Location: Hatakeyama, Kimura, Naka, Kawasaki, Yumoto, Ichikawa, Kim, Saito, Saeki, Shirouzu, Yokoyama, Konagaya, 2003 @ e5fc28738fa1 / hatakeyama_kimura_naka_kawasaki_yumoto_ichikawa_kim_saito_saeki_shirouzu_yokoyama_konagaya_2003.cellml

Author:
pmr2.import <nobody@models.cellml.org>
Date:
2007-08-27 00:03:04+12:00
Desc:
committing version01 of hatakeyama_kimura_naka_kawasaki_yumoto_ichikawa_kim_saito_saeki_shirouzu_yokoyama_konagaya_2003
Permanent Source URI:
https://models.cellml.org/workspace/hatakeyama_kimura_naka_kawasaki_yumoto_ichikawa_kim_saito_saeki_shirouzu_yokoyama_konagaya_2003/rawfile/e5fc28738fa147afd3e8a1b702a8b52cee8dc515/hatakeyama_kimura_naka_kawasaki_yumoto_ichikawa_kim_saito_saeki_shirouzu_yokoyama_konagaya_2003.cellml

<?xml version='1.0' encoding='utf-8'?>
<!--
This CellML file was generated on 20/06/2007 at 12:39:18 at a.m. using:

COR (0.9.31.649)
Copyright 2002-2007 Dr Alan Garny
http://COR.physiol.ox.ac.uk/ - COR@physiol.ox.ac.uk

CellML 1.0 was used to generate this cellular model
http://www.CellML.org/
--><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="bhalla_model_1999" name="bi_model_1999_version01">

<documentation xmlns="http://cellml.org/tmp-documentation">
<article>
  <articleinfo>
  <title>A computational model on the modulation of mitogen-activated protein kinase (MAPK) and Akt pathways in heregulin-induced ErbB signalling</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 version of the model has been checked and it runs in PCEnv.
    </para>
  </section>
  <sect1 id="sec_structure">
<title>Model Structure</title>

<para>
ErbB receptor tyrosine kinases play an essential role in the proliferation and differentiation of cells.  The ErbB receptor family includes ErbB1 - also known as the epidermal growth factor receptor (EGFR) - and the signalling pathways which involve this receptor have been extensively analysed, both experimentally and also via mathematical modelling.  ErbB receptors share a common ability to bind a diverse range of ligands, in turn producing a wide range of biological responses.  In the study described here, Mariko Hatakeyama <emphasis>et al.</emphasis> examined heregulin (HRG)-induced signal transduction of the ErbB4 receptor, and they produced a mathematical model to capture the features of the signal transduction cascade (described in more detail in the figure below).  This model is described here in CellML.
</para>

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

<para>
<ulink url="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&amp;pubmedid=12691603">A computational model on the modulation of mitogen-activated protein kinase (MAPK) and Akt pathways in heregulin-induced ErbB signalling</ulink>, Mariko Hatakeyama, Shuhei Kimura, Takashi Naka, Takuji Kawasaki, Noriko Yumoto, Mio Ichikawa, Jae-Hoon Kim, Kazuki Saito, Mihoro Saeki, Mikako Shirouzu, Shigeyuki Yokoyama, and Akihiko Konagaya, 2003, <ulink url="http://www.biochemj.org/bj/">
            <emphasis>The Biochemical Journal</emphasis>
          </ulink>, 373, 451-463. (A <ulink url="http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=12691603&amp;blobtype=pdf">PDF</ulink> of the article is available free for download from the PubMed website.)  <ulink url="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;list_uids=16445978&amp;dopt=Abstract">PubMed ID: 12691603</ulink> 
</para>


<informalfigure float="0" id="fig_pathway_diagram">
<mediaobject>
  <imageobject>
    <objectinfo>
      <title>model diagram</title>
    </objectinfo>
    <imagedata fileref="hatakeyama_networkdiagram_scaled_2003.png"/>
  </imageobject>
</mediaobject>
<caption>A schematic diagram of the complete signalling network.</caption>
</informalfigure>

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




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                     <ci>kf25</ci>
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                  <apply>
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                     <ci>kb25</ci>
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            </apply>
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         <apply>
            <eq/>
            <apply>
               <diff/>
               <bvar>
                  <ci>t</ci>
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               <ci>PI3Kstar</ci>
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            <apply>
               <minus/>
               <apply>
                  <minus/>
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                     <times/>
                     <ci>kf25</ci>
                     <ci>R_PI3Kstar</ci>
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                  <apply>
                     <times/>
                     <ci>kb25</ci>
                     <ci>RP</ci>
                     <ci>PI3Kstar</ci>
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               </apply>
               <apply>
                  <divide/>
                  <apply>
                     <times/>
                     <ci>V26</ci>
                     <ci>PI3Kstar</ci>
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                  <apply>
                     <plus/>
                     <ci>k26</ci>
                     <ci>PI3Kstar</ci>
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               </apply>
            </apply>
         </apply>
      </math>
   </component>
   <component name="RasGDPtoRasGTP">
      <variable units="s" public_interface="in" name="t"/>
      <variable units="nm" public_interface="in" name="ShGS"/>
      <variable units="nm" public_interface="out" name="RasGTP" initial_value="0"/>
      <variable units="per_nm_s" name="kf11" initial_value="0.222"/>
      <variable units="nm" name="k11" initial_value="0.181"/>
      <variable units="nm_per_s" name="V12" initial_value="0.289"/>
      <variable units="nm" name="k12" initial_value="0.0571"/>
      <variable units="nm" name="RasGDP" initial_value="120"/>
      <math xmlns="http://www.w3.org/1998/Math/MathML">
         <apply>
            <eq/>
            <apply>
               <diff/>
               <bvar>
                  <ci>t</ci>
               </bvar>
               <ci>RasGDP</ci>
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            <apply>
               <plus/>
               <apply>
                  <minus/>
                  <apply>
                     <divide/>
                     <apply>
                        <times/>
                        <ci>kf11</ci>
                        <ci>ShGS</ci>
                        <ci>RasGDP</ci>
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                        <plus/>
                        <ci>k11</ci>
                        <ci>RasGDP</ci>
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               <apply>
                  <divide/>
                  <apply>
                     <times/>
                     <ci>V12</ci>
                     <ci>RasGTP</ci>
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                  <apply>
                     <plus/>
                     <ci>k12</ci>
                     <ci>RasGTP</ci>
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            <eq/>
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               <diff/>
               <bvar>
                  <ci>t</ci>
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               <ci>RasGTP</ci>
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            <apply>
               <minus/>
               <apply>
                  <divide/>
                  <apply>
                     <times/>
                     <ci>kf11</ci>
                     <ci>ShGS</ci>
                     <ci>RasGDP</ci>
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                  <apply>
                     <plus/>
                     <ci>k11</ci>
                     <ci>RasGDP</ci>
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               <apply>
                  <divide/>
                  <apply>
                     <times/>
                     <ci>V12</ci>
                     <ci>RasGTP</ci>
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                  <apply>
                     <plus/>
                     <ci>k12</ci>
                     <ci>RasGTP</ci>
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               </apply>
            </apply>
         </apply>
      </math>
   </component>
   <component name="RAF">
      <variable units="s" public_interface="in" name="t"/>
      <variable units="nm" public_interface="in" name="RasGTP"/>
      <variable units="nm" public_interface="in" name="Akt_PIPP"/>
      <variable units="nm" public_interface="out" name="RAF_star" initial_value="100"/>
      <variable units="per_nm_s" name="kf13" initial_value="1.53"/>
      <variable units="nm" name="k13" initial_value="11.7"/>
      <variable units="per_nm_s" name="kf14" initial_value="0.00673"/>
      <variable units="nm" name="k14" initial_value="8.07"/>
      <variable units="nm" name="E" initial_value="7"/>
      <variable units="nm" name="RAF" initial_value="0"/>
      <math xmlns="http://www.w3.org/1998/Math/MathML">
         <apply>
            <eq/>
            <apply>
               <diff/>
               <bvar>
                  <ci>t</ci>
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               <ci>RAF</ci>
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            <apply>
               <minus/>
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                  <divide/>
                  <apply>
                     <times/>
                     <ci>kf14</ci>
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                        <plus/>
                        <ci>Akt_PIPP</ci>
                        <ci>E</ci>
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                     <plus/>
                     <ci>k14</ci>
                     <ci>RAF_star</ci>
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               <apply>
                  <divide/>
                  <apply>
                     <times/>
                     <ci>kf13</ci>
                     <ci>RasGTP</ci>
                     <ci>RAF</ci>
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                     <plus/>
                     <ci>k13</ci>
                     <ci>RAF</ci>
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            </apply>
         </apply>
         <apply>
            <eq/>
            <apply>
               <diff/>
               <bvar>
                  <ci>t</ci>
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               <ci>RAF_star</ci>
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            <apply>
               <plus/>
               <apply>
                  <minus/>
                  <apply>
                     <divide/>
                     <apply>
                        <times/>
                        <ci>kf14</ci>
                        <apply>
                           <plus/>
                           <ci>Akt_PIPP</ci>
                           <ci>E</ci>
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                        <ci>RAF_star</ci>
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                     <apply>
                        <plus/>
                        <ci>k14</ci>
                        <ci>RAF_star</ci>
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                  </apply>
               </apply>
               <apply>
                  <divide/>
                  <apply>
                     <times/>
                     <ci>kf13</ci>
                     <ci>RasGTP</ci>
                     <ci>RAF</ci>
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                  <apply>
                     <plus/>
                     <ci>k13</ci>
                     <ci>RAF</ci>
                  </apply>
               </apply>
            </apply>
         </apply>
      </math>
   </component>
   <component name="Akt">
      <variable units="s" public_interface="in" name="t"/>
      <variable units="nm" public_interface="in" name="PI3Kstar"/>
      <variable units="nm" public_interface="out" name="Akt_PIPP"/>
      <variable units="nm" public_interface="in" name="MEKP"/>
      <variable units="nm" public_interface="in" name="MEKPP"/>
      <variable units="per_nm_s" name="kf27" initial_value="16.9"/>
      <variable units="nm" name="k27" initial_value="39.1"/>
      <variable units="nm_per_s" name="V28" initial_value="17000"/>
      <variable units="nm" name="k28" initial_value="9.02"/>
      <variable units="per_nm_s" name="kf29" initial_value="507"/>
      <variable units="per_s" name="kb29" initial_value="234"/>
      <variable units="nm_per_s" name="V30" initial_value="20000"/>
      <variable units="nm" name="k30" initial_value="80000"/>
      <variable units="per_nm_s" name="kf31" initial_value="0.107"/>
      <variable units="nm" name="k31" initial_value="4.35"/>
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      <variable units="nm" name="k32" initial_value="80000"/>
      <variable units="per_nm_s" name="kf33" initial_value="0.211"/>
      <variable units="nm" name="k33" initial_value="12"/>
      <variable units="nm" name="k16" initial_value="2200"/>
      <variable units="nm" name="k18" initial_value="60"/>
      <variable units="nm" name="P" initial_value="800"/>
      <variable units="nm" name="PIP3" initial_value="0"/>
      <variable units="nm" name="Akt" initial_value="10"/>
      <variable units="nm" name="Akt_PIP3" initial_value="0"/>
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      <variable units="nm" public_interface="out" name="Akt_PIP" initial_value="0"/>
      <variable units="nm" name="PP2A" initial_value="11.4"/>
      <variable units="dimensionless" name="one" initial_value="1"/>
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         <apply>
            <eq/>
            <apply>
               <diff/>
               <bvar>
                  <ci>t</ci>
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               <ci>P</ci>
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            <apply>
               <minus/>
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                  <divide/>
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                     <times/>
                     <ci>V28</ci>
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                     <ci>k28</ci>
                     <ci>PIP3</ci>
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                  <divide/>
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                     <times/>
                     <ci>kf27</ci>
                     <ci>PI3Kstar</ci>
                     <ci>P</ci>
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                     <plus/>
                     <ci>k27</ci>
                     <ci>P</ci>
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            <eq/>
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               <diff/>
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                  <ci>t</ci>
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               <ci>PIP3</ci>
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               <minus/>
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                  <plus/>
                  <apply>
                     <minus/>
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                        <divide/>
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                           <times/>
                           <ci>V28</ci>
                           <ci>PIP3</ci>
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                           <plus/>
                           <ci>k28</ci>
                           <ci>PIP3</ci>
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                  <apply>
                     <divide/>
                     <apply>
                        <times/>
                        <ci>kf27</ci>
                        <ci>PI3Kstar</ci>
                        <ci>P</ci>
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                     <apply>
                        <plus/>
                        <ci>k27</ci>
                        <ci>P</ci>
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               <apply>
                  <minus/>
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                     <times/>
                     <ci>kf29</ci>
                     <ci>PIP3</ci>
                     <ci>Akt</ci>
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                  <apply>
                     <times/>
                     <ci>kb29</ci>
                     <ci>Akt_PIP3</ci>
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               </apply>
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         <apply>
            <eq/>
            <apply>
               <diff/>
               <bvar>
                  <ci>t</ci>
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               <ci>Akt</ci>
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            <apply>
               <minus/>
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                  <minus/>
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                     <times/>
                     <ci>kf29</ci>
                     <ci>PIP3</ci>
                     <ci>Akt</ci>
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                  <apply>
                     <times/>
                     <ci>kb29</ci>
                     <ci>Akt_PIP3</ci>
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               </apply>
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            <eq/>
            <apply>
               <diff/>
               <bvar>
                  <ci>t</ci>
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               <ci>Akt_PIP3</ci>
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               <plus/>
               <apply>
                  <minus/>
                  <apply>
                     <minus/>
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                        <times/>
                        <ci>kf29</ci>
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                        <ci>Akt</ci>
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                        <times/>
                        <ci>kb29</ci>
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                        <times/>
                        <ci>V30</ci>
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                        <plus/>
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                           <times/>
                           <ci>k30</ci>
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                              <ci>one</ci>
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                                 <divide/>
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                     <ci>kf31</ci>
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                        <times/>
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                           <ci>one</ci>
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                              <divide/>
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                              <ci>k16</ci>
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                              <ci>k18</ci>
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                        <divide/>
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                           <ci>V30</ci>
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                           <plus/>
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                              <times/>
                              <ci>k30</ci>
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                                    <divide/>
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                     <apply>
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                           <times/>
                           <ci>kf31</ci>
                           <ci>PP2A</ci>
                           <ci>Akt_PIP</ci>
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                           <plus/>
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                              <times/>
                              <ci>k31</ci>
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                                 <plus/>
                                 <ci>one</ci>
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                                    <divide/>
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                                    <ci>k16</ci>
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                                 <apply>
                                    <divide/>
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                                    <ci>k18</ci>
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                                 <apply>
                                    <divide/>
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                                    <ci>k33</ci>
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                           <ci>Akt_PIP</ci>
                        </apply>
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                  <apply>
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                        <times/>
                        <ci>V32</ci>
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                        <plus/>
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                           <times/>
                           <ci>k32</ci>
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                              <plus/>
                              <ci>one</ci>
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                                 <divide/>
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                                 <ci>k30</ci>
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                     <times/>
                     <ci>kf33</ci>
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                     <ci>Akt_PIPP</ci>
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                     <plus/>
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                        <times/>
                        <ci>k33</ci>
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                           <plus/>
                           <ci>one</ci>
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                              <divide/>
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                              <ci>k16</ci>
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                              <divide/>
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                        <times/>
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                           <ci>one</ci>
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      <variable units="nm" public_interface="in" name="Akt_PIP"/>
      <variable units="nm" public_interface="in" name="Akt_PIPP"/>
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      <variable units="per_nm_s" name="kf17" initial_value="2.9"/>
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               <diff/>
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                  <ci>t</ci>
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               <plus/>
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                  <minus/>
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                        <times/>
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                        <plus/>
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                           <times/>
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                              <plus/>
                              <ci>one</ci>
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                                 <divide/>
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                                 <ci>k17</ci>
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                     <times/>
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                     <ci>MEKP</ci>
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                     <plus/>
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                        <times/>
                        <ci>k16</ci>
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                           <plus/>
                           <ci>one</ci>
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                              <divide/>
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                              <ci>k18</ci>
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                           <apply>
                              <divide/>
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                              <ci>k31</ci>
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                              <divide/>
                              <ci>Akt_PIPP</ci>
                              <ci>k33</ci>
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                     <ci>MEKP</ci>
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            <eq/>
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               <diff/>
               <bvar>
                  <ci>t</ci>
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               <ci>MEKP</ci>
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               <plus/>
               <apply>
                  <minus/>
                  <apply>
                     <minus/>
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                        <divide/>
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                           <times/>
                           <ci>kf15</ci>
                           <ci>RAF_star</ci>
                           <ci>MEK</ci>
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                        <apply>
                           <plus/>
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                              <times/>
                              <ci>k15</ci>
                              <apply>
                                 <plus/>
                                 <ci>one</ci>
                                 <apply>
                                    <divide/>
                                    <ci>MEKP</ci>
                                    <ci>k17</ci>
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                           <ci>MEK</ci>
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                     <apply>
                        <divide/>
                        <apply>
                           <times/>
                           <ci>kf16</ci>
                           <ci>PP2A</ci>
                           <ci>MEKP</ci>
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                        <apply>
                           <plus/>
                           <apply>
                              <times/>
                              <ci>k16</ci>
                              <apply>
                                 <plus/>
                                 <ci>one</ci>
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                                    <divide/>
                                    <ci>MEKPP</ci>
                                    <ci>k18</ci>
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                                 <apply>
                                    <divide/>
                                    <ci>Akt_PIP</ci>
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    <vCard:Given>Mikako</vCard:Given>
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    <dc:creator rdf:resource="rdf:#ee118ad6-fcc9-4e1f-a1e6-1bc6c1b98aea"/>
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    <vCard:Given>Mariko</vCard:Given>
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  <rdf:Description rdf:about="rdf:#cde4f27f-f734-44cc-bd3f-22c8792ccd12">
    <dc:title>The Biochemical Journal</dc:title>
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    <vCard:Given>Mio</vCard:Given>
    <vCard:Family>Ichikawa</vCard:Family>
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