- Author:
- Hanne <Hanne@hanne-nielsens-macbook.local>
- Date:
- 2009-12-14 17:10:52+13:00
- Desc:
- Added images in ai and svg format
- Permanent Source URI:
- https://models.physiomeproject.org/workspace/teusink_passarge_reijenga_esgalhado_vanderweijden_schepper_walsh_bakker_vandam_westerhoff_snoep_2000/rawfile/be6f425765c2cb1bbd00ea6a811374211db9bbb8/teusink_passarge_reijenga_esgalhado_vanderweijden_schepper_walsh_bakker_vandam_westerhoff_snoep_2000.cellml
<?xml version='1.0' encoding='utf-8'?>
<!-- FILE : teusink_model_2000.xml
CREATED : 12th May 2003
LAST MODIFIED : 20th April 2005
AUTHOR : Catherine Lloyd
Bioengineering Institute
The University of Auckland
MODEL STATUS : This model conforms to the CellML 1.0 Specification released on
10th August 2001, and the 16/1/02 CellML Metadata 1.0 Specification.
DESCRIPTION : This file contains a CellML description of Teusink et al.'s 2000 model for glycolysis in yeast.
CHANGES:
20/04/2005 - PJV - Updated syntax to conform with cellml1.1 specs
--><model xmlns="http://www.cellml.org/cellml/1.0#" xmlns:cmeta="http://www.cellml.org/metadata/1.0#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqs="http://www.cellml.org/bqs/1.0#" xmlns:cellml="http://www.cellml.org/cellml/1.0#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" cmeta:id="teusink_model_2000" name="teusink_model_2000">
<documentation xmlns="http://cellml.org/tmp-documentation">
<article>
<articleinfo>
<title>Understanding Yeast Glycolysis in Terms of the in vitro Kinetics of the Constituent Enzymes</title>
<author>
<firstname>Catherine</firstname>
<surname>Lloyd</surname>
<affiliation>
<shortaffil>Bioengineering Institute, University of Auckland</shortaffil>
</affiliation>
</author>
</articleinfo>
<section id="sec_status">
<title>Model Status</title>
<para>
This CellML runs in both PCEnv and COR to recreate the published results. The units have been checked and they are consistent. This particular CellML model is based on a Matlab file which, in turn, was exported from the working SBML file in the BioModels database. There are several subtle differences between the published paper and the working Matlab code which have been previously documented by the BioModels curators. In brief these are:
in the kinetic law for ADH the species a should denote NAD and b Ethanol the last term in the equation should read bpq/(Kib Kiq Kp) and the rate equation for the PFK contains two errors: the R term should read: R = 1 + lambda1 + lambda2 + gR lambda1 lambda2 and the last term in the L equation should be squared.
Also there are slight differences in the parameterisation of the model depending on whether it comes from the JWS or the BioModels database and, for Vmax values, please note that there is a conversion factor of approxinately 270 to convert from U/mg-protein as shown in Table 1 of the paper to mmol/(min*L_cytosol).
</para>
</section>
<sect1 id="sec_structure">
<title>Model Structure</title>
<para>
In April 2003 the human genome sequence was completed. One of the greatest challenges currently facing biologists is the elucidation of the molecular function of the proteins encoded by the genes. Traditionally, the approach has been to isolate these proteins and then characterise them <emphasis>in vitro</emphasis>. More recently, scientists have begun to question whether this will generate an accurate picture of how these proteins behave within a functional cell (<emphasis>in vivo</emphasis>). It is highly likely that the environment within a living cell is very different from the conditions within a test tube. Interacting metabolites, intracellular compartmentation, and enzyme concentrations are all likely to differ. The question to be asked is whether these differences between <emphasis>in vitro</emphasis> and <emphasis>in vivo</emphasis> conditions seriously affect scientists' understanding of the functional behaviour of the living cell.
</para>
<para>
The paper described here by Teusink <emphasis>et al.</emphasis> (2000) asks the question: can the behaviour of biochemical pathways be described by simply combining the properties of the components in isolation? In other words, can the <emphasis>in vivo</emphasis> behaviour of yeast glycolysis be understood in terms of the <emphasis>in vitro</emphasis> kinetic properties of the constituent enzymes? Based on <emphasis>in vitro</emphasis>, experimentally determined enzyme kinetics data, they developed a mathematical model of the glycolysis pathway in the yeast <emphasis>Saccharomyces cerevisiae</emphasis>. The simulation results from this model were then compared with recorded fluxes and metabolite levels in living cells under similar conditions. They employed mathematical modelling to test whether knowledge of the <emphasis>in vitro</emphasis> kinetic properties of the glycolytic enzymes allows a good understanding of the overall pathway behaviour <emphasis>in vivo</emphasis>.
</para>
<para>
The model includes most enzymes in the glycolysis pathway (see the figure below). A set of ordinary differential equations was used to represent the time-dependence of the metabolite concentrations. Reversible Michaelis-Menten and irreversible Hill kinetics were amongst the types of enzymes kinetics included in the model equations.
</para>
<para>
The complete original paper reference is cited below:
</para>
<para>
Can yeast glycolysis be understood in terms of <emphasis>in vitro</emphasis> kinetics of the constituent enzymes? Testing biochemistry, Bas Teusink, Jutta Passarge, Corinne A. Reijenga, Eugenia Esgalhado, Coen C. van der Weijden, Mike Schepper, Michael C. Walsh, Barbara M. Bakker, Karel van Dam, Hans V. Westerhoff, and Jacky L. Snoep, 2000, <emphasis>European Journal of Biochemistry</emphasis>, 267, 5313-5329. <ulink url="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10951190&dopt=Abstract">PubMed ID: 10951190</ulink>
</para>
<informalfigure float="0" id="fig_reaction_diagram">
<mediaobject>
<imageobject>
<objectinfo>
<title>reaction diagram</title>
</objectinfo>
<imagedata fileref="teusink_2000.png"/>
</imageobject>
</mediaobject>
<caption>A schematic diagram of the reactions included in the Teusink <emphasis>et al.</emphasis> 2000 model of the glycolysis pathway in the yeast <emphasis>Saccharomyces cerevisiae</emphasis>.</caption>
</informalfigure>
<para>
Model simulations revealed that the orginal question posed does not have a simple answer. For half of the enzymes studied, the <emphasis>in vitro</emphasis> kinetics did describe the <emphasis>in vivo</emphasis> activity. However, the other half of the enzymes analysed, they were larger deviations between their <emphasis>in vitro</emphasis> and <emphasis>in vivo</emphasis> characteristics.
</para>
</sect1>
</article>
</documentation>
<units name="millimolar">
<unit units="mole" prefix="milli"/>
<unit units="litre" exponent="-1"/>
</units>
<units name="millimolar2">
<unit units="millimolar" exponent="2"/>
</units>
<units name="per_millimolar2">
<unit units="millimolar" exponent="-2"/>
</units>
<units name="minute">
<unit units="second" multiplier="60.0"/>
</units>
<units name="flux">
<unit units="millimolar"/>
<unit units="minute" exponent="-1"/>
</units>
<units name="first_order_rate_constant">
<unit units="minute" exponent="-1"/>
</units>
<component name="environment">
<variable units="minute" public_interface="out" name="time"/>
</component>
<!--
The following components describe all the reactants and products involved in
reactions.
-->
<component cmeta:id="GLCo" name="GLCo">
<rdf:RDF>
<rdf:Description rdf:about="GLCo">
<dc:title>GLCo</dc:title>
<dcterms:alternative>extracellular glucose</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
<variable units="millimolar" public_interface="out" name="GLCo" initial_value="50.0"/>
</component>
<component cmeta:id="GLCi" name="GLCi">
<rdf:RDF>
<rdf:Description rdf:about="GLCi">
<dc:title>GLCi</dc:title>
<dcterms:alternative>intracellular glucose</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
<variable units="millimolar" public_interface="out" name="GLCi" initial_value="0.087"/>
<variable units="flux" public_interface="in" name="v_GLT"/>
<variable units="flux" public_interface="in" name="v_GLK"/>
<variable units="minute" public_interface="in" name="time"/>
<math xmlns="http://www.w3.org/1998/Math/MathML" id="2">
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci> time </ci>
</bvar>
<ci> GLCi </ci>
</apply>
<apply>
<minus/>
<ci> v_GLT </ci>
<ci> v_GLK </ci>
</apply>
</apply>
</math>
</component>
<component cmeta:id="G6P" name="G6P">
<rdf:RDF>
<rdf:Description rdf:about="G6P">
<dc:title>G6P</dc:title>
<dcterms:alternative>glucose 6-phosphate</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
<variable units="millimolar" public_interface="out" name="G6P" initial_value="2.45"/>
<variable units="flux" public_interface="in" name="v_GLK"/>
<variable units="flux" public_interface="in" name="v_PGI"/>
<variable units="flux" public_interface="in" name="v_trehalose"/>
<variable units="flux" public_interface="in" name="v_glycogen"/>
<variable units="minute" public_interface="in" name="time"/>
<math xmlns="http://www.w3.org/1998/Math/MathML" id="3">
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>G6P</ci>
</apply>
<apply>
<minus/>
<ci> v_GLK </ci>
<apply>
<plus/>
<ci> v_PGI </ci>
<apply>
<times/>
<cn cellml:units="dimensionless"> 2.0 </cn>
<ci> v_trehalose </ci>
</apply>
<ci> v_glycogen </ci>
</apply>
</apply>
</apply>
</math>
</component>
<component cmeta:id="F6P" name="F6P">
<rdf:RDF>
<rdf:Description rdf:about="F6P">
<dc:title>F6P</dc:title>
<dcterms:alternative>fructose 6-phosphate</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
<variable units="millimolar" public_interface="out" name="F6P" initial_value="0.62"/>
<variable units="flux" public_interface="in" name="v_PGI"/>
<variable units="flux" public_interface="in" name="v_PFK"/>
<variable units="minute" public_interface="in" name="time"/>
<math xmlns="http://www.w3.org/1998/Math/MathML" id="4">
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>F6P</ci>
</apply>
<apply>
<minus/>
<ci>v_PGI</ci>
<ci>v_PFK</ci>
</apply>
</apply>
</math>
</component>
<component cmeta:id="F16P" name="F16P">
<rdf:RDF>
<rdf:Description rdf:about="F16P">
<dc:title>F16P</dc:title>
<dcterms:alternative>fructose 1,6-bisphosphate</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
<variable units="millimolar" public_interface="out" name="F16P" initial_value="5.51"/>
<variable units="flux" public_interface="in" name="v_PFK"/>
<variable units="flux" public_interface="in" name="v_ALD"/>
<variable units="minute" public_interface="in" name="time"/>
<math xmlns="http://www.w3.org/1998/Math/MathML" id="5">
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>F16P</ci>
</apply>
<apply>
<minus/>
<ci>v_PFK</ci>
<ci>v_ALD</ci>
</apply>
</apply>
</math>
</component>
<component cmeta:id="F26P" name="F26P">
<rdf:RDF>
<rdf:Description rdf:about="F26P">
<dc:title>F26P</dc:title>
<dcterms:alternative>fructose 2,6-bisphosphate</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
<variable units="millimolar" public_interface="out" name="F26P" initial_value="0.02"/>
</component>
<component cmeta:id="TRIO" name="TRIO">
<rdf:RDF>
<rdf:Description rdf:about="TRIO">
<dc:title>TRIO</dc:title>
<dcterms:alternative>triosphosphate</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
<variable units="millimolar" public_interface="out" name="TRIO" initial_value="0.96"/>
<variable units="flux" public_interface="in" name="v_ALD"/>
<variable units="flux" public_interface="in" name="v_GAPDH"/>
<variable units="flux" public_interface="in" name="v_G3PDH"/>
<variable units="minute" public_interface="in" name="time"/>
<math xmlns="http://www.w3.org/1998/Math/MathML" id="6">
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>TRIO</ci>
</apply>
<apply>
<minus/>
<apply>
<times/>
<cn cellml:units="dimensionless"> 2.0 </cn>
<ci> v_ALD </ci>
</apply>
<apply>
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<ci> v_GAPDH </ci>
<ci> v_G3PDH </ci>
</apply>
</apply>
</apply>
</math>
</component>
<component cmeta:id="BPG" name="BPG">
<rdf:RDF>
<rdf:Description rdf:about="BPG">
<dc:title>BPG</dc:title>
<dcterms:alternative>1,3-bisphosphoglycerate</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
<variable units="millimolar" public_interface="out" name="BPG" initial_value="0.0"/>
<variable units="flux" public_interface="in" name="v_GAPDH"/>
<variable units="flux" public_interface="in" name="v_PGK"/>
<variable units="minute" public_interface="in" name="time"/>
<math xmlns="http://www.w3.org/1998/Math/MathML" id="7">
<apply>
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<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>BPG</ci>
</apply>
<apply>
<minus/>
<ci>v_GAPDH</ci>
<ci>v_PGK</ci>
</apply>
</apply>
</math>
</component>
<component cmeta:id="P3G" name="P3G">
<rdf:RDF>
<rdf:Description rdf:about="P3G">
<dc:title>P3G</dc:title>
<dcterms:alternative>3-phosphoglycerate</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
<variable units="millimolar" public_interface="out" name="P3G" initial_value="0.9"/>
<variable units="flux" public_interface="in" name="v_PGK"/>
<variable units="flux" public_interface="in" name="v_PGM"/>
<variable units="minute" public_interface="in" name="time"/>
<math xmlns="http://www.w3.org/1998/Math/MathML" id="8">
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>P3G</ci>
</apply>
<apply>
<minus/>
<ci>v_PGK</ci>
<ci>v_PGM</ci>
</apply>
</apply>
</math>
</component>
<component cmeta:id="P2G" name="P2G">
<rdf:RDF>
<rdf:Description rdf:about="P2G">
<dc:title>P2G</dc:title>
<dcterms:alternative>2-phosphoglycerate</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
<variable units="millimolar" public_interface="out" name="P2G" initial_value="0.12"/>
<variable units="flux" public_interface="in" name="v_PGM"/>
<variable units="flux" public_interface="in" name="v_ENO"/>
<variable units="minute" public_interface="in" name="time"/>
<math xmlns="http://www.w3.org/1998/Math/MathML" id="9">
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>P2G</ci>
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<apply>
<minus/>
<ci>v_PGM</ci>
<ci>v_ENO</ci>
</apply>
</apply>
</math>
</component>
<component cmeta:id="PEP" name="PEP">
<rdf:RDF>
<rdf:Description rdf:about="PEP">
<dc:title>PEP</dc:title>
<dcterms:alternative>phosphoenolpyruvate</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
<variable units="millimolar" public_interface="out" name="PEP" initial_value="0.07"/>
<variable units="flux" public_interface="in" name="v_ENO"/>
<variable units="flux" public_interface="in" name="v_PYK"/>
<variable units="minute" public_interface="in" name="time"/>
<math xmlns="http://www.w3.org/1998/Math/MathML" id="10">
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<ci>PEP</ci>
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<apply>
<minus/>
<ci>v_ENO</ci>
<ci>v_PYK</ci>
</apply>
</apply>
</math>
</component>
<component cmeta:id="PYR" name="PYR">
<rdf:RDF>
<rdf:Description rdf:about="PYR">
<dc:title>PYR</dc:title>
<dcterms:alternative>pyruvate</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
<variable units="millimolar" public_interface="out" name="PYR" initial_value="1.85"/>
<variable units="flux" public_interface="in" name="v_PYK"/>
<variable units="flux" public_interface="in" name="v_PDC"/>
<variable units="minute" public_interface="in" name="time"/>
<math xmlns="http://www.w3.org/1998/Math/MathML" id="11">
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<apply>
<diff/>
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</bvar>
<ci>PYR</ci>
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<apply>
<minus/>
<ci>v_PYK</ci>
<ci>v_PDC</ci>
</apply>
</apply>
</math>
</component>
<component cmeta:id="ACE" name="ACE">
<rdf:RDF>
<rdf:Description rdf:about="ACE">
<dc:title>ACE</dc:title>
<dcterms:alternative>acetaldehyde</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
<variable units="millimolar" public_interface="out" name="ACE" initial_value="0.17"/>
<variable units="flux" public_interface="in" name="v_PDC"/>
<variable units="flux" public_interface="in" name="v_ADH"/>
<variable units="flux" public_interface="in" name="v_succinate"/>
<variable units="minute" public_interface="in" name="time"/>
<math xmlns="http://www.w3.org/1998/Math/MathML" id="12">
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<eq/>
<apply>
<diff/>
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<ci>time</ci>
</bvar>
<ci>ACE</ci>
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<apply>
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<ci>v_PDC</ci>
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<ci>v_ADH</ci>
<apply>
<times/>
<cn cellml:units="dimensionless"> 2.0 </cn>
<ci>v_succinate</ci>
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</apply>
</apply>
</apply>
</math>
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<rdf:RDF>
<rdf:Description rdf:about="P">
<dc:title>P</dc:title>
<dcterms:alternative>high energy phosphates</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
<variable units="millimolar" public_interface="out" name="P" initial_value="6.31"/>
<variable units="flux" public_interface="in" name="v_GLK"/>
<variable units="flux" public_interface="in" name="v_PFK"/>
<variable units="flux" public_interface="in" name="v_PGK"/>
<variable units="flux" public_interface="in" name="v_PYK"/>
<variable units="flux" public_interface="in" name="v_ATP"/>
<variable units="flux" public_interface="in" name="v_trehalose"/>
<variable units="flux" public_interface="in" name="v_glycogen"/>
<variable units="flux" public_interface="in" name="v_succinate"/>
<variable units="minute" public_interface="in" name="time"/>
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<apply>
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</bvar>
<ci>P</ci>
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<apply>
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<ci> v_PGK </ci>
<ci> v_PYK </ci>
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<apply>
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<ci> v_GLK </ci>
<ci> v_PFK </ci>
<ci> v_ATP </ci>
<ci> v_trehalose </ci>
<ci> v_glycogen </ci>
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<times/>
<cn cellml:units="dimensionless"> 4.0 </cn>
<ci>v_succinate</ci>
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</component>
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<rdf:RDF>
<rdf:Description rdf:about="NADH">
<dc:title>NADH</dc:title>
<dcterms:alternative>
nicotinamide adenine dinucleotide
</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
<variable units="millimolar" public_interface="out" name="NADH" initial_value="0.39"/>
<variable units="flux" public_interface="in" name="v_GAPDH"/>
<variable units="flux" public_interface="in" name="v_ADH"/>
<variable units="flux" public_interface="in" name="v_G3PDH"/>
<variable units="flux" public_interface="in" name="v_succinate"/>
<variable units="minute" public_interface="in" name="time"/>
<math xmlns="http://www.w3.org/1998/Math/MathML" id="14">
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<ci>time</ci>
</bvar>
<ci>NADH</ci>
</apply>
<apply>
<minus/>
<apply>
<plus/>
<ci>v_GAPDH</ci>
<apply>
<times/>
<cn cellml:units="dimensionless"> 3.0 </cn>
<ci>v_succinate</ci>
</apply>
</apply>
<apply>
<plus/>
<ci>v_ADH</ci>
<ci>v_G3PDH</ci>
</apply>
</apply>
</apply>
</math>
</component>
<component cmeta:id="NAD" name="NAD">
<rdf:RDF>
<rdf:Description rdf:about="NAD">
<dc:title>NAD</dc:title>
<dcterms:alternative>
charged nicotinamide adenine dinucleotide
</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
<variable units="millimolar" public_interface="out" name="NAD" initial_value="1.20"/>
<variable units="flux" public_interface="in" name="v_GAPDH"/>
<variable units="flux" public_interface="in" name="v_ADH"/>
<variable units="flux" public_interface="in" name="v_G3PDH"/>
<variable units="flux" public_interface="in" name="v_succinate"/>
<variable units="minute" public_interface="in" name="time"/>
<math xmlns="http://www.w3.org/1998/Math/MathML" id="15">
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<ci>NAD</ci>
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<apply>
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<ci>v_ADH</ci>
<ci>v_G3PDH</ci>
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<apply>
<plus/>
<ci>v_GAPDH</ci>
<apply>
<times/>
<cn cellml:units="dimensionless"> 3.0 </cn>
<ci>v_succinate</ci>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
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<variable units="millimolar" public_interface="out" name="DHAP"/>
<variable units="dimensionless" public_interface="out" name="Keq_TPI" initial_value="0.045"/>
<variable units="millimolar" public_interface="in" name="TRIO"/>
<math xmlns="http://www.w3.org/1998/Math/MathML" id="16">
<apply>
<eq/>
<ci>DHAP</ci>
<apply>
<divide/>
<ci>TRIO</ci>
<apply>
<plus/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<ci>Keq_TPI</ci>
</apply>
</apply>
</apply>
</math>
</component>
<component cmeta:id="GAP" name="GAP">
<rdf:RDF>
<rdf:Description rdf:about="GAP">
<dc:title>GAP</dc:title>
<dcterms:alternative>D-glyceraldehyde-3-phosphate</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
<variable units="millimolar" public_interface="out" name="GAP"/>
<variable units="dimensionless" public_interface="in" name="Keq_TPI"/>
<variable units="millimolar" public_interface="in" name="TRIO"/>
<math xmlns="http://www.w3.org/1998/Math/MathML" id="17">
<apply>
<eq/>
<ci>GAP</ci>
<apply>
<divide/>
<apply>
<times/>
<ci>TRIO</ci>
<ci>Keq_TPI</ci>
</apply>
<apply>
<plus/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<ci>Keq_TPI</ci>
</apply>
</apply>
</apply>
</math>
</component>
<component cmeta:id="ADP" name="ADP">
<rdf:RDF>
<rdf:Description rdf:about="ADP">
<dc:title>ADP</dc:title>
<dcterms:alternative>adenosine diphoshate</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
<variable units="millimolar" public_interface="out" name="ADP"/>
<variable units="millimolar" public_interface="out" initial_value="4.1" name="SUM_P"/>
<variable units="dimensionless" initial_value="0.450" name="Keq_AK"/>
<variable units="millimolar" public_interface="in" name="P"/>
<math xmlns="http://www.w3.org/1998/Math/MathML" id="18">
<apply><eq/>
<ci>ADP</ci>
<apply><divide/>
<apply><minus/>
<ci>SUM_P</ci>
<apply><root/>
<apply><plus/>
<apply><times/>
<apply><power/>
<ci>P</ci>
<cn cellml:units="dimensionless"> 2 </cn>
</apply>
<apply><minus/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<apply><times/>
<cn cellml:units="dimensionless"> 4.0 </cn>
<ci>Keq_AK</ci>
</apply>
</apply>
</apply>
<apply><times/>
<cn cellml:units="dimensionless"> 2 </cn>
<ci>SUM_P</ci>
<ci>P</ci>
<apply><minus/>
<apply><times/>
<cn cellml:units="dimensionless"> 4.0 </cn>
<ci>Keq_AK</ci>
</apply>
<cn cellml:units="dimensionless"> 1.0 </cn>
</apply>
</apply>
<apply><power/>
<ci>SUM_P</ci>
<cn cellml:units="dimensionless"> 2 </cn>
</apply>
</apply>
</apply>
</apply>
<apply><minus/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<apply><times/>
<cn cellml:units="dimensionless"> 4.0 </cn>
<ci>Keq_AK</ci>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<component cmeta:id="ATP" name="ATP">
<rdf:RDF>
<rdf:Description rdf:about="ATP">
<dc:title>ATP</dc:title>
<dcterms:alternative>adenosine triphosphate</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
<variable units="millimolar" public_interface="out" name="ATP"/>
<variable units="millimolar" public_interface="in" name="P"/>
<variable units="millimolar" public_interface="in" name="ADP"/>
<math xmlns="http://www.w3.org/1998/Math/MathML" id="19">
<apply><eq/>
<ci>ATP</ci>
<apply><divide/>
<apply><minus/>
<ci>P</ci>
<ci>ADP</ci>
</apply>
<cn cellml:units="dimensionless"> 2 </cn>
</apply>
</apply>
</math>
</component>
<component cmeta:id="AMP" name="AMP">
<rdf:RDF>
<rdf:Description rdf:about="AMP">
<dc:title>AMP</dc:title>
<dcterms:alternative>adenosine monophoshate</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
<variable units="millimolar" public_interface="out" name="AMP"/>
<variable units="millimolar" public_interface="in" name="SUM_P"/>
<variable units="millimolar" public_interface="in" name="ADP"/>
<variable units="millimolar" public_interface="in" name="ATP"/>
<math xmlns="http://www.w3.org/1998/Math/MathML" id="20">
<apply><eq/>
<ci>AMP</ci>
<apply><minus/>
<ci>SUM_P</ci>
<apply><plus/>
<ci>ATP</ci>
<ci>ADP</ci>
</apply>
</apply>
</apply>
</math>
</component>
<component cmeta:id="ETOH" name="ETOH">
<rdf:RDF>
<rdf:Description rdf:about="ETOH">
<dc:title>ETOH</dc:title>
<dcterms:alternative>ethanol</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
<variable units="millimolar" public_interface="out" name="ETOH" initial_value="50.0"/>
</component>
<component cmeta:id="GLY" name="GLY">
<rdf:RDF>
<rdf:Description rdf:about="GLY">
<dc:title>GLY</dc:title>
<dcterms:alternative>glycerol</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
<variable units="millimolar" public_interface="out" name="GLY" initial_value="0.15"/>
</component>
<!--
The following components describe the reactions of the core, unbranched model.
-->
<component name="v_PGI">
<variable units="flux" public_interface="out" name="v_PGI"/>
<variable units="millimolar" name="Km_G6P" initial_value="1.4"/>
<variable units="millimolar" name="Km_F6P" initial_value="0.3"/>
<variable units="dimensionless" name="Keq_PGI" initial_value="0.314"/>
<variable units="flux" name="v_max" initial_value="339.677"/>
<variable units="millimolar" public_interface="in" name="G6P"/>
<variable units="millimolar" public_interface="in" name="F6P"/>
<math xmlns="http://www.w3.org/1998/Math/MathML" id="25">
<apply id="v_PGI_calculation"><eq/>
<ci> v_PGI </ci>
<apply><divide/>
<apply><times/>
<apply><divide/>
<ci> v_max </ci>
<ci> Km_G6P </ci>
</apply>
<apply><minus/>
<ci> G6P </ci>
<apply><divide/>
<ci> F6P </ci>
<ci> Keq_PGI </ci>
</apply>
</apply>
</apply>
<apply><plus/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<apply><divide/>
<ci> G6P </ci>
<ci> Km_G6P </ci>
</apply>
<apply><divide/>
<ci> F6P </ci>
<ci> Km_F6P </ci>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<component name="v_PGM">
<variable units="flux" public_interface="out" name="v_PGM"/>
<variable units="millimolar" name="Km_P3G" initial_value="1.2"/>
<variable units="millimolar" name="Km_P2G" initial_value="0.08"/>
<variable units="dimensionless" name="Keq_PGM" initial_value="0.19"/>
<variable units="flux" name="v_max" initial_value="2525.81"/>
<variable units="millimolar" public_interface="in" name="P2G"/>
<variable units="millimolar" public_interface="in" name="P3G"/>
<math xmlns="http://www.w3.org/1998/Math/MathML" id="26">
<apply id="v_PGM_calculation"><eq/>
<ci> v_PGM </ci>
<apply><divide/>
<apply><times/>
<apply><divide/>
<ci> v_max </ci>
<ci> Km_P3G </ci>
</apply>
<apply><minus/>
<ci> P3G </ci>
<apply><divide/>
<ci> P2G </ci>
<ci> Keq_PGM </ci>
</apply>
</apply>
</apply>
<apply><plus/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<apply><divide/>
<ci> P3G </ci>
<ci> Km_P3G </ci>
</apply>
<apply><divide/>
<ci> P2G </ci>
<ci> Km_P2G </ci>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<component name="v_ENO">
<variable units="flux" public_interface="out" name="v_ENO"/>
<variable units="millimolar" name="Km_P2G" initial_value="0.04"/>
<variable units="millimolar" name="Km_PEP" initial_value="0.5"/>
<variable units="dimensionless" name="Keq_ENO" initial_value="6.7"/>
<variable units="flux" name="v_max" initial_value="365.806"/>
<variable units="millimolar" public_interface="in" name="PEP"/>
<variable units="millimolar" public_interface="in" name="P2G"/>
<math xmlns="http://www.w3.org/1998/Math/MathML" id="27">
<apply id="v_ENO_calculation"><eq/>
<ci> v_ENO </ci>
<apply><divide/>
<apply><times/>
<apply><divide/>
<ci> v_max </ci>
<ci> Km_P2G </ci>
</apply>
<apply><minus/>
<ci> P2G </ci>
<apply><divide/>
<ci> PEP </ci>
<ci> Keq_ENO </ci>
</apply>
</apply>
</apply>
<apply><plus/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<apply><divide/>
<ci> P2G </ci>
<ci> Km_P2G </ci>
</apply>
<apply><divide/>
<ci> PEP </ci>
<ci> Km_PEP </ci>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<component name="v_GLK">
<variable units="flux" public_interface="out" name="v_GLK"/>
<variable units="millimolar" name="Km_GLCi" initial_value="0.08"/>
<variable units="millimolar" name="Km_G6P" initial_value="30.0"/>
<variable units="millimolar" name="Km_ATP" initial_value="0.15"/>
<variable units="millimolar" name="Km_ADP" initial_value="0.23"/>
<variable units="dimensionless" name="Keq_GLK" initial_value="3800"/>
<variable units="flux" name="v_max" initial_value="226.452"/>
<variable units="millimolar" public_interface="in" name="G6P"/>
<variable units="millimolar" public_interface="in" name="GLCi"/>
<variable units="millimolar" public_interface="in" name="ATP"/>
<variable units="millimolar" public_interface="in" name="ADP"/>
<math xmlns="http://www.w3.org/1998/Math/MathML" id="28">
<apply id="v_GLK_calculation"><eq/>
<ci> v_GLK </ci>
<apply><divide/>
<apply><times/>
<apply><divide/>
<ci> v_max </ci>
<apply><times/>
<ci> Km_GLCi </ci>
<ci> Km_ATP </ci>
</apply>
</apply>
<apply><minus/>
<apply><times/>
<ci> GLCi </ci>
<ci> ATP </ci>
</apply>
<apply><divide/>
<apply><times/>
<ci> G6P </ci>
<ci> ADP </ci>
</apply>
<ci> Keq_GLK </ci>
</apply>
</apply>
</apply>
<apply><times/>
<apply><plus/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<apply><divide/>
<ci> GLCi </ci>
<ci> Km_GLCi </ci>
</apply>
<apply><divide/>
<ci> G6P </ci>
<ci> Km_G6P </ci>
</apply>
</apply>
<apply><plus/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<apply><divide/>
<ci> ATP </ci>
<ci> Km_ATP </ci>
</apply>
<apply><divide/>
<ci> ADP </ci>
<ci> Km_ADP </ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<component name="v_GAPDH">
<variable units="flux" public_interface="out" name="v_GAPDH"/>
<variable units="millimolar" name="Km_GAP" initial_value="0.21"/>
<variable units="millimolar" name="Km_BPG" initial_value="0.0098"/>
<variable units="millimolar" name="Km_NAD" initial_value="0.09"/>
<variable units="millimolar" name="Km_NADH" initial_value="0.06"/>
<variable units="flux" name="v_max_f" initial_value="1184.52"/>
<variable units="flux" name="v_max_r" initial_value="6549.68"/>
<variable units="dimensionless" public_interface="in" name="Keq_TPI"/>
<variable units="millimolar" public_interface="in" name="BPG"/>
<variable units="millimolar" public_interface="in" name="TRIO"/>
<variable units="millimolar" public_interface="in" name="NAD"/>
<variable units="millimolar" public_interface="in" name="NADH"/>
<math xmlns="http://www.w3.org/1998/Math/MathML" id="29">
<apply id="v_GAPDH_calculation"><eq/>
<ci> v_GAPDH </ci>
<apply><divide/>
<apply><minus/>
<apply><divide/>
<apply><times/>
<ci> v_max_f </ci>
<apply><divide/>
<ci> Keq_TPI </ci>
<apply><plus/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<ci> Keq_TPI </ci>
</apply>
</apply>
<ci> TRIO </ci>
<ci> NAD </ci>
</apply>
<apply><times/>
<ci> Km_GAP </ci>
<ci> Km_NAD </ci>
</apply>
</apply>
<apply><divide/>
<apply><times/>
<ci> v_max_r </ci>
<ci> BPG </ci>
<ci> NADH </ci>
</apply>
<apply><times/>
<ci> Km_BPG </ci>
<ci> Km_NADH </ci>
</apply>
</apply>
</apply>
<apply><times/>
<apply><plus/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<apply><divide/>
<apply><times/>
<apply><divide/>
<ci> Keq_TPI </ci>
<apply><plus/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<ci> Keq_TPI </ci>
</apply>
</apply>
<ci> TRIO </ci>
</apply>
<ci> Km_GAP </ci>
</apply>
<apply><divide/>
<ci> BPG </ci>
<ci> Km_BPG </ci>
</apply>
</apply>
<apply><plus/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<apply><divide/>
<ci> NAD </ci>
<ci> Km_NAD </ci>
</apply>
<apply><divide/>
<ci> NADH </ci>
<ci> Km_NADH </ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<component name="v_PGK">
<variable units="flux" public_interface="out" name="v_PGK"/>
<variable units="millimolar" name="Km_BPG" initial_value="0.003"/>
<variable units="millimolar" name="Km_P3G" initial_value="0.53"/>
<variable units="millimolar" name="Km_ADP" initial_value="0.2"/>
<variable units="millimolar" name="Km_ATP" initial_value="0.3"/>
<variable units="dimensionless" name="Keq_PGK" initial_value="3200"/>
<variable units="flux" name="v_max" initial_value="1306.45"/>
<variable units="millimolar" public_interface="in" name="P3G"/>
<variable units="millimolar" public_interface="in" name="BPG"/>
<variable units="millimolar" public_interface="in" name="ATP"/>
<variable units="millimolar" public_interface="in" name="ADP"/>
<math xmlns="http://www.w3.org/1998/Math/MathML" id="30">
<apply id="v_PGK_calculation"><eq/>
<ci> v_PGK </ci>
<apply><divide/>
<apply><times/>
<apply><divide/>
<ci> v_max </ci>
<apply><times/>
<ci> Km_P3G </ci>
<ci> Km_ATP </ci>
</apply>
</apply>
<apply><minus/>
<apply><times/>
<ci> Keq_PGK </ci>
<ci> BPG </ci>
<ci> ADP </ci>
</apply>
<apply><times/>
<ci> P3G </ci>
<ci> ATP </ci>
</apply>
</apply>
</apply>
<apply><times/>
<apply><plus/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<apply><divide/>
<ci> BPG </ci>
<ci> Km_BPG </ci>
</apply>
<apply><divide/>
<ci> P3G </ci>
<ci> Km_P3G </ci>
</apply>
</apply>
<apply><plus/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<apply><divide/>
<ci> ATP </ci>
<ci> Km_ATP </ci>
</apply>
<apply><divide/>
<ci> ADP</ci>
<ci> Km_ADP </ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<component name="v_PYK">
<variable units="flux" public_interface="out" name="v_PYK"/>
<variable units="millimolar" name="Km_PEP" initial_value="0.14"/>
<variable units="millimolar" name="Km_PYR" initial_value="21.0"/>
<variable units="millimolar" name="Km_ADP" initial_value="0.53"/>
<variable units="millimolar" name="Km_ATP" initial_value="1.5"/>
<variable units="dimensionless" name="Keq_PYK" initial_value="6500"/>
<variable units="flux" name="v_max" initial_value="1088.71"/>
<variable units="millimolar" public_interface="in" name="PYR"/>
<variable units="millimolar" public_interface="in" name="PEP"/>
<variable units="millimolar" public_interface="in" name="ADP"/>
<variable units="millimolar" public_interface="in" name="ATP"/>
<math xmlns="http://www.w3.org/1998/Math/MathML" id="31">
<apply id="v_PYK_calculation"><eq/>
<ci> v_PYK </ci>
<apply><divide/>
<apply><times/>
<apply><divide/>
<ci> v_max </ci>
<apply><times/>
<ci> Km_PEP </ci>
<ci> Km_ADP </ci>
</apply>
</apply>
<apply><minus/>
<apply><times/>
<ci> PEP </ci>
<ci> ADP </ci>
</apply>
<apply><divide/>
<apply><times/>
<ci> PYR </ci>
<ci> ATP </ci>
</apply>
<ci> Keq_PYK </ci>
</apply>
</apply>
</apply>
<apply><times/>
<apply><plus/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<apply><divide/>
<ci> PEP </ci>
<ci> Km_PEP </ci>
</apply>
<apply><divide/>
<ci> PYR </ci>
<ci> Km_PYR </ci>
</apply>
</apply>
<apply><plus/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<apply><divide/>
<ci> ATP </ci>
<ci> Km_ATP </ci>
</apply>
<apply><divide/>
<ci> ADP</ci>
<ci> Km_ADP </ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<component name="v_GLT">
<variable units="flux" public_interface="out" name="v_GLT"/>
<variable units="millimolar" name="Km_Glco" initial_value="1.1918"/>
<variable units="millimolar" name="Km_Glci" initial_value="1.1918"/>
<variable units="dimensionless" name="Keq_Glc" initial_value="1"/>
<variable units="flux" name="v_max" initial_value="97.264"/>
<variable units="millimolar" public_interface="in" name="GLCo"/>
<variable units="millimolar" public_interface="in" name="GLCi"/>
<math xmlns="http://www.w3.org/1998/Math/MathML" id="32">
<apply id="v_GLT_calculation"><eq/>
<ci> v_GLT </ci>
<apply><divide/>
<apply><times/>
<ci> v_max </ci>
<apply><minus/>
<ci> GLCo </ci>
<apply><divide/>
<ci> GLCi </ci>
<ci> Keq_Glc </ci>
</apply>
</apply>
</apply>
<apply><times/>
<ci> Km_Glco </ci>
<apply><plus/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<apply><divide/>
<ci> GLCo </ci>
<ci> Km_Glco </ci>
</apply>
<apply><divide/>
<ci> GLCi </ci>
<ci> Km_Glci </ci>
</apply>
<apply><divide/>
<apply><times/>
<cn cellml:units="dimensionless"> 0.91 </cn>
<ci> GLCo </ci>
<ci> GLCi </ci>
</apply>
<apply><times/>
<ci> Km_Glci </ci>
<ci> Km_Glco </ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<component name="v_ALD">
<variable units="flux" public_interface="out" name="v_ALD"/>
<variable units="millimolar" name="Km_F16P" initial_value="0.3"/>
<variable units="millimolar" name="Km_GAP" initial_value="2.0"/>
<variable units="millimolar" name="Km_GAPi" initial_value="10.0"/>
<variable units="millimolar" name="Km_DHAP" initial_value="2.4"/>
<variable units="millimolar" name="Keq_ALD" initial_value="0.069"/>
<variable units="flux" name="v_max" initial_value="322.258"/>
<variable units="dimensionless" public_interface="in" name="Keq_TPI"/>
<variable units="millimolar" public_interface="in" name="TRIO"/>
<variable units="millimolar" public_interface="in" name="F16P"/>
<math xmlns="http://www.w3.org/1998/Math/MathML" id="33">
<apply><eq/>
<ci> v_ALD </ci>
<apply><divide/>
<apply><times/>
<apply><divide/>
<ci> v_max </ci>
<ci> Km_F16P </ci>
</apply>
<apply><minus/>
<ci> F16P </ci>
<apply><divide/>
<apply><times/>
<apply><divide/>
<ci> Keq_TPI </ci>
<apply><plus/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<ci> Keq_TPI </ci>
</apply>
</apply>
<ci> TRIO </ci>
<apply><divide/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<apply><plus/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<ci> Keq_TPI </ci>
</apply>
</apply>
<ci> TRIO </ci>
</apply>
<ci> Keq_ALD </ci>
</apply>
</apply>
</apply>
<apply><plus/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<apply><divide/>
<ci> F16P </ci>
<ci> Km_F16P </ci>
</apply>
<apply><divide/>
<apply><times/>
<apply><divide/>
<ci> Keq_TPI </ci>
<apply><plus/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<ci> Keq_TPI </ci>
</apply>
</apply>
<ci> TRIO </ci>
</apply>
<ci> Km_GAP </ci>
</apply>
<apply><divide/>
<apply><times/>
<apply><divide/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<apply><plus/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<ci> Keq_TPI </ci>
</apply>
</apply>
<ci> TRIO </ci>
</apply>
<ci> Km_DHAP </ci>
</apply>
<apply><divide/>
<apply><times/>
<apply><divide/>
<ci> Keq_TPI </ci>
<apply><plus/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<ci> Keq_TPI </ci>
</apply>
</apply>
<ci> TRIO </ci>
<apply><divide/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<apply><plus/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<ci> Keq_TPI </ci>
</apply>
</apply>
<ci> TRIO </ci>
</apply>
<apply><times/>
<ci> Km_GAP </ci>
<ci> Km_DHAP </ci>
</apply>
</apply>
<apply><divide/>
<apply><times/>
<ci> F16P </ci>
<apply><divide/>
<ci> Keq_TPI </ci>
<apply><plus/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<ci> Keq_TPI </ci>
</apply>
</apply>
<ci> TRIO </ci>
</apply>
<apply><times/>
<ci> Km_GAPi </ci>
<ci> Km_F16P </ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<component name="v_PDC">
<variable units="flux" public_interface="out" name="v_PDC"/>
<variable units="dimensionless" name="nPDC" initial_value="1.9"/>
<variable units="millimolar" name="Km_PYR" initial_value="4.33"/>
<variable units="flux" name="v_max" initial_value="174.194"/>
<variable units="millimolar" public_interface="in" name="PYR"/>
<math xmlns="http://www.w3.org/1998/Math/MathML" id="34">
<apply><eq/>
<ci> v_PDC </ci>
<apply><divide/>
<apply><times/>
<ci> v_max </ci>
<apply><divide/>
<apply><power/>
<ci> PYR </ci>
<ci> nPDC </ci>
</apply>
<apply><power/>
<ci> Km_PYR </ci>
<ci> nPDC </ci>
</apply>
</apply>
</apply>
<apply><plus/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<apply><divide/>
<apply><power/>
<ci> PYR </ci>
<ci> nPDC </ci>
</apply>
<apply><power/>
<ci> Km_PYR </ci>
<ci> nPDC </ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<component name="v_ADH">
<variable units="flux" public_interface="out" name="v_ADH"/>
<variable units="millimolar" name="Km_NAD" initial_value="0.17"/>
<variable units="millimolar" name="Km_NADH" initial_value="0.11"/>
<variable units="millimolar" name="Km_ACE" initial_value="1.11"/>
<variable units="millimolar" name="Km_ETOH" initial_value="17.0"/>
<variable units="millimolar" name="Ki_NADH" initial_value="0.031"/>
<variable units="millimolar" name="Ki_NAD" initial_value="0.92"/>
<variable units="millimolar" name="Ki_ACE" initial_value="1.1"/>
<variable units="millimolar" name="Ki_ETOH" initial_value="90.0"/>
<variable units="flux" name="v_max" initial_value="810.0"/>
<variable units="dimensionless" name="Keq_ADH" initial_value="0.000069"/>
<variable units="millimolar" public_interface="in" name="ETOH"/>
<variable units="millimolar" public_interface="in" name="ACE"/>
<variable units="millimolar" public_interface="in" name="NADH"/>
<variable units="millimolar" public_interface="in" name="NAD"/>
<math xmlns="http://www.w3.org/1998/Math/MathML" id="35">
<apply id="v_ADH_calculation"><eq/>
<ci> v_ADH </ci>
<apply><minus/>
<apply><times/>
<apply><divide/>
<ci> v_max </ci>
<apply><times/>
<ci> Ki_NAD </ci>
<ci> Km_ETOH </ci>
</apply>
</apply>
<apply><divide/>
<apply><minus/>
<apply><times/>
<ci> NAD </ci>
<ci> ETOH </ci>
</apply>
<apply><divide/>
<apply><times/>
<ci> NADH </ci>
<ci> ACE </ci>
</apply>
<ci> Keq_ADH </ci>
</apply>
</apply>
<apply><plus/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<apply><divide/>
<ci> NAD </ci>
<ci> Ki_NAD </ci>
</apply>
<apply><divide/>
<apply><times/>
<ci> Km_NAD </ci>
<ci> ETOH </ci>
</apply>
<apply><times/>
<ci> Ki_NAD </ci>
<ci> Km_ETOH </ci>
</apply>
</apply>
<apply><divide/>
<apply><times/>
<ci> Km_NADH </ci>
<ci> ACE </ci>
</apply>
<apply><times/>
<ci> Ki_NADH </ci>
<ci> Km_ACE </ci>
</apply>
</apply>
<apply><divide/>
<ci> NADH </ci>
<ci> Ki_NADH </ci>
</apply>
<apply><divide/>
<apply><times/>
<ci> NAD </ci>
<ci> ETOH </ci>
</apply>
<apply><times/>
<ci> Ki_NAD </ci>
<ci> Km_ETOH </ci>
</apply>
</apply>
<apply><divide/>
<apply><times/>
<ci> Km_NADH </ci>
<ci> NAD </ci>
<ci> ACE </ci>
</apply>
<apply><times/>
<ci> Ki_NAD </ci>
<ci> Ki_NADH </ci>
<ci> Km_ACE </ci>
</apply>
</apply>
<apply><divide/>
<apply><times/>
<ci> Km_NAD </ci>
<ci> ETOH </ci>
<ci> NADH </ci>
</apply>
<apply><times/>
<ci> Ki_NAD </ci>
<ci> Km_ETOH</ci>
<ci> Ki_NADH </ci>
</apply>
</apply>
<apply><divide/>
<apply><times/>
<ci> NADH </ci>
<ci> ACE </ci>
</apply>
<apply><times/>
<ci> Ki_NADH </ci>
<ci> Km_ACE </ci>
</apply>
</apply>
<apply><divide/>
<apply><times/>
<ci> NAD </ci>
<ci> ETOH </ci>
<ci> ACE </ci>
</apply>
<apply><times/>
<ci> Ki_NAD </ci>
<ci> Km_ETOH </ci>
<ci> Ki_ACE </ci>
</apply>
</apply>
<apply><divide/>
<apply><times/>
<ci> ETOH </ci>
<ci> NADH </ci>
<ci> ACE </ci>
</apply>
<apply><times/>
<ci> Ki_ETOH </ci>
<ci> Ki_NADH </ci>
<ci> Km_ACE </ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<component name="v_ATP">
<variable units="flux" public_interface="out" name="v_ATP"/>
<variable units="first_order_rate_constant" name="Km_ATPase" initial_value="33.7"/>
<variable units="millimolar" public_interface="in" name="ATP"/>
<math xmlns="http://www.w3.org/1998/Math/MathML" id="36">
<apply>
<eq/>
<ci> v_ATP </ci>
<apply>
<times/>
<ci> Km_ATPase </ci>
<ci> ATP </ci>
</apply>
</apply>
</math>
</component>
<component name="v_PFK">
<variable units="flux" public_interface="out" name="v_PFK"/>
<variable units="flux" name="v_max" initial_value="182.903"/>
<variable units="dimensionless" name="gR" initial_value="5.12"/>
<variable units="per_millimolar2" name="L0" initial_value="0.66"/>
<variable units="millimolar" name="Km_F6P" initial_value="0.1"/>
<variable units="millimolar" name="Km_ATP" initial_value="0.71"/>
<variable units="millimolar" name="CATP" initial_value="3.0"/>
<variable units="millimolar" name="Km_AMP" initial_value="0.0995"/>
<variable units="dimensionless" name="CAMP" initial_value="0.0845"/>
<variable units="millimolar" name="Ki_ATP" initial_value="0.65"/>
<variable units="dimensionless" name="Ci_ATP" initial_value="100.0"/>
<variable units="millimolar" name="Km_F26BP" initial_value="0.000682"/>
<variable units="dimensionless" name="CF26BP" initial_value="0.0174"/>
<variable units="millimolar" name="Km_F16BP" initial_value="0.111"/>
<variable units="dimensionless" name="CF16BP" initial_value="0.397"/>
<variable units="per_millimolar2" name="L"/>
<variable units="dimensionless" name="R"/>
<variable units="millimolar" name="T"/>
<variable units="millimolar" public_interface="in" name="F6P"/>
<variable units="millimolar" public_interface="in" name="F16P"/>
<variable units="millimolar" public_interface="in" name="F26P"/>
<variable units="millimolar" public_interface="in" name="ATP"/>
<variable units="millimolar" public_interface="in" name="AMP"/>
<math xmlns="http://www.w3.org/1998/Math/MathML" id="37">
<apply id="v_PFKm_calculation"><eq/>
<ci> v_PFK </ci>
<apply><times/>
<ci> v_max </ci>
<ci> gR </ci>
<apply><divide/>
<ci> F6P </ci>
<ci> Km_F6P </ci>
</apply>
<apply><divide/>
<ci> ATP </ci>
<ci> Km_ATP </ci>
</apply>
<apply><divide/>
<ci> R </ci>
<apply><plus/>
<apply><power/>
<ci> R </ci>
<cn cellml:units="dimensionless"> 2 </cn>
</apply>
<apply><times/>
<ci> L </ci>
<apply><power/>
<ci> T </ci>
<cn cellml:units="dimensionless"> 2 </cn>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
</math>
<math xmlns="http://www.w3.org/1998/Math/MathML" id="38">
<apply id="R_calculation"><eq/>
<ci> R </ci>
<apply><plus/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<apply><divide/>
<ci> F6P </ci>
<ci> Km_F6P </ci>
</apply>
<apply><divide/>
<ci> ATP </ci>
<ci> Km_ATP </ci>
</apply>
<apply><times/>
<ci> gR </ci>
<apply><divide/>
<ci> F6P </ci>
<ci> Km_F6P </ci>
</apply>
<apply><divide/>
<ci> ATP </ci>
<ci> Km_ATP </ci>
</apply>
</apply>
</apply>
</apply>
</math>
<math xmlns="http://www.w3.org/1998/Math/MathML" id="39">
<apply id="L_calculation"><eq/>
<ci> L </ci>
<apply><times/>
<ci> L0 </ci>
<apply><power/>
<apply><divide/>
<apply><plus/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<apply><times/>
<ci> Ci_ATP </ci>
<apply><divide/>
<ci> ATP </ci>
<ci> Ki_ATP </ci>
</apply>
</apply>
</apply>
<apply><plus/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<apply><divide/>
<ci> ATP </ci>
<ci> Ki_ATP </ci>
</apply>
</apply>
</apply>
<cn cellml:units="dimensionless"> 2.0 </cn>
</apply>
<apply><power/>
<apply><divide/>
<apply><plus/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<apply><times/>
<ci> CAMP </ci>
<apply><divide/>
<ci> AMP </ci>
<ci> Km_AMP </ci>
</apply>
</apply>
</apply>
<apply><plus/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<apply><divide/>
<ci> AMP </ci>
<ci> Km_AMP </ci>
</apply>
</apply>
</apply>
<cn cellml:units="dimensionless"> 2.0 </cn>
</apply>
<apply><power/>
<apply><divide/>
<apply><plus/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<apply><times/>
<ci> CF26BP </ci>
<apply><divide/>
<ci> F26P </ci>
<ci> Km_F26BP </ci>
</apply>
</apply>
<apply><times/>
<ci> CF16BP </ci>
<apply><divide/>
<ci> F16P </ci>
<ci> Km_F16BP </ci>
</apply>
</apply>
</apply>
<apply><plus/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<apply><divide/>
<ci> F26P </ci>
<ci> Km_F26BP </ci>
</apply>
<apply><divide/>
<ci> F16P </ci>
<ci> Km_F16BP </ci>
</apply>
</apply>
</apply>
<cn cellml:units="dimensionless"> 2 </cn>
</apply>
</apply>
</apply>
</math>
<math xmlns="http://www.w3.org/1998/Math/MathML" id="40">
<apply id="T_calculation"><eq/>
<ci> T </ci>
<apply><plus/>
<cn cellml:units="millimolar"> 1.0 </cn>
<apply><times/>
<ci> CATP </ci>
<apply><divide/>
<ci> ATP </ci>
<ci> Km_ATP </ci>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<!--
The following components describe the reactions of the branches introduced in the extended model. For simplicity, fluxes to glycogen and trehalose are introduced as experimentally derived constants.
-->
<component name="v_G3PDH">
<variable units="flux" public_interface="out" name="v_G3PDH"/>
<variable units="millimolar" name="Km_DHAP" initial_value="0.4"/>
<variable units="millimolar" name="Km_GLY" initial_value="1"/>
<variable units="millimolar" name="Km_NADH" initial_value="0.023"/>
<variable units="millimolar" name="Km_NAD" initial_value="0.93"/>
<variable units="dimensionless" name="Keq_G3PDH" initial_value="4300"/>
<variable units="flux" name="v_max" initial_value="70.15"/>
<variable units="dimensionless" public_interface="in" name="Keq_TPI"/>
<variable units="millimolar" public_interface="in" name="TRIO"/>
<variable units="millimolar" public_interface="in" name="GLY"/>
<variable units="millimolar" public_interface="in" name="NADH"/>
<variable units="millimolar" public_interface="in" name="NAD"/>
<math xmlns="http://www.w3.org/1998/Math/MathML" id="43">
<apply><eq/>
<ci>v_G3PDH</ci>
<apply><divide/>
<apply><times/>
<apply><divide/>
<ci> v_max </ci>
<apply><times/>
<ci> Km_DHAP </ci>
<ci> Km_NADH </ci>
</apply>
</apply>
<apply><minus/>
<apply><times/>
<apply><divide/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<apply><plus/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<ci> Keq_TPI </ci>
</apply>
</apply>
<ci> TRIO </ci>
<ci> NADH </ci>
</apply>
<apply><divide/>
<apply><times/>
<ci> GLY </ci>
<ci> NAD </ci>
</apply>
<ci> Keq_G3PDH </ci>
</apply>
</apply>
</apply>
<apply><times/>
<apply><plus/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<apply><divide/>
<apply><times/>
<apply><divide/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<apply><plus/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<ci> Keq_TPI </ci>
</apply>
</apply>
<ci> TRIO </ci>
</apply>
<ci> Km_DHAP </ci>
</apply>
<apply><divide/>
<ci> GLY </ci>
<ci> Km_GLY </ci>
</apply>
</apply>
<apply><plus/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<apply><divide/>
<ci> NADH </ci>
<ci> Km_NADH </ci>
</apply>
<apply><divide/>
<ci> NAD </ci>
<ci> Km_NAD </ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<component name="v_succinate">
<variable units="flux" public_interface="out" name="v_succinate"/>
<variable units="first_order_rate_constant" name="Km_succinate" initial_value="21.4"/>
<variable units="millimolar" public_interface="in" name="ACE"/>
<math xmlns="http://www.w3.org/1998/Math/MathML" id="44">
<apply>
<eq/>
<ci>v_succinate</ci>
<apply>
<times/>
<ci> Km_succinate </ci>
<ci> ACE </ci>
</apply>
</apply>
</math>
</component>
<component name="v_glycogen">
<variable units="flux" public_interface="out" name="v_glycogen" initial_value="6.0"/>
</component>
<component name="v_trehalose">
<variable units="flux" public_interface="out" name="v_trehalose" initial_value="2.4"/>
</component>
<!-- Connections -->
<connection>
<map_components component_2="environment" component_1="GLCi"/>
<map_variables variable_2="time" variable_1="time"/>
</connection>
<connection>
<map_components component_2="environment" component_1="G6P"/>
<map_variables variable_2="time" variable_1="time"/>
</connection>
<connection>
<map_components component_2="environment" component_1="F6P"/>
<map_variables variable_2="time" variable_1="time"/>
</connection>
<connection>
<map_components component_2="environment" component_1="F16P"/>
<map_variables variable_2="time" variable_1="time"/>
</connection>
<connection>
<map_components component_2="environment" component_1="TRIO"/>
<map_variables variable_2="time" variable_1="time"/>
</connection>
<connection>
<map_components component_2="environment" component_1="BPG"/>
<map_variables variable_2="time" variable_1="time"/>
</connection>
<connection>
<map_components component_2="environment" component_1="P3G"/>
<map_variables variable_2="time" variable_1="time"/>
</connection>
<connection>
<map_components component_2="environment" component_1="P2G"/>
<map_variables variable_2="time" variable_1="time"/>
</connection>
<connection>
<map_components component_2="environment" component_1="PEP"/>
<map_variables variable_2="time" variable_1="time"/>
</connection>
<connection>
<map_components component_2="environment" component_1="PYR"/>
<map_variables variable_2="time" variable_1="time"/>
</connection>
<connection>
<map_components component_2="environment" component_1="ACE"/>
<map_variables variable_2="time" variable_1="time"/>
</connection>
<connection>
<map_components component_2="environment" component_1="P"/>
<map_variables variable_2="time" variable_1="time"/>
</connection>
<connection>
<map_components component_2="environment" component_1="NADH"/>
<map_variables variable_2="time" variable_1="time"/>
</connection>
<connection>
<map_components component_2="environment" component_1="NAD"/>
<map_variables variable_2="time" variable_1="time"/>
</connection>
<connection>
<map_components component_2="v_GLT" component_1="GLCo"/>
<map_variables variable_2="GLCo" variable_1="GLCo"/>
</connection>
<connection>
<map_components component_2="v_GLT" component_1="GLCi"/>
<map_variables variable_2="GLCi" variable_1="GLCi"/>
<map_variables variable_2="v_GLT" variable_1="v_GLT"/>
</connection>
<connection>
<map_components component_2="v_GLK" component_1="GLCi"/>
<map_variables variable_2="GLCi" variable_1="GLCi"/>
<map_variables variable_2="v_GLK" variable_1="v_GLK"/>
</connection>
<connection>
<map_components component_2="v_GLK" component_1="G6P"/>
<map_variables variable_2="G6P" variable_1="G6P"/>
<map_variables variable_2="v_GLK" variable_1="v_GLK"/>
</connection>
<connection>
<map_components component_2="v_PGI" component_1="G6P"/>
<map_variables variable_2="G6P" variable_1="G6P"/>
<map_variables variable_2="v_PGI" variable_1="v_PGI"/>
</connection>
<connection>
<map_components component_2="v_trehalose" component_1="G6P"/>
<map_variables variable_2="v_trehalose" variable_1="v_trehalose"/>
</connection>
<connection>
<map_components component_2="v_glycogen" component_1="G6P"/>
<map_variables variable_2="v_glycogen" variable_1="v_glycogen"/>
</connection>
<connection>
<map_components component_2="v_PGI" component_1="F6P"/>
<map_variables variable_2="F6P" variable_1="F6P"/>
<map_variables variable_2="v_PGI" variable_1="v_PGI"/>
</connection>
<connection>
<map_components component_2="v_PFK" component_1="F6P"/>
<map_variables variable_2="F6P" variable_1="F6P"/>
<map_variables variable_2="v_PFK" variable_1="v_PFK"/>
</connection>
<connection>
<map_components component_2="v_PFK" component_1="F16P"/>
<map_variables variable_2="F16P" variable_1="F16P"/>
<map_variables variable_2="v_PFK" variable_1="v_PFK"/>
</connection>
<connection>
<map_components component_2="v_ALD" component_1="F16P"/>
<map_variables variable_2="F16P" variable_1="F16P"/>
<map_variables variable_2="v_ALD" variable_1="v_ALD"/>
</connection>
<connection>
<map_components component_2="v_PFK" component_1="F26P"/>
<map_variables variable_2="F26P" variable_1="F26P"/>
</connection>
<connection>
<map_components component_2="v_ALD" component_1="TRIO"/>
<map_variables variable_2="v_ALD" variable_1="v_ALD"/>
<map_variables variable_2="TRIO" variable_1="TRIO"/>
</connection>
<connection>
<map_components component_2="v_GAPDH" component_1="TRIO"/>
<map_variables variable_2="v_GAPDH" variable_1="v_GAPDH"/>
<map_variables variable_2="TRIO" variable_1="TRIO"/>
</connection>
<connection>
<map_components component_2="v_G3PDH" component_1="TRIO"/>
<map_variables variable_2="v_G3PDH" variable_1="v_G3PDH"/>
<map_variables variable_2="TRIO" variable_1="TRIO"/>
</connection>
<connection>
<map_components component_2="v_GAPDH" component_1="BPG"/>
<map_variables variable_2="BPG" variable_1="BPG"/>
<map_variables variable_2="v_GAPDH" variable_1="v_GAPDH"/>
</connection>
<connection>
<map_components component_2="v_PGK" component_1="BPG"/>
<map_variables variable_2="BPG" variable_1="BPG"/>
<map_variables variable_2="v_PGK" variable_1="v_PGK"/>
</connection>
<connection>
<map_components component_2="v_PGK" component_1="P3G"/>
<map_variables variable_2="P3G" variable_1="P3G"/>
<map_variables variable_2="v_PGK" variable_1="v_PGK"/>
</connection>
<connection>
<map_components component_2="v_PGM" component_1="P3G"/>
<map_variables variable_2="P3G" variable_1="P3G"/>
<map_variables variable_2="v_PGM" variable_1="v_PGM"/>
</connection>
<connection>
<map_components component_2="v_PGM" component_1="P2G"/>
<map_variables variable_2="P2G" variable_1="P2G"/>
<map_variables variable_2="v_PGM" variable_1="v_PGM"/>
</connection>
<connection>
<map_components component_2="v_ENO" component_1="P2G"/>
<map_variables variable_2="P2G" variable_1="P2G"/>
<map_variables variable_2="v_ENO" variable_1="v_ENO"/>
</connection>
<connection>
<map_components component_2="v_ENO" component_1="PEP"/>
<map_variables variable_2="PEP" variable_1="PEP"/>
<map_variables variable_2="v_ENO" variable_1="v_ENO"/>
</connection>
<connection>
<map_components component_2="v_PYK" component_1="PEP"/>
<map_variables variable_2="PEP" variable_1="PEP"/>
<map_variables variable_2="v_PYK" variable_1="v_PYK"/>
</connection>
<connection>
<map_components component_2="v_PYK" component_1="PYR"/>
<map_variables variable_2="PYR" variable_1="PYR"/>
<map_variables variable_2="v_PYK" variable_1="v_PYK"/>
</connection>
<connection>
<map_components component_2="v_PDC" component_1="PYR"/>
<map_variables variable_2="PYR" variable_1="PYR"/>
<map_variables variable_2="v_PDC" variable_1="v_PDC"/>
</connection>
<connection>
<map_components component_2="v_PDC" component_1="ACE"/>
<map_variables variable_2="v_PDC" variable_1="v_PDC"/>
</connection>
<connection>
<map_components component_2="v_ADH" component_1="ACE"/>
<map_variables variable_2="ACE" variable_1="ACE"/>
<map_variables variable_2="v_ADH" variable_1="v_ADH"/>
</connection>
<connection>
<map_components component_2="v_succinate" component_1="ACE"/>
<map_variables variable_2="ACE" variable_1="ACE"/>
<map_variables variable_2="v_succinate" variable_1="v_succinate"/>
</connection>
<connection>
<map_components component_2="v_GLK" component_1="P"/>
<map_variables variable_2="v_GLK" variable_1="v_GLK"/>
</connection>
<connection>
<map_components component_2="v_PFK" component_1="P"/>
<map_variables variable_2="v_PFK" variable_1="v_PFK"/>
</connection>
<connection>
<map_components component_2="v_PGK" component_1="P"/>
<map_variables variable_2="v_PGK" variable_1="v_PGK"/>
</connection>
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