Rendering of the source text

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<documentation xmlns="http://cellml.org/tmp-documentation">
<article>
  <articleinfo>
  <title>The Pentose Phosphate Pathway in Saccharomyces cerevisiae</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 model is known to run in both PCEnv and COR, however at present it does not seem to be recreating the published results - possibly beause we need to include a description of a glucose pulse in the CellML model.  We are continuing to work on the model. The units have been checked and they are consistent.</para>
			</section>
  <sect1 id="sec_structure">
<title>Model Structure</title>

<para>
Metabolic networks are highly complex nonlinear reaction systems whose functions are tightly co-ordinated and regulated by feedback mechanisms to meet the physiological demands of living organisms.  Dynamic mathematical models of metabolic networks allow prediction as to how metabolism will respond to manipulation.
</para>

<para>
The pentose phosphate pathway can provide an alternative to glycolysis plus the TCA cycle for the complete oxidation of glucose.  However, it is thought that its main role is not glucose oxidation, but to provide the cell with a source of NADPH for biosynthetic reactions and to supply pentose phosphate for the synthesis of nucleotides.
</para>

<para>
In 1999, Sam Vaseghi, Anja Baumeister, Manfred Rizzi and Matthias Reuss published a kinetic model of the pentose phosphate pathway in the yeast <emphasis>Saccharomyces cerevisiae</emphasis> (see <xref linkend="fig_pathway_diagram"/> below).  They studied the <emphasis>in vivo</emphasis> dynamics of the pathway under conditions of continuous culture in order to elucidate important regulation phenomena responsible for co-ordinating the fluxes between glycolysis and the pentose phosphate pathway.  They constructed the model by combining knowledge about enzyme kinetics with the stoichiometry of metabolic pathways based on the same principles used by Rizzi <emphasis>et al</emphasis> in their model of glycolysis (1997) (see <ulink url="${HTML_EXMPL_GLYCOLYSIS_1997}">The Glycolysis Pathway Model, 1997</ulink>). 
</para>

<para>
The complete original paper reference is cited below:
</para>

<para>
<ulink url="http://www.sciencedirect.com/science?_ob=ArticleURL&amp;_udi=B6WN3-45GMXTM-2&amp;_user=140507&amp;_coverDate=04%2F30%2F1999&amp;_alid=185462660&amp;_rdoc=1&amp;_fmt=summary&amp;_orig=search&amp;_qd=1&amp;_cdi=6951&amp;_sort=d&amp;_docanchor=&amp;view=c&amp;_acct=C000011498&amp;_version=1&amp;_urlVersion=0&amp;_userid=140507&amp;md5=618c9e292e1d213b8aa38e60c0f03db3">
            <emphasis>In Vivo</emphasis> Dynamics of the Pentose Phosphate Pathway in <emphasis>Saccharomyces cerevisiae</emphasis>
          </ulink>, Sam Vaseghi, Anja Baumeister, Manfred Rizzi and Matthias Reuss, 1999, <ulink url="http://www.sciencedirect.com/science?_ob=JournalURL&amp;_cdi=6951&amp;_auth=y&amp;_acct=C000011498&amp;_version=1&amp;_urlVersion=0&amp;_userid=140507&amp;md5=960dfeca7fc4aabf0cf2dcfe0b2c41c0">
            <emphasis>Metabolic Engineering</emphasis>
          </ulink>, 1, 128-140.  (A PDF version of the article is available to subscribers on the <emphasis>Metabolic Engineering</emphasis> website.)  <ulink url="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;list_uids=10935926&amp;dopt=Abstract">PubMed ID: 10935926</ulink>
</para>

<para>
The raw CellML description of the pentose phosphate pathway model can be downloaded in various formats as described in <xref linkend="sec_download_this_model"/>.  For an example of a more complete documentation of another real reaction pathway, see <ulink url="${HTML_EXMPL_BI_EGF_INTRO}">The Bhalla Iyengar EGF Pathway Model, 1999</ulink>. 
</para>

<informalfigure float="0" id="fig_pathway_diagram">
<mediaobject>
  <imageobject>
    <objectinfo>
      <title>the conventional rendering of the pentose phosphate pathway in Saccharomyces cerevisiae</title>
    </objectinfo>
    <imagedata fileref="vaseghi_1999.png"/>
  </imageobject>
</mediaobject>
<caption>A rendering of the pentose phosphate pathway in <emphasis>Saccharomyces cerevisiae</emphasis>. Metabolites are represented by rounded rectangles, catalysts are represented by ellipses and reactions by arrows.  The action of the inhibitor MgATP on the enzymes G6PDH and 6PGDH is represented by dashed lines.</caption>
</informalfigure>

<para>
In CellML, models are thought of as connected networks of discrete components. These components may correspond to physiologically separated regions or chemically distinct objects, or may be useful modelling abstractions. This model has 36 components representing chemically distinct objects (15 metabolites, 10 enzymes one inhibitor and 10 reactions) and one component defined for modelling convenience which stores the universal variable time.  Because this model has so many components, its CellML rendering would be complex.  For an example of a CellML rendering of a reaction pathway see <ulink url="${HTML_EXMPL_BI_EGF_INTRO}">The Bhalla Iyengar EGF Pathway Model, 1999</ulink>.  
</para>

</sect1>
</article>
</documentation>

  
  
  
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                    <ci>time</ci>
                  </apply>
                  <apply>
                    <times/>
                    <cn cellml:units="per_second2">0.05</cn>
                    <apply>
                      <power/>
                      <ci>time</ci>
                      <cn cellml:units="dimensionless">2</cn>
                    </apply>
                  </apply>
                </apply>
              </apply>
            </apply>
            <apply>
              <plus/>
              <cn cellml:units="dimensionless">13.42</cn>
              <apply>
                <times/>
                <cn cellml:units="per_second">0.1</cn>
                <ci>time</ci>
              </apply>
            </apply>
          </apply>
        </apply>
      </apply>
    </math> 
  </component>

  <component name="rG6PDH">
     <variable units="flux" public_interface="out" name="rG6PDH"/>
     
     <variable units="millimolar" public_interface="in" name="C_NADP"/>
     <variable units="millimolar" public_interface="in" name="C_NADPH"/>
     <variable units="millimolar" public_interface="in" name="C_MgATP"/>
     
     <variable units="millimolar" name="K_NADP_1" initial_value="0.116"/>
     <variable units="millimolar" name="Ki_NADPH_1" initial_value="1.702"/>
     <variable units="millimolar" name="Ki_MgATP_1" initial_value="0.33"/>
     <variable units="dimensionless" name="I_NADPH_1"/>
     <variable units="dimensionless" name="I_MgATP_1"/>
     <variable units="flux" name="rmax_G6PDH" initial_value="44.19"/>

     <math xmlns="http://www.w3.org/1998/Math/MathML">
       <apply>
        <eq/>
         <ci> rG6PDH </ci>
         <apply>
          <times/>
           <ci> rmax_G6PDH </ci>
           <apply>
            <divide/>
             <ci> C_NADP </ci>
             <apply>
              <times/>
               <apply>
                <plus/>
                 <ci> C_NADP </ci>
                 <apply>
                  <times/>
                   <ci> K_NADP_1 </ci>
                   <ci> I_NADPH_1 </ci>
                 </apply>
               </apply>
               <ci> I_MgATP_1 </ci>
             </apply>
           </apply>
         </apply>
       </apply>
              
       <apply>
        <eq/>
         <ci> I_NADPH_1 </ci>
         <apply>
          <plus/>
           <cn cellml:units="dimensionless">1.0</cn>
           <apply>
            <divide/>
             <ci> C_NADPH </ci>
             <ci> Ki_NADPH_1 </ci>
           </apply>
         </apply>
       </apply>

       <apply>
        <eq/>
         <ci> I_MgATP_1 </ci>
         <apply>
          <plus/>
           <cn cellml:units="dimensionless">1.0</cn>
           <apply>
            <divide/>
             <ci> C_MgATP </ci>
             <ci> Ki_MgATP_1 </ci>
           </apply>
         </apply>
       </apply>
     </math>  
  </component>

  <component name="r6PGDH">
     <variable units="flux" public_interface="out" name="r6PGDH"/>
     
     <variable units="millimolar" public_interface="in" name="C_NADP"/>
     <variable units="millimolar" public_interface="in" name="C_NADPH"/>
     <variable units="millimolar" public_interface="in" name="C_MgATP"/>     

     <variable units="millimolar" name="K_NADP_2" initial_value="1.848"/>
     <variable units="millimolar" name="Ki_NADPH_2" initial_value="0.055"/>
     <variable units="millimolar" name="Ki_MgATP_2" initial_value="0.109"/>
     <variable units="dimensionless" name="I_NADPH_2"/>
     <variable units="dimensionless" name="I_MgATP_2"/>
     <variable units="flux" name="rmax_6PGDH" initial_value="0.654"/>
 
     <math xmlns="http://www.w3.org/1998/Math/MathML">
       <apply>
        <eq/>
         <ci> r6PGDH </ci>
         <apply>
          <times/>
           <ci> rmax_6PGDH </ci>
           <apply>
            <divide/>
             <ci> C_NADP </ci>
             <apply>
              <times/>
               <apply>
                <plus/>
                 <ci> C_NADP </ci>
                 <apply>
                  <times/>
                   <ci> K_NADP_2 </ci>
                   <ci> I_NADPH_2 </ci>
                 </apply>
               </apply>
               <ci> I_MgATP_2 </ci>
             </apply>
           </apply>
         </apply>
       </apply>

       <apply>
        <eq/>
         <ci> I_NADPH_2 </ci>
         <apply>
          <plus/>
           <cn cellml:units="dimensionless">1.0</cn>
           <apply>
            <divide/>
             <ci> C_NADPH </ci>
             <ci> Ki_NADPH_2 </ci>
           </apply>
         </apply>
       </apply>

       <apply>
        <eq/>
         <ci> I_MgATP_2 </ci>
         <apply>
          <plus/>
           <cn cellml:units="dimensionless">1.0</cn>
           <apply>
            <divide/>
             <ci> C_MgATP </ci>
             <ci> Ki_MgATP_2 </ci>
           </apply>
         </apply>
       </apply>
     </math>  
  </component>
  
  <component name="rR5PI">
     <variable units="flux" public_interface="out" name="rR5PI"/>
     
     <variable units="millimolar" public_interface="in" name="C_Ru5P"/>
     <variable units="millimole_per_second" name="rmax_R5PI" initial_value="0.57"/>
     
     <math xmlns="http://www.w3.org/1998/Math/MathML">
       <apply>
        <eq/>
         <ci> rR5PI </ci>
         <apply>
          <times/>
           <cn cellml:units="per_millimole">1</cn>
		   <ci> rmax_R5PI </ci>
           <ci> C_Ru5P </ci>
         </apply>
       </apply>
     </math>
  </component>

  <component name="rRu5PE">
     <variable units="flux" public_interface="out" name="rRu5PE"/>
     
     <variable units="millimolar" public_interface="in" name="C_Ru5P"/>
     <variable units="millimole_per_second" name="rmax_Ru5PE" initial_value="0.85"/>
     
     <math xmlns="http://www.w3.org/1998/Math/MathML">
       <apply>
        <eq/>
         <ci> rRu5PE </ci>
         <apply>
          <times/>
		   <cn cellml:units="per_millimole">1</cn>
           <ci> rmax_Ru5PE </ci>
           <ci> C_Ru5P </ci>
         </apply>
       </apply>
     </math>
  </component>

  <component name="rTKL1">
     <variable units="flux" public_interface="out" name="rTKL1"/>
     
     <variable units="millimolar" public_interface="in" name="C_X5P"/>
     <variable units="millimolar" public_interface="in" name="C_R5P"/>
     <variable units="millimole_per_second" name="rmax_TKL1" initial_value="3.24"/>
     
     <math xmlns="http://www.w3.org/1998/Math/MathML">
       <apply>
        <eq/>
         <ci> rTKL1 </ci>
         <apply>
          <times/>
		   <cn cellml:units="litre_per_millimole2">1</cn>
           <ci> rmax_TKL1 </ci>
           <ci> C_X5P </ci>
           <ci> C_R5P </ci>
         </apply>
       </apply>
     </math>
  </component>

  <component name="rTAL">
     <variable units="flux" public_interface="out" name="rTAL"/>
     
     <variable units="millimolar" public_interface="in" name="C_GAP"/>
     <variable units="millimolar" public_interface="in" name="C_S7P"/>
     <variable units="millimole_per_second" name="rmax_TAL" initial_value="3.0"/>
     
     <math xmlns="http://www.w3.org/1998/Math/MathML">
       <apply>
        <eq/>
         <ci> rTAL </ci>
         <apply>
          <times/>
           <cn cellml:units="litre_per_millimole2">1</cn>
		   <ci> rmax_TAL </ci>
           <ci> C_GAP </ci>
           <ci> C_S7P </ci>
         </apply>
       </apply>
     </math>
  </component>

  <component name="rTKL2">
     <variable units="flux" public_interface="out" name="rTKL2"/>
     
     <variable units="millimolar" public_interface="in" name="C_E4P"/>
     <variable units="millimolar" public_interface="in" name="C_X5P"/>
     <variable units="millimole_per_second" name="rmax_TKL2" initial_value="10.5"/>
     
     <math xmlns="http://www.w3.org/1998/Math/MathML">
       <apply>
        <eq/>
         <ci> rTKL2 </ci>
         <apply>
          <times/>
           <cn cellml:units="litre_per_millimole2">1</cn>
		   <ci> rmax_TKL2 </ci>
           <ci> C_E4P </ci>
           <ci> C_X5P </ci>
         </apply>
       </apply>
     </math>
  </component>

  <component name="rPKDA">
     <variable units="flux" public_interface="out" name="rPKDA"/>
     
     <variable units="millimolar" public_interface="in" name="C_E4P"/>
     
     <variable units="millimolar" name="K_PKDA" initial_value="0.0032"/>
     <variable units="millimole_per_second" name="rmax_PKDA" initial_value="0.004"/>
     
     <math xmlns="http://www.w3.org/1998/Math/MathML">
       <apply>
        <eq/>
         <ci> rPKDA </ci>
         <apply>
          <times/>
           <cn cellml:units="per_litre">1</cn>
		   <ci> rmax_PKDA </ci>
           <apply>
            <divide/>
             <ci> C_E4P </ci>
             <apply>
              <plus/>
               <ci> C_E4P </ci>
               <ci> K_PKDA </ci>
             </apply>
           </apply>
         </apply>
       </apply>
     </math>
  </component>

  <component name="rRPPK">
     <variable units="flux" public_interface="out" name="rRPPK"/>
     
     <variable units="millimolar" public_interface="in" name="C_R5P"/>
     
     <variable units="millimolar" name="K_RPPK" initial_value="0.0034"/>
     <variable units="millimole_per_second" name="rmax_RPPK" initial_value="0.003"/>
     
     <math xmlns="http://www.w3.org/1998/Math/MathML">
       <apply>
        <eq/>
         <ci> rRPPK </ci>
         <apply>
          <times/>
           <cn cellml:units="per_litre">1</cn>
		   <ci> rmax_RPPK </ci>
           <apply>
            <divide/>
             <ci> C_R5P </ci>
             <apply>
              <plus/>
               <ci> C_R5P </ci>
               <ci> K_RPPK </ci>
             </apply>
           </apply>
         </apply>
       </apply>
     </math>
  </component>

  <component name="rHK">
     <variable units="flux" name="rHK"/>
     
     <variable units="flux" public_interface="in" name="qs"/>
     
     <math xmlns="http://www.w3.org/1998/Math/MathML">
       <apply>
        <eq/>
         <ci> rHK </ci>
         <ci> qs </ci>
       </apply>
     </math>
  </component>

  <component name="rPGI">
     <variable units="flux" public_interface="out" name="rPGI"/>
     
	 <variable units="flux" public_interface="in" name="dC_G6P_dt"/>
     <variable units="per_hour" public_interface="in" name="mu"/>
     <variable units="flux" public_interface="in" name="rG6PDH"/>
     <variable units="millimolar" public_interface="in" name="C_G6P"/>
     <variable units="flux" public_interface="in" name="qs"/>
	 <variable units="second" public_interface="in" name="time"/>
     
     <math xmlns="http://www.w3.org/1998/Math/MathML">
       <apply>
        <eq/>
         <ci> rPGI </ci>
         <apply>
          <minus/>
           <ci> qs </ci> 
           <apply>
            <plus/>
             <ci> rG6PDH </ci>
             <apply>
              <times/>
               <ci> mu </ci>
               <ci> C_G6P </ci>
             </apply>
			 <ci> dC_G6P_dt </ci>
           </apply>
         </apply> 
       </apply>
     </math> 
  </component>

  <component name="model_constants">
    <variable units="per_hour" public_interface="out" name="mu" initial_value="1.0"/>
    <variable units="flux" public_interface="out" name="qs"/>
    <variable units="millimolar" public_interface="out" name="C_GAP" initial_value="0.064"/>

    <variable units="second" public_interface="in" name="time"/>
    
    <math xmlns="http://www.w3.org/1998/Math/MathML">
      <apply>
        <eq/>
        <ci> qs </ci>
        <piecewise>
          <piece>
            <cn cellml:units="flux"> 0.131 </cn>
            <apply>
              <lt/>
              <ci> time </ci>
              <cn cellml:units="second"> 0.0 </cn>
            </apply>
          </piece>
          <otherwise>
            <cn cellml:units="flux"> 0.546 </cn>
          </otherwise>
        </piecewise>
      </apply>   
    </math>
  </component>  

  <connection>
     <map_components component_2="environment" component_1="C_6PG"/>
     <map_variables variable_2="time" variable_1="time"/>
  </connection>

  <connection>
     <map_components component_2="environment" component_1="C_Ru5P"/>
     <map_variables variable_2="time" variable_1="time"/>
  </connection>

  <connection>
     <map_components component_2="environment" component_1="C_R5P"/>
     <map_variables variable_2="time" variable_1="time"/>
  </connection>

  <connection>
     <map_components component_2="environment" component_1="C_X5P"/>
     <map_variables variable_2="time" variable_1="time"/>
  </connection>

  <connection>
     <map_components component_2="environment" component_1="C_S7P"/>
     <map_variables variable_2="time" variable_1="time"/>
  </connection>

  <connection>
     <map_components component_2="environment" component_1="C_E4P"/>
     <map_variables variable_2="time" variable_1="time"/>
  </connection>

  <connection>
     <map_components component_2="environment" component_1="C_NADP"/>
     <map_variables variable_2="time" variable_1="time"/>
  </connection>

  <connection>
     <map_components component_2="environment" component_1="C_NADPH"/>
     <map_variables variable_2="time" variable_1="time"/>
  </connection>

  <connection>
     <map_components component_2="environment" component_1="C_MgATP"/>
     <map_variables variable_2="time" variable_1="time"/>
  </connection>

  <connection>
     <map_components component_2="environment" component_1="C_G6P"/>
     <map_variables variable_2="time" variable_1="time"/>
  </connection>

  <connection>
     <map_components component_2="environment" component_1="rPGI"/>
     <map_variables variable_2="time" variable_1="time"/>
  </connection>

  <connection>
     <map_components component_2="environment" component_1="model_constants"/>
     <map_variables variable_2="time" variable_1="time"/>
  </connection>

  <connection>
     <map_components component_2="rPGI" component_1="C_G6P"/>
     <map_variables variable_2="C_G6P" variable_1="C_G6P"/>
	 <map_variables variable_2="dC_G6P_dt" variable_1="dC_G6P_dt"/>
  </connection>

  <connection>
     <map_components component_2="rG6PDH" component_1="rPGI"/>
     <map_variables variable_2="rG6PDH" variable_1="rG6PDH"/>
  </connection>

  <connection>
     <map_components component_2="rG6PDH" component_1="C_6PG"/>
     <map_variables variable_2="rG6PDH" variable_1="rG6PDH"/>
  </connection>

  <connection>
     <map_components component_2="r6PGDH" component_1="C_6PG"/>
     <map_variables variable_2="r6PGDH" variable_1="r6PGDH"/>
  </connection>

  <connection>
     <map_components component_2="r6PGDH" component_1="C_Ru5P"/>
     <map_variables variable_2="r6PGDH" variable_1="r6PGDH"/>
  </connection>

  <connection>
     <map_components component_2="rR5PI" component_1="C_Ru5P"/>
     <map_variables variable_2="C_Ru5P" variable_1="C_Ru5P"/>
     <map_variables variable_2="rR5PI" variable_1="rR5PI"/>
  </connection>

  <connection>
     <map_components component_2="rRu5PE" component_1="C_Ru5P"/>
     <map_variables variable_2="C_Ru5P" variable_1="C_Ru5P"/>
     <map_variables variable_2="rRu5PE" variable_1="rRu5PE"/>
  </connection>

  <connection>
     <map_components component_2="rR5PI" component_1="C_R5P"/>
     <map_variables variable_2="rR5PI" variable_1="rR5PI"/>
  </connection>

  <connection>
     <map_components component_2="rTKL1" component_1="C_R5P"/>
     <map_variables variable_2="C_R5P" variable_1="C_R5P"/>
     <map_variables variable_2="rTKL1" variable_1="rTKL1"/>
  </connection>

  <connection>
     <map_components component_2="rRPPK" component_1="C_R5P"/>
     <map_variables variable_2="C_R5P" variable_1="C_R5P"/>
     <map_variables variable_2="rRPPK" variable_1="rRPPK"/>
  </connection>

  <connection>
     <map_components component_2="rRu5PE" component_1="C_X5P"/>
     <map_variables variable_2="rRu5PE" variable_1="rRu5PE"/>
  </connection>

  <connection>
     <map_components component_2="rTKL1" component_1="C_X5P"/>
     <map_variables variable_2="C_X5P" variable_1="C_X5P"/>
     <map_variables variable_2="rTKL1" variable_1="rTKL1"/>
  </connection>

  <connection>
     <map_components component_2="rTKL2" component_1="C_X5P"/>
     <map_variables variable_2="C_X5P" variable_1="C_X5P"/>
     <map_variables variable_2="rTKL2" variable_1="rTKL2"/>
  </connection>

  <connection>
     <map_components component_2="rTKL1" component_1="C_S7P"/>
     <map_variables variable_2="rTKL1" variable_1="rTKL1"/>
  </connection>

  <connection>
     <map_components component_2="rTAL" component_1="C_S7P"/>
     <map_variables variable_2="C_S7P" variable_1="C_S7P"/>
     <map_variables variable_2="rTAL" variable_1="rTAL"/>
  </connection>

  <connection>
     <map_components component_2="rTAL" component_1="C_E4P"/>
     <map_variables variable_2="rTAL" variable_1="rTAL"/>
  </connection>

  <connection>
     <map_components component_2="rTKL2" component_1="C_E4P"/>
     <map_variables variable_2="C_E4P" variable_1="C_E4P"/>
     <map_variables variable_2="rTKL2" variable_1="rTKL2"/>
  </connection>

  <connection>
     <map_components component_2="rPKDA" component_1="C_E4P"/>
     <map_variables variable_2="C_E4P" variable_1="C_E4P"/>
     <map_variables variable_2="rPKDA" variable_1="rPKDA"/>
  </connection>

  <connection>
     <map_components component_2="rG6PDH" component_1="C_NADP"/>
     <map_variables variable_2="C_NADP" variable_1="C_NADP"/>
  </connection>

  <connection>
     <map_components component_2="rG6PDH" component_1="C_NADPH"/>
     <map_variables variable_2="C_NADPH" variable_1="C_NADPH"/>
  </connection>

  <connection>
     <map_components component_2="rG6PDH" component_1="C_MgATP"/>
     <map_variables variable_2="C_MgATP" variable_1="C_MgATP"/>
  </connection>

  <connection>
     <map_components component_2="r6PGDH" component_1="C_NADP"/>
     <map_variables variable_2="C_NADP" variable_1="C_NADP"/>
  </connection>

  <connection>
     <map_components component_2="r6PGDH" component_1="C_NADPH"/>
     <map_variables variable_2="C_NADPH" variable_1="C_NADPH"/>
  </connection>

  <connection>
     <map_components component_2="r6PGDH" component_1="C_MgATP"/>
     <map_variables variable_2="C_MgATP" variable_1="C_MgATP"/>
  </connection>

  <connection>
    <map_components component_2="model_constants" component_1="C_6PG"/>
    <map_variables variable_2="mu" variable_1="mu"/>
  </connection>

  <connection>
    <map_components component_2="model_constants" component_1="C_Ru5P"/>
    <map_variables variable_2="mu" variable_1="mu"/>
  </connection>

  <connection>
    <map_components component_2="model_constants" component_1="C_R5P"/>
    <map_variables variable_2="mu" variable_1="mu"/>
  </connection>

  <connection>
    <map_components component_2="model_constants" component_1="C_X5P"/>
    <map_variables variable_2="mu" variable_1="mu"/>
  </connection>

  <connection>
    <map_components component_2="model_constants" component_1="C_S7P"/>
    <map_variables variable_2="mu" variable_1="mu"/>
  </connection>

  <connection>
    <map_components component_2="model_constants" component_1="C_E4P"/>
    <map_variables variable_2="mu" variable_1="mu"/>
  </connection>

  <connection>
    <map_components component_2="model_constants" component_1="rPGI"/>
    <map_variables variable_2="mu" variable_1="mu"/>
    <map_variables variable_2="qs" variable_1="qs"/>
  </connection>

  <connection>
    <map_components component_2="model_constants" component_1="rHK"/>
    <map_variables variable_2="qs" variable_1="qs"/>
  </connection>

  <connection>
    <map_components component_2="model_constants" component_1="rTAL"/>
    <map_variables variable_2="C_GAP" variable_1="C_GAP"/>
  </connection>
   


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    <dc:publisher>The University of Auckland, Bioengineering Institute</dc:publisher>
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    <dcterms:modified rdf:resource="rdf:#92a65782-cc1a-45de-9b0a-c37a44662457"/>
    <rdf:value>Replaced the reaction element with simple MathML equations to better describe the original publication.</rdf:value>
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    <dcterms:W3CDTF>2008-11-03T15:02:03+13:00</dcterms:W3CDTF>
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    <dc:creator rdf:resource="rdf:#5b6d1e48-8e34-4cc6-93c4-9201b35527bb"/>
    <dc:title>In Vivo Dynamics of the Pentose Phosphate Pathway in Saccharomyces cerevisiae</dc:title>
    <bqs:volume>1</bqs:volume>
    <bqs:first_page>128</bqs:first_page>
    <bqs:Journal rdf:resource="rdf:#b790e299-3675-4c56-9143-fdee6cc3decf"/>
    <dcterms:issued rdf:resource="rdf:#62bbfdad-62e2-4d55-9ab9-dda00a8acbec"/>
    <bqs:last_page>140</bqs:last_page>
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    <dcterms:alternative>glucose-6-phosphate</dcterms:alternative>
    <dc:title>G6P</dc:title>
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    <ns7:boundIntervals rdf:resource="rdf:#$meq3i2"/>
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    <dcterms:alternative>erythrose 4-phosphate</dcterms:alternative>
    <dc:title>C_E4P</dc:title>
  </rdf:Description>
  <rdf:Description rdf:about="rdf:#9add5da4-149b-4f23-9953-9920b9b11d5b">
    <dcterms:W3CDTF>2007-06-20T11:42:32+12:00</dcterms:W3CDTF>
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  <rdf:Description rdf:about="rdf:#2383ca30-7756-46dd-a0ad-061c94596d5c">
    <vCard:Given>Catherine</vCard:Given>
    <vCard:Family>Lloyd</vCard:Family>
    <vCard:Other>May</vCard:Other>
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  <rdf:Description rdf:about="rdf:#090a4a67-9f67-47e1-b29f-c49d77c59f5a">
    <vCard:Given>Matthias</vCard:Given>
    <vCard:Family>Reuss</vCard:Family>
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  <rdf:Description rdf:about="rdf:#95dd941a-163c-431a-b88f-12c6a1d0e687">
    <vCard:Given>Catherine</vCard:Given>
    <vCard:Family>Lloyd</vCard:Family>
    <vCard:Other>May</vCard:Other>
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    <vCard:ORG rdf:resource="rdf:#9e5830e0-e822-47bb-a778-79c1fb5fdf62"/>
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  <rdf:Description rdf:about="rdf:#77017cdb-b868-4d31-8902-c2d2aeee45dc">
    <vCard:FN>Catherine Lloyd</vCard:FN>
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  <rdf:Description rdf:about="rdf:#e895912c-efb1-4220-b652-65afac577f3e">
    <dcterms:W3CDTF>2007-06-13T00:00:00+00:00</dcterms:W3CDTF>
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  <rdf:Description rdf:about="rdf:#62bbfdad-62e2-4d55-9ab9-dda00a8acbec">
    <dcterms:W3CDTF>1999-04</dcterms:W3CDTF>
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  <rdf:Description rdf:about="rdf:#8593756e-a98e-4f89-a344-3b0e1b07f4a3">
    <vCard:Given>Yizhi</vCard:Given>
    <vCard:Family>Cai</vCard:Family>
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    <bqs:Pubmed_id>10935926</bqs:Pubmed_id>
    <bqs:JournalArticle rdf:resource="rdf:#9b3b7cc5-c9ff-4c7e-b629-394a5ae89a75"/>
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    <vCard:Given>Anja</vCard:Given>
    <vCard:Family>Baumeister</vCard:Family>
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  <rdf:Description rdf:about="#C_6PG">
    <dcterms:alternative>6-phosphogluconate</dcterms:alternative>
    <dc:title>C_6PG</dc:title>
  </rdf:Description>
  <rdf:Description rdf:about="rdf:#d3a4410c-487c-4bdd-81b6-a73d067fa822">
    <dc:creator rdf:resource="rdf:#77017cdb-b868-4d31-8902-c2d2aeee45dc"/>
    <rdf:value>This is the CellML description of Vaseghi et al's mathematical model of the pentose phosphate pathway in the yeast Saccharomyces cerevisiae (1999).</rdf:value>
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  <rdf:Description rdf:about="#pentose_phosphate_pathway_1999_version02">
    <ns7:simulation rdf:resource="rdf:#$leq3i2"/>
    <dc:title>A model of the pentose phosphate pathway in the yeast Saccharomyces
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    <dc:title>Metabolic Engineering</dc:title>
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  <rdf:Description rdf:about="rdf:#c1c096b7-a8dd-41f9-af3e-3c4f5d6e48f6">
    <vCard:FN>Catherine Lloyd</vCard:FN>
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    <dc:creator rdf:resource="rdf:#c1c096b7-a8dd-41f9-af3e-3c4f5d6e48f6"/>
    <rdf:value>This CellML model is known to run in both PCEnv and COR, however at present it does not seem to be recreating the published results - possibly beause we need to include a description of a glucose pulse in the CellML model.  We are continuing to work on the model. The units have been checked and they are consistent.</rdf:value>
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  <rdf:Description rdf:about="rdf:#cc31d5c5-655d-4015-a38d-ec5821f8d595">
    <vCard:Given>Catherine</vCard:Given>
    <vCard:Family>Lloyd</vCard:Family>
    <vCard:Other>May</vCard:Other>
  </rdf:Description>
  <rdf:Description rdf:about="rdf:#92a65782-cc1a-45de-9b0a-c37a44662457">
    <dcterms:W3CDTF>2007-06-14T08:03:30+12:00</dcterms:W3CDTF>
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  <rdf:Description rdf:about="rdf:#2774bd1a-79c5-47f6-a5fb-41e06f0b14d9">
    <vCard:Given>Manfred</vCard:Given>
    <vCard:Family>Rizzi</vCard:Family>
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  <rdf:Description rdf:about="rdf:#$meq3i2">
    <rdf:rest rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>
    <rdf:first rdf:resource="rdf:#$neq3i2"/>
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  <rdf:Description rdf:about="rdf:#$neq3i2">
    <ns7:endingValue>100000.0</ns7:endingValue>
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  <rdf:Description rdf:about="rdf:#31b3aca3-5483-47f2-b138-42e7433ef672">
    <vCard:Given>Sam</vCard:Given>
    <vCard:Family>Vaseghi</vCard:Family>
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  <rdf:Description rdf:about="rdf:#ab54e2ad-439b-47e5-b84a-c5046dfbce93">
    <dcterms:modified rdf:resource="rdf:#9add5da4-149b-4f23-9953-9920b9b11d5b"/>
    <rdf:value>Corrected some of the equations so the CellML model now reflects the model in the original publication.</rdf:value>
    <cmeta:modifier rdf:resource="rdf:#6d4b2a1f-acf3-4ee5-a514-a3070f61a9b5"/>
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  <rdf:Description rdf:about="rdf:#9e5830e0-e822-47bb-a778-79c1fb5fdf62">
    <vCard:Orgname>The University of Auckland</vCard:Orgname>
    <vCard:Orgunit>The Bioengineering Institute</vCard:Orgunit>
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  <rdf:Description rdf:about="#C_S7P">
    <dcterms:alternative>sedoheptulose 7-phosphate</dcterms:alternative>
    <dc:title>C_S7P</dc:title>
  </rdf:Description>
  <rdf:Description rdf:about="#C_Ru5P">
    <dcterms:alternative>ribulose 5-phosphate</dcterms:alternative>
    <dc:title>C_Ru5P</dc:title>
  </rdf:Description>
  <rdf:Description rdf:about="rdf:#7016c3d4-66c7-4c2d-ad8e-dc08d5e1669e">
    <dcterms:modified rdf:resource="rdf:#19988b83-cd26-49d2-957f-b9a5788a453e"/>
    <rdf:value>Added some initial conditions to the ODEs, altered some equations to better reflect the paper, and unit balanced several equations.</rdf:value>
    <cmeta:modifier rdf:resource="rdf:#7395f4f4-392b-4d42-8e1e-b04265b24c63"/>
  </rdf:Description>
  <rdf:Description rdf:about="#C_X5P">
    <dcterms:alternative>xylulose 5-phosphate</dcterms:alternative>
    <dc:title>C_X5P</dc:title>
  </rdf:Description>
  <rdf:Description rdf:about="rdf:#edc00ec2-458a-4b74-ab12-bfa8bed8d80f">
    <rdf:type rdf:resource="http://www.cellml.org/bqs/1.0#Person"/>
    <vCard:N rdf:resource="rdf:#1bf29046-443d-4e9f-907b-3e221b2b48c3"/>
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    <bqs:subject_type>keyword</bqs:subject_type>
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      <rdf:Bag>
        <rdf:li>metabolism</rdf:li>
        <rdf:li>yeast</rdf:li>
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  </rdf:Description>
  <rdf:Description rdf:about="#R5P">
    <dcterms:alternative>ribose 5-phosphate</dcterms:alternative>
    <dc:title>C_R5P</dc:title>
  </rdf:Description>
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