comment regarding the model. -->
<cmeta:comment rdf:parseType="Resource">
<rdf:value>
This is the CellML description of Mulquiney, Bubb and Kuchel's
mathematical model of the 2,3-BPG shunt in human erythrocytes (1999).
</rdf:value>
<!-- The creator of the comment. -->
<dc:creator rdf:parseType="Resource">
<vCard:FN>Catherine Lloyd</vCard:FN>
</dc:creator>
</cmeta:comment>
<!-- The model is relevant to human erythrocytes. -->
<cmeta:species>Homo Sapiens</cmeta:species>
<!-- This model is specific to erythrocytes. -->
<cmeta:bio_entity>erythrocyte</cmeta:bio_entity>
<!-- Keyword(s) -->
<bqs:reference rdf:parseType="Resource">
<dc:subject rdf:parseType="Resource">
<bqs:subject_type>keyword</bqs:subject_type>
<rdf:value>metabolism</rdf:value>
</dc:subject>
</bqs:reference>
<!--
The CellML Metadata Specification recommends that bibliographic metadata
is used to provide information about the original model reference. The
"identifier" attribute on the "BibliographicReference" class provides an
elegant way to identify a cited reference using a database identifier such as Pubmed. All associated data such as author, journal title,
date, etc can be looked up on the database.
-->
<bqs:reference rdf:parseType="Resource">
<bqs:Pubmed_id>10477268</bqs:Pubmed_id>
<bqs:JournalArticle rdf:parseType="Resource">
<dc:creator>
<rdf:Seq>
<rdf:li rdf:parseType="Resource">
<bqs:Person rdf:parseType="Resource">
<vCard:N rdf:parseType="Resource">
<vCard:Family>Mulquiney</vCard:Family>
<vCard:Given>Peter</vCard:Given>
<vCard:Other>J</vCard:Other>
</vCard:N>
</bqs:Person>
</rdf:li>
<rdf:li rdf:parseType="Resource">
<bqs:Person rdf:parseType="Resource">
<vCard:N rdf:parseType="Resource">
<vCard:Family>Bubb</vCard:Family>
<vCard:Given>William</vCard:Given>
<vCard:Other>A</vCard:Other>
</vCard:N>
</bqs:Person>
</rdf:li>
<rdf:li rdf:parseType="Resource">
<bqs:Person rdf:parseType="Resource">
<vCard:N rdf:parseType="Resource">
<vCard:Family>Kuchel</vCard:Family>
<vCard:Given>Philip</vCard:Given>
<vCard:Other>W</vCard:Other>
</vCard:N>
</bqs:Person>
</rdf:li>
</rdf:Seq>
</dc:creator>
<dc:title>
Model of 2,3-bisphosphoglycerate metabolism in the human erythrocyte based on detailed enzyme kinetic equations: in vivo kinetic
characterisation of 2,3-bisphosphoglycerate synthase/phosphatase
using 13C and 31P NMR
</dc:title>
<dcterms:issued rdf:parseType="Resource">
<dcterms:W3CDTF>1999-09-15</dcterms:W3CDTF>
</dcterms:issued>
<bqs:Journal rdf:parseType="Resource">
<dc:title>Biochemical Journal</dc:title>
</bqs:Journal>
<bqs:volume>342</bqs:volume>
<bqs:first_page>567</bqs:first_page>
<bqs:last_page>580</bqs:last_page>
</bqs:JournalArticle>
</bqs:reference>
</rdf:Description>
</rdf:RDF>
<!--
We start the model definition with a definition of some named
sets of units for use throughout the model.
-->
<units name="molar">
<unit units="mole" />
<unit units="litre" exponent="-1" />
</units>
<units name="millimolar">
<unit prefix="milli" units="molar" />
</units>
<units name="flux">
<unit prefix="milli" units="mole" />
<unit units="second" exponent="-1" />
</units>
<units name="first_order_rate_constant">
<unit units="second" exponent="-1" />
</units>
<units name="second_order_rate_constant">
<unit units="molar" exponent="-1" />
<unit units="second" exponent="-1" />
</units>
<!--
The following component is defined for modelling convenience. It contains
all the universal variables, in this case, only time.
-->
<component name="global_variables">
<variable name="time" public_interface="out" units="second" />
</component>
<!--
The following components describe all the substrates, enzymes,
enzyme-substrate complexes and products in the 2,3-BPG shunt.
-->
<component name="E" cmeta:id="E">
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/">
<rdf:Description rdf:about="E">
<dc:title>E</dc:title>
<dcterms:alternative>free PGM</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
<variable name="E" public_interface="out" units="millimolar" />
<variable name="delta_E_rxn3" public_interface="in" units="flux" />
<variable name="delta_E_rxn3a" public_interface="in" units="flux" />
<variable name="delta_E_rxn4" public_interface="in" units="flux" />
<variable name="delta_E_rxn0" public_interface="in" units="flux" />
<variable name="time" public_interface="in" units="second" />
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq />
<apply>
<diff />
<bvar>
<ci>time</ci>
</bvar>
<ci>E</ci>
</apply>
<apply>
<plus />
<ci>delta_E_rxn3</ci>
<ci>delta_E_rxn3a</ci>
<ci>delta_E_rxn4</ci>
<ci>delta_E_rxn0</ci>
</apply>
</apply>
</math>
</component>
<component name="A" cmeta:id="A">
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/">
<rdf:Description rdf:about="A">
<dc:title>A</dc:title>
<dcterms:alternative>1,3-BPG</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
<variable name="A" public_interface="out" units="millimolar" />
<variable name="delta_A_rxn0" public_interface="in" units="flux" />
<variable name="time" public_interface="in" units="second" />
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq />
<apply>
<diff />
<bvar>
<ci>time</ci>
</bvar>
<ci>A</ci>
</apply>
<ci>delta_A_rxn0</ci>
</apply>
</math>
</component>
<component name="EA">
<variable name="EA" public_interface="out" units="millimolar" />
<variable name="delta_EA_rxn0" public_interface="in" units="flux" />
<variable name="delta_EA_rxn1" public_interface="in" units="flux" />
<variable name="time" public_interface="in" units="second" />
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq />
<apply>
<diff />
<bvar>
<ci>time</ci>
</bvar>
<ci>EA</ci>
</apply>
<apply>
<plus />
<ci>delta_EA_rxn0</ci>
<ci>delta_EA_rxn1</ci>
</apply>
</apply>
</math>
</component>
<component name="F" cmeta:id="F">
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/">
<rdf:Description rdf:about="F">
<dc:title>F</dc:title>
<dcterms:alternative>phosphorylated PGM</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
<variable name="F" public_interface="out" units="millimolar" />
<variable name="delta_F_rxn1" public_interface="in" units="flux" />
<variable name="delta_F_rxn2" public_interface="in" units="flux" />
<variable name="delta_F_rxn2a" public_interface="in" units="flux" />
<variable name="delta_F_rxn5" public_interface="in" units="flux" />
<variable name="delta_F_rxn6" public_interface="in" units="flux" />
<variable name="time" public_interface="in" units="second" />
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq />
<apply>
<diff />
<bvar>
<ci>time</ci>
</bvar>
<ci>F</ci>
</apply>
<apply>
<plus />
<ci>delta_F_rxn1</ci>
<ci>delta_F_rxn2</ci>
<ci>delta_F_rxn2a</ci>
<ci>delta_F_rxn5</ci>
<ci>delta_F_rxn6</ci>
</apply>
</apply>
</math>
</component>
<component name="Pi" cmeta:id="Pi">
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/">
<rdf:Description rdf:about="Pi">
<dc:title>Pi</dc:title>
<dcterms:alternative>inorganic phosphate</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
<variable name="Pi" public_interface="out" units="millimolar" />
<variable name="delta_Pi_rxn2" public_interface="in" units="flux" />
<variable name="time" public_interface="in" units="second" />
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq />
<apply>
<diff />
<bvar>
<ci>time</ci>
</bvar>
<ci>Pi</ci>
</apply>
<ci>delta_Pi_rxn2</ci>
</apply>
</math>
</component>
<component name="two_PGly">
<variable name="two_PGly" public_interface="out" units="millimolar" />
<variable name="delta_two_PGly_rxn2a" public_interface="in" units="flux" />
<variable name="time" public_interface="in" units="second" />
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq />
<apply>
<diff />
<bvar>
<ci>time</ci>
</bvar>
<ci>two_PGly</ci>
</apply>
<ci>delta_two_PGly_rxn2a</ci>
</apply>
</math>
</component>
<component name="FPi">
<variable name="FPi" public_interface="out" units="millimolar" />
<variable name="delta_FPi_rxn2" public_interface="in" units="flux" />
<variable name="delta_FPi_rxn3" public_interface="in" units="flux" />
<variable name="time" public_interface="in" units="second" />
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq />
<apply>
<diff />
<bvar>
<ci>time</ci>
</bvar>
<ci>FPi</ci>
</apply>
<apply>
<plus />
<ci>delta_FPi_rxn2</ci>
<ci>delta_FPi_rxn3</ci>
</apply>
</apply>
</math>
</component>
<component name="Ftwo_PGly">
<variable name="Ftwo_PGly" public_interface="out" units="millimolar" />
<variable name="delta_Ftwo_PGly_rxn2a" public_interface="in" units="flux" />
<variable name="delta_Ftwo_PGly_rxn3a" public_interface="in" units="flux" />
<variable name="time" public_interface="in" units="second" />
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq />
<apply>
<diff />
<bvar>
<ci>time</ci>
</bvar>
<ci>Ftwo_PGly</ci>
</apply>
<apply>
<plus />
<ci>delta_Ftwo_PGly_rxn2a</ci>
<ci>delta_Ftwo_PGly_rxn3a</ci>
</apply>
</apply>
</math>
</component>
<component name="D" cmeta:id="D">
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/">
<rdf:Description rdf:about="D">
<dc:title>D</dc:title>
<dcterms:alternative>2,3-BPG</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
<variable name="D" public_interface="out" units="millimolar" />
<variable name="delta_D_rxn4" public_interface="in" units="flux" />
<variable name="time" public_interface="in" units="second" />
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq />
<apply>
<diff />
<bvar>
<ci>time</ci>
</bvar>
<ci>D</ci>
</apply>
<ci>delta_D_rxn4</ci>
</apply>
</math>
</component>
<component name="ED">
<variable name="ED" public_interface="out" units="millimolar" />
<variable name="delta_ED_rxn7" public_interface="in" units="flux" />
<variable name="delta_ED_rxn8" public_interface="in" units="flux" />
<variable name="delta_ED_rxn4" public_interface="in" units="flux" />
<variable name="time" public_interface="in" units="second" />
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq />
<apply>
<diff />
<bvar>
<ci>time</ci>
</bvar>
<ci>ED</ci>
</apply>
<apply>
<plus />
<ci>delta_ED_rxn7</ci>
<ci>delta_ED_rxn8</ci>
<ci>delta_ED_rxn4</ci>
</apply>
</apply>
</math>
</component>
<component name="B" cmeta:id="B">
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/">
<rdf:Description rdf:about="B">
<dc:title>B</dc:title>
<dcterms:alternative>3-PGA</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
<variable name="B" public_interface="out" units="millimolar" />
<variable name="delta_B_rxn5" public_interface="in" units="flux" />
<variable name="time" public_interface="in" units="second" />
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq />
<apply>
<diff />
<bvar>
<ci>time</ci>
</bvar>
<ci>B</ci>
</apply>
<ci>delta_B_rxn5</ci>
</apply>
</math>
</component>
<component name="FB">
<variable name="FB" public_interface="out" units="millimolar" />
<variable name="delta_FB_rxn5" public_interface="in" units="flux" />
<variable name="delta_FB_rxn7" public_interface="in" units="flux" />
<variable name="time" public_interface="in" units="second" />
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq />
<apply>
<diff />
<bvar>
<ci>time</ci>
</bvar>
<ci>FB</ci>
</apply>
<apply>
<plus />
<ci>delta_FB_rxn5</ci>
<ci>delta_FB_rxn7</ci>
</apply>
</apply>
</math>
</component>
<component name="C" cmeta:id="C">
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/">
<rdf:Description rdf:about="C">
<dc:title>C</dc:title>
<dcterms:alternative>2-PGA</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
<variable name="C" public_interface="out" units="millimolar" />
<variable name="delta_C_rxn6" public_interface="in" units="flux" />
<variable name="time" public_interface="in" units="second" />
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq />
<apply>
<diff />
<bvar>
<ci>time</ci>
</bvar>
<ci>C</ci>
</apply>
<ci>delta_C_rxn6</ci>
</apply>
</math>
</component>
<component name="FC">
<variable name="FC" public_interface="out" units="millimolar" />
<variable name="delta_FC_rxn6" public_interface="in" units="flux" />
<variable name="delta_FC_rxn8" public_interface="in" units="flux" />
<variable name="time" public_interface="in" units="second" />
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq />
<apply>
<diff />
<bvar>
<ci>time</ci>
</bvar>
<ci>FC</ci>
</apply>
<apply>
<plus />
<ci>delta_FC_rxn6</ci>
<ci>delta_FC_rxn8</ci>
</apply>
</apply>
</math>
</component>
<!--
The following components represent the individual reaction steps of the
2,3-BPG shunt.
-->
<component name="reaction0">
<variable <