<?xml version="1.0"?>
<!-- FILE : transamination_model.xml
CREATED : 4th June 2002
LAST MODIFIED : 20nd April 2005
AUTHOR : Catherine Lloyd
The Bioengineering Institute
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 a generic model of
transamination.
CHANGES:
22/07/2002 - CML - Added more metadata.
20/04/2005 - PJV - Updated syntax to conform with cellml1.1 specs
-->
<model name="transamination_model" pathway_editor:rendering_config_file="transamination_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>2002-06-04</dcterms:W3CDTF>
</dcterms:created>
<!--
The Last Modified Date metadata. This is the date on which
the model was last changed.
-->
<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 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>2002-07-22</dcterms:W3CDTF>
</dcterms:modified>
</cmeta:modification>
<!-- The Publisher metadata. -->
<dc:publisher>
The University of Auckland, Bioengineering Institute
</dc:publisher>
</rdf:Description>
<!--
The following metadata refers to the model itself, as indicated by the
reference to the ID "transamination_model", which is declared on the
<model> element.
-->
<rdf:Description rdf:about="#transamination_model">
<!-- A human readable name for the model. -->
<dc:title>A Generic Model Of Transamination</dc:title>
<!-- A comment regarding the model. -->
<cmeta:comment rdf:parseType="Resource">
<rdf:value>
Below is a CellML description of a general model of transamination.
It is not based on a specific published mathematical model, but
instead it is based on a textbook defined pathway. The general
sequential structure and all the reactant, product and enzyme
components are included. Michaelis-Menten enzyme kinetics are
assumed.
The purpose of this description is to illustrate how CellML can be
used to model a general metabolic pathway.
</rdf:value>
<!-- The creator of the comment. -->
<dc:creator>
<vCard:FN>Catherine Lloyd</vCard:FN>
</dc:creator>
</cmeta:comment>
<cmeta:species>Homo sapiens</cmeta:species>
<!-- 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>
<bqs:Book rdf:parseType="Resource">
<dc:creator rdf:parseType="Resource">
<bqs:Person rdf:parseType="Resource">
<vCard:N rdf:parseType="Resource">
<vCard:Family>Bronk</vCard:Family>
<vCard:Given>J</vCard:Given>
<vCard:Other>Ramsey</vCard:Other>
</vCard:N>
</bqs:Person>
</dc:creator>
<dc:title>Human Metabolism</dc:title>
<dcterms:issued rdf:parseType="Resource">
<dcterms:W3CDTF>1999</dcterms:W3CDTF>
</dcterms:issued>
<dc:publisher rdf:parseType="Resource">
<bqs:Organisation>Addison Wesley Longman Limited</bqs:Organisation>
<bqs:Property rdf:parseType="Resource">
<bqs:property_type>location</bqs:property_type>
<rdf:value>England</rdf:value>
</bqs:Property>
</dc:publisher>
</bqs:Book>
</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="micromolar">
<unit prefix="micro" units="mole" />
<unit units="litre" exponent="-1" />
</units>
<units name="flux">
<unit units="micromolar" />
<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="micromolar" exponent="-1" />
<unit units="second" exponent="-1" />
</units>
<units name="third_order_rate_constant">
<unit units="micromolar" exponent="-2" />
<unit units="second" exponent="-1" />
</units>
<units name="fourth_order_rate_constant">
<unit units="micromolar" exponent="-3" />
<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 metabolites - both reactants and
products - involved in transamination.
-->
<component name="Oxaloacetate" cmeta:id="Oxaloacetate">
<variable name="Oxaloacetate" public_interface="out" initial_value="1.0" units="micromolar" />
<variable name="delta_Oxaloacetate_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>Oxaloacetate</ci>
</apply>
<ci>delta_Oxaloacetate_rxn0</ci>
</apply>
</math>
</component>
<component name="Aspartate" cmeta:id="Aspartate">
<variable name="Aspartate" public_interface="out" initial_value="1.0" units="micromolar" />
<variable name="delta_Aspartate_rxn0" public_interface="in" units="flux" />
<variable name="delta_Aspartate_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>Aspartate</ci>
</apply>
<apply>
<plus />
<ci>delta_Aspartate_rxn0</ci>
<ci>delta_Aspartate_rxn5</ci>
</apply>
</apply>
</math>
</component>
<component name="alpha_amino_acid" cmeta:id="alpha_amino_acid">
<variable name="alpha_amino_acid" public_interface="out" initial_value="1.0" units="micromolar" />
<variable name="delta_alpha_amino_acid_rxn0" public_interface="in" units="flux" />
<variable name="delta_alpha_amino_acid_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>alpha_amino_acid</ci>
</apply>
<apply>
<plus />
<ci>delta_alpha_amino_acid_rxn0</ci>
<ci>delta_alpha_amino_acid_rxn1</ci>
</apply>
</apply>
</math>
</component>
<component name="Oxo_2_acid" cmeta:id="Oxo_2_acid">
<variable name="Oxo_2_acid" public_interface="out" initial_value="1.0" units="micromolar" />
<variable name="delta_Oxo_2_acid_rxn0" public_interface="in" units="flux" />
<variable name="delta_Oxo_2_acid_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>Oxo_2_acid</ci>
</apply>
<apply>
<plus />
<ci>delta_Oxo_2_acid_rxn0</ci>
<ci>delta_Oxo_2_acid_rxn1</ci>
</apply>
</apply>
</math>
</component>
<component name="Oxoglutarate_2" cmeta:id="Oxoglutarate_2">
<variable name="Oxoglutarate_2" public_interface="out" initial_value="1.0" units="micromolar" />
<variable name="delta_Oxoglutarate_2_rxn2" public_interface="in" units="flux" />
<variable name="delta_Oxoglutarate_2_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>Oxoglutarate_2</ci>
</apply>
<apply>
<plus />
<ci>delta_Oxoglutarate_2_rxn2</ci>
<ci>delta_Oxoglutarate_2_rxn1</ci>
</apply>
</apply>
</math>
</component>
<component name="Glutamate" cmeta:id="Glutamate">
<variable name="Glutamate" public_interface="out" initial_value="1.0" units="micromolar" />
<variable name="delta_Glutamate_rxn1" public_interface="in" units="flux" />
<variable name="delta_Glutamate_rxn4" public_interface="in" units="flux" />
<variable name="delta_Glutamate_rxn2" public_interface="in" units="flux" />
<variable name="delta_Glutamate_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>Glutamate</ci>
</apply>
<apply>
<plus />
<ci>delta_Glutamate_rxn1</ci>
<ci>delta_Glutamate_rxn4</ci>
<ci>delta_Glutamate_rxn2</ci>
<ci>delta_Glutamate_rxn3</ci>
</apply>
</apply>
</math>
</component>
<component name="NADH" cmeta:id="NADH">
<variable name="NADH" public_interface="out" initial_value="1.0" units="micromolar" />
<variable name="delta_NADH_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>NADH</ci>
</apply>
<ci>delta_NADH_rxn2</ci>
</apply>
</math>
</component>
<component name="NH4" cmeta:id="NH4">
<variable name="NH4" public_interface="out" initial_value="1.0" units="micromolar" />
<variable name="delta_NH4_rxn2" public_interface="in" units="flux" />
<variable name="delta_NH4_rxn4" public_interface="in" units="flux" />
<variable name="delta_NH4_rxn3" public_interface="in" units="flux" />
<variable name="delta_NH4_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>NH4</ci>
</apply>
<apply>
<plus />
<ci>delta_NH4_rxn2</ci>
<ci>delta_NH4_rxn4</ci>
<ci>delta_NH4_rxn3</ci>
<ci>delta_NH4_rxn8</ci>
</apply>
</apply>
</math>
</component>
<component name="H" cmeta:id="H">
<variable name="H" public_interface="out" initial_value="1.0" units="micromolar" />
<variable name="delta_H_rxn2" public_interface="in" units="flux" />
<variable name="delta_H_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>H</ci>
</apply>
<apply>
<plus />
<ci>delta_H_rxn2</ci>
<ci>delta_H_rxn3</ci>
</apply>
</apply>
</math>
</component>
<component name="NAD" cmeta:id="NAD">
<variable name="NAD" public_interface="out" initial_value="1.0" units="micromolar" />
<variable name="delta_NAD_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>NAD</ci>
</apply>
<ci>delta_NAD_rxn2</ci>
</apply>
</math>
</component>
<component name="H2O" cmeta:id="H2O">
<variable name="H2O" public_interface="out" initial_value="1.0" units="micromolar" />
<variable name="delta_H2O_rxn2" public_interface="in" units="flux" />
<variable name="delta_H2O_rxn4" public_interface="in" units="flux" />
<variable name="delta_H2O_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>H2O</ci>
</apply>
<apply>
<plus />
<ci>delta_H2O_rxn2</ci>
<ci>delta_H2O_rxn4</ci>
<ci>delta_H2O_rxn6</ci>
</apply>
</apply>
</math>
</component>
<component name="Glutamine" cmeta:id="Glutamine">
<variable name="Glutamine" public_interface="out" initial_value="1.0" units="micromolar" />
<variable name="delta_Glutamine_rxn3" public_interface="in" units="flux" />
<variable name="delta_Glutamine_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>Glutamine</ci>
</apply>
<apply>
<plus />
<ci>delta_Glutamine_rxn3</ci>
<ci>delta_Glutamine_rxn4</ci>
</apply>
</apply>
</math>
</component>
<component name="ATP" cmeta:id="ATP">
<variable name="ATP" public_interface="out" initial_value="1.0" units="micromolar" />
<variable name="delta_ATP_rxn3" public_interface="in" units="flux" />
<variable name="delta_ATP_rxn5" public_interface="in" units="flux" />
<variable name="delta_ATP_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>ATP</ci>
</apply>
<apply>
<plus />
<ci>delta_ATP_rxn3</ci>
<ci>delta_ATP_rxn5</ci>
<ci>delta_ATP_rxn8</ci>
</apply>
</apply>
</math>
</component>
<component name="ADP" cmeta:id="ADP">
<variable name="ADP" public_interface="out" initial_value="1.0" units="micromolar" />
<variable name="delta_ADP_rxn3" public_interface="in" units="flux" />
<variable name="delta_ADP_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>ADP</ci>
</apply>
<apply>
<plus />
<ci>delta_ADP_rxn3</ci>
<ci>delta_ADP_rxn8</ci>
</apply>
</apply>
</math>
</component>
<component name="Pi" cmeta:id="Pi">
<variable name="Pi" public_interface="out" initial_value="1.0" units="micromolar" />
<variable name="delta_Pi_rxn3" public_interface="in" units="flux" />
<variable name="delta_Pi_rxn5" public_interface="in" units="flux" />
<variable name="delta_Pi_rxn7" public_interface="in" units="flux" />
<variable name="delta_Pi_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>Pi</ci>
</apply>
<apply>
<plus />
<ci>delta_Pi_rxn3</ci>
<ci>delta_Pi_rxn5</ci>
<ci>delta_Pi_rxn7</ci>
<ci>delta_Pi_rxn8</ci>
</apply>
</apply>
</math>
</component>
<component name="Fumarate" cmeta:id="Fumarate">
<variable name="Fumarate" public_interface="out" initial_value="1.0" units="micromolar" />
<variable name="delta_Fumarate_rxn5b" 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>Fumarate</ci>
</apply>
<ci>delta_Fumarate_rxn5b</ci>
</apply>
</math>
</component>
<component name="AMP" cmeta:id="AMP">
<variable name="AMP" public_interface="out" initial_value="1.0" units="micromolar" />
<variable name="delta_AMP_rxn5" public_interface="in" units="flux" />
<variable name="time" public_interface="in" units="second" />
<math