Location: Vempati, Karagiannis, Popel, 2007 @ 17c90dc4e1b1 / vempati_karagiannis_popel_2007.cellml

Author:
Catherine Lloyd <c.lloyd@auckland.ac.nz>
Date:
2010-07-30 19:56:28+12:00
Desc:
Fixed broken structure of the documentation.
Permanent Source URI:
https://models.cellml.org/workspace/vempati_karagiannis_popel_2007/rawfile/17c90dc4e1b18a662af86c12379323ea21b0481b/vempati_karagiannis_popel_2007.cellml

<?xml version="1.0"?>
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	<documentation xmlns="http://cellml.org/tmp-documentation">
		<article>
			<articleinfo>
				<title>A Biochemical Model of Matrix Metalloproteinase 9 Activation and Inhibition</title>
				<author>
					<firstname>Catherine</firstname>
					<surname>Lloyd</surname>
					<affiliation>
						<shortaffil>Auckland Bioengineering Institute, The 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 OpenCell and COR to recreate the results in the published paper.  The units have been checked and they are consistent. Please note that many of the figures in the paper are complex and requite special simulation conditions. This particular CellML model represents the basic core model presented in the paper. Initial conditions can be modified to generate more complex results.  We thank the model author Prakash Vempati for his assistance in getting this CellML model to run.
          </para>
  </section>
  <sect1 id="sec_structure">
				<title>Model Structure</title>

<para>ABSTRACT: Matrix metalloproteinases (MMPs) are a class of extracellular and membrane-bound proteases involved in an array of physiological processes including angiogenesis. We present a detailed computational model of MMP9 activation and inhibition. Our model is validated to existing biochemical experimental data. We determine kinetic rate constants for the processes of MMP9 activation by MMP3, MMP10, MMP13, and trypsin, inhibition by the tissue inhibitors of metalloproteinases (TIMPs) TIMP1 and TIMP2, and MMP9 deactivation. This computational approach allows us to investigate discrepancies in our understanding of the MMP9</para>
				
<para>
The original paper reference is cited below:
</para>
				<para>
A Biochemical Model of Matrix Metalloproteinase 9 Activation and Inhibition, Prakash Vempati, Emmanouil D. Karagiannis, and Aleksander S. Popel , 2007, <emphasis>The Journal of Biological Chemistry</emphasis>
, 282, 37585-37596.  <ulink url="http://www.ncbi.nlm.nih.gov/pubmed/17848556">PubMed ID: 17848556</ulink>
				</para>
				
<informalfigure float="0" id="fig_reaction_diagram">
<mediaobject>
  <imageobject>
    <objectinfo>
      <title>model diagram</title>
    </objectinfo>
    <imagedata fileref="vempati_2007.png"/>
  </imageobject>
</mediaobject>
<caption>Schematic diagram of the biochemical reaction network for MMP9 activation and inhibition spanning MMP9, MMP3, TIMP1, and TIMP2.  pM9, pro-MMP9; M3, MMP3; M9, MMP9; T1, TIMP1; T2, TIMP2; Tr, Trypsin.</caption>
</informalfigure>
				
				
			</sect1>
		</article>
	</documentation>
	
	
	
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                  <ci>v3</ci>
                  <ci>v5</ci>
                  <ci>v10</ci>
                  <ci>v12</ci>
               </apply>
            </apply>
         </apply>
      </math>
   </component>
   <component name="M3_pM9">
      <variable cmeta:id="M3_pM9_M3_pM9" initial_value="0" name="M3_pM9" public_interface="out" units="molar"/>
      <variable name="v1" public_interface="in" units="flux"/>
      <variable name="v2" public_interface="in" units="flux"/>
      <variable name="time" public_interface="in" units="second"/>
      <math xmlns="http://www.w3.org/1998/Math/MathML">
         <apply>
            <eq/>
            <apply>
               <diff/>
               <bvar>
                  <ci>time</ci>
               </bvar>
               <ci>M3_pM9</ci>
            </apply>
            <apply>
               <minus/>
               <ci>v1</ci>
               <ci>v2</ci>
            </apply>
         </apply>
      </math>
   </component>
   <component name="T1">
      <variable cmeta:id="T1_T1" initial_value="3e-7" name="T1" public_interface="out" units="molar"/>
      <variable name="v3" public_interface="in" units="flux"/>
      <variable name="v4" public_interface="in" units="flux"/>
      <variable name="v7" public_interface="in" units="flux"/>
      <variable name="time" public_interface="in" units="second"/>
      <math xmlns="http://www.w3.org/1998/Math/MathML">
         <apply>
            <eq/>
            <apply>
               <diff/>
               <bvar>
                  <ci>time</ci>
               </bvar>
               <ci>T1</ci>
            </apply>
            <apply>
               <minus/>
               <apply>
                  <plus/>
                  <ci>v3</ci>
                  <ci>v4</ci>
                  <ci>v7</ci>
               </apply>
            </apply>
         </apply>
      </math>
   </component>
   <component name="M3_T1">
      <variable cmeta:id="M3_T1_M3_T1" initial_value="0" name="M3_T1" public_interface="out" units="molar"/>
      <variable name="v3" public_interface="in" units="flux"/>
      <variable name="v9" public_interface="in" units="flux"/>
      <variable name="v11" public_interface="in" units="flux"/>
      <variable name="time" public_interface="in" units="second"/>
      <math xmlns="http://www.w3.org/1998/Math/MathML">
         <apply>
            <eq/>
            <apply>
               <diff/>
               <bvar>
                  <ci>time</ci>
               </bvar>
               <ci>M3_T1</ci>
            </apply>
            <apply>
               <minus/>
               <apply>
                  <plus/>
                  <ci>v3</ci>
                  <ci>v9</ci>
               </apply>
               <ci>v11</ci>
            </apply>
         </apply>
      </math>
   </component>
   <component name="pM9_T1">
      <variable cmeta:id="pM9_T1_pM9_T1" initial_value="0" name="pM9_T1" public_interface="out" units="molar"/>
      <variable name="v4" public_interface="in" units="flux"/>
      <variable name="v5" public_interface="in" units="flux"/>
      <variable name="v10" public_interface="in" units="flux"/>
      <variable name="v17" public_interface="in" units="flux"/>
      <variable name="time" public_interface="in" units="second"/>
      <math xmlns="http://www.w3.org/1998/Math/MathML">
         <apply>
            <eq/>
            <apply>
               <diff/>
               <bvar>
                  <ci>time</ci>
               </bvar>
               <ci>pM9_T1</ci>
            </apply>
            <apply>
               <minus/>
               <ci>v4</ci>
               <apply>
                  <plus/>
                  <ci>v5</ci>
                  <ci>v10</ci>
                  <ci>v17</ci>
               </apply>
            </apply>
         </apply>
      </math>
   </component>
   <component name="M3_pM9_T1">
      <variable cmeta:id="M3_pM9_T1_M3_pM9_T1" initial_value="0" name="M3_pM9_T1" public_interface="out" units="molar"/>
      <variable name="v5" public_interface="in" units="flux"/>
      <variable name="v6" public_interface="in" units="flux"/>
      <variable name="time" public_interface="in" units="second"/>
      <math xmlns="http://www.w3.org/1998/Math/MathML">
         <apply>
            <eq/>
            <apply>
               <diff/>
               <bvar>
                  <ci>time</ci>
               </bvar>
               <ci>M3_pM9_T1</ci>
            </apply>
            <apply>
               <minus/>
               <ci>v5</ci>
               <ci>v6</ci>
            </apply>
         </apply>
      </math>
   </component>
   <component name="M9_T1_star">
      <variable cmeta:id="M9_T1_star_M9_T1_star" initial_value="0" name="M9_T1_star" public_interface="out" units="molar"/>
      <variable name="v7" public_interface="in" units="flux"/>
      <variable name="v14" public_interface="in" units="flux"/>
      <variable name="v8" public_interface="in" units="flux"/>
      <variable name="time" public_interface="in" units="second"/>
      <math xmlns="http://www.w3.org/1998/Math/MathML">
         <apply>
            <eq/>
            <apply>
               <diff/>
               <bvar>
                  <ci>time</ci>
               </bvar>
               <ci>M9_T1_star</ci>
            </apply>
            <apply>
               <minus/>
               <apply>
                  <plus/>
                  <ci>v7</ci>
                  <ci>v14</ci>
               </apply>
               <ci>v8</ci>
            </apply>
         </apply>
      </math>
   </component>
   <component name="M9">
      <variable cmeta:id="M9_M9" initial_value="0" name="M9" public_interface="out" units="molar"/>
      <variable name="v2" public_interface="in" units="flux"/>
      <variable name="v7" public_interface="in" units="flux"/>
      <variable name="v9" public_interface="in" units="flux"/>
      <variable name="v16" public_interface="in" units="flux"/>
      <variable name="time" public_interface="in" units="second"/>
      <math xmlns="http://www.w3.org/1998/Math/MathML">
         <apply>
            <eq/>
            <apply>
               <diff/>
               <bvar>
                  <ci>time</ci>
               </bvar>
               <ci>M9</ci>
            </apply>
            <apply>
               <minus/>
               <apply>
                  <plus/>
                  <ci>v2</ci>
                  <ci>v9</ci>
                  <ci>v16</ci>
               </apply>
               <ci>v7</ci>
            </apply>
         </apply>
      </math>
   </component>
   <component name="M9_T1">
      <variable cmeta:id="M9_T1_M9_T1" initial_value="0" name="M9_T1" public_interface="out" units="molar"/>
      <variable name="v8" public_interface="in" units="flux"/>
      <variable name="v18" public_interface="in" units="flux"/>
      <variable name="time" public_interface="in" units="second"/>
      <math xmlns="http://www.w3.org/1998/Math/MathML">
         <apply>
            <eq/>
            <apply>
               <diff/>
               <bvar>
                  <ci>time</ci>
               </bvar>
               <ci>M9_T1</ci>
            </apply>
            <apply>
               <plus/>
               <ci>v8</ci>
               <ci>v18</ci>
            </apply>
         </apply>
      </math>
   </component>
   <component name="pM9_T1_M3">
      <variable cmeta:id="pM9_T1_M3_pM9_T1_M3" initial_value="0" name="pM9_T1_M3" public_interface="out" units="molar"/>
      <variable name="v10" public_interface="in" units="flux"/>
      <variable name="v11" public_interface="in" units="flux"/>
      <variable name="v12" public_interface="in" units="flux"/>
      <variable name="v19" public_interface="in" units="flux"/>
      <variable name="time" public_interface="in" units="second"/>
      <math xmlns="http://www.w3.org/1998/Math/MathML">
         <apply>
            <eq/>
            <apply>
               <diff/>
               <bvar>
                  <ci>time</ci>
               </bvar>
               <ci>pM9_T1_M3</ci>
            </apply>
            <apply>
               <minus/>
               <apply>
                  <plus/>
                  <ci>v10</ci>
                  <ci>v11</ci>
               </apply>
               <apply>
                  <plus/>
                  <ci>v12</ci>
                  <ci>v19</ci>
               </apply>
            </apply>
         </apply>
      </math>
   </component>
   <component name="M3_pM9_T1_M3">
      <variable cmeta:id="M3_pM9_T1_M3_M3_pM9_T1_M3" initial_value="0" name="M3_pM9_T1_M3" public_interface="out" units="molar"/>
      <variable name="v13" public_interface="in" units="flux"/>
      <variable name="v12" public_interface="in" units="flux"/>
      <variable name="time" public_interface="in" units="second"/>
      <math xmlns="http://www.w3.org/1998/Math/MathML">
         <apply>
            <eq/>
            <apply>
               <diff/>
               <bvar>
                  <ci>time</ci>
               </bvar>
               <ci>M3_pM9_T1_M3</ci>
            </apply>
            <apply>
               <minus/>
               <ci>v12</ci>
               <ci>v13</ci>
            </apply>
         </apply>
      </math>
   </component>
   <component name="M9_T1_M3">
      <variable cmeta:id="M9_T1_M3_M9_T1_M3" initial_value="0" name="M9_T1_M3" public_interface="out" units="molar"/>
      <variable name="v9" public_interface="in" units="flux"/>
      <variable name="v13" public_interface="in" units="flux"/>
      <variable name="v14" public_interface="in" units="flux"/>
      <variable name="v20" public_interface="in" units="flux"/>
      <variable name="time" public_interface="in" units="second"/>
      <math xmlns="http://www.w3.org/1998/Math/MathML">
         <apply>
            <eq/>
            <apply>
               <diff/>
               <bvar>
                  <ci>time</ci>
               </bvar>
               <ci>M9_T1_M3</ci>
            </apply>
            <apply>
               <minus/>
               <apply>
                  <plus/>
                  <ci>v13</ci>
                  <ci>v20</ci>
               </apply>
               <apply>
                  <plus/>
                  <ci>v14</ci>
                  <ci>v9</ci>
               </apply>
            </apply>
         </apply>
      </math>
   </component>
   <component name="Tr">
      <variable cmeta:id="Tr_Tr" initial_value="1e-7" name="Tr" public_interface="out" units="molar"/>
      <variable name="v15" public_interface="in" units="flux"/>
      <variable name="v16" public_interface="in" units="flux"/>
      <variable name="v17" public_interface="in" units="flux"/>
      <variable name="v18" public_interface="in" units="flux"/>
      <variable name="v19" public_interface="in" units="flux"/>
      <variable name="v20" public_interface="in" units="flux"/>
      <variable name="time" public_interface="in" units="second"/>
      <math xmlns="http://www.w3.org/1998/Math/MathML">
         <apply>
            <eq/>
            <apply>
               <diff/>
               <bvar>
                  <ci>time</ci>
               </bvar>
               <ci>Tr</ci>
            </apply>
            <apply>
               <minus/>
               <apply>
                  <plus/>
                  <ci>v16</ci>
                  <ci>v18</ci>
                  <ci>v20</ci>
               </apply>
               <apply>
                  <plus/>
                  <ci>v15</ci>
                  <ci>v17</ci>
                  <ci>v19</ci>
               </apply>
            </apply>
         </apply>
      </math>
   </component>
   <component name="Tr_pM9">
      <variable cmeta:id="Tr_pM9_Tr_pM9" initial_value="0" name="Tr_pM9" public_interface="out" units="molar"/>
      <variable name="v15" public_interface="in" units="flux"/>
      <variable name="v16" public_interface="in" units="flux"/>
      <variable name="time" public_interface="in" units="second"/>
      <math xmlns="http://www.w3.org/1998/Math/MathML">
         <apply>
            <eq/>
            <apply>
               <diff/>
               <bvar>
                  <ci>time</ci>
               </bvar>
               <ci>Tr_pM9</ci>
            </apply>
            <apply>
               <minus/>
               <ci>v15</ci>
               <ci>v16</ci>
            </apply>
         </apply>
      </math>
   </component>
   <component name="Tr_pM9_T1">
      <variable cmeta:id="Tr_pM9_T1_Tr_pM9_T1" initial_value="0" name="Tr_pM9_T1" public_interface="out" units="molar"/>
      <variable name="v17" public_interface="in" units="flux"/>
      <variable name="v18" public_interface="in" units="flux"/>
      <variable name="time" public_interface="in" units="second"/>
      <math xmlns="http://www.w3.org/1998/Math/MathML">
         <apply>
            <eq/>
            <apply>
               <diff/>
               <bvar>
                  <ci>time</ci>
               </bvar>
               <ci>Tr_pM9_T1</ci>
            </apply>
            <apply>
               <minus/>
               <ci>v17</ci>
               <ci>v18</ci>
            </apply>
         </apply>
      </math>
   </component>
   <component name="Tr_pM9_T1_M3">
      <variable cmeta:id="Tr_pM9_T1_M3_Tr_pM9_T1_M3" initial_value="0" name="Tr_pM9_T1_M3" public_interface="out" units="molar"/>
      <variable name="v19" public_interface="in" units="flux"/>
      <variable name="v20" public_interface="in" units="flux"/>
      <variable name="time" public_interface="in" units="second"/>
      <math xmlns="http://www.w3.org/1998/Math/MathML">
         <apply>
            <eq/>
            <apply>
               <diff/>
               <bvar>
                  <ci>time</ci>
               </bvar>
               <ci>Tr_pM9_T1_M3</ci>
            </apply>
            <apply>
               <minus/>
               <ci>v19</ci>
               <ci>v20</ci>
            </apply>
         </apply>
      </math>
   </component>
   <component name="kinetic_parameters">
      <variable initial_value="3.4e4" name="kon_pM9T1" public_interface="out" units="second_order_rate_constant"/>
      <variable initial_value="7.48e-5" name="koff_pM9T1" public_interface="out" units="first_order_rate_constant"/>
	  <variable initial_value="3.4e4" name="kon_pM9T1M3" public_interface="out" units="second_order_rate_constant"/>
      <variable initial_value="7.48e-5" name="koff_pM9T1M3" public_interface="out" units="first_order_rate_constant"/>
	  <variable initial_value="1e4" name="kon_M3pM9" public_interface="out" units="second_order_rate_constant"/>
      <variable initial_value="0.001" name="koff_M3pM9" public_interface="out" units="first_order_rate_constant"/>
      <variable initial_value="1e4" name="kon_M3pM9T1" public_interface="out" units="second_order_rate_constant"/>
      <variable initial_value="0.001" name="koff_M3pM9T1" public_interface="out" units="first_order_rate_constant"/>
	  <variable initial_value="1e4" name="kon_M3pM9T1M3" public_interface="out" units="second_order_rate_constant"/>
      <variable initial_value="0.001" name="koff_M3pM9T1M3" public_interface="out" units="first_order_rate_constant"/>
	  <variable initial_value="1.9e6" name="kon_M3T1" public_interface="out" units="second_order_rate_constant"/>
      <variable initial_value="1.26e-4" name="koff_M3T1" public_interface="out" units="first_order_rate_constant"/>
	  <variable initial_value="5.6e6" name="kon_M9T1_star" public_interface="out" units="second_order_rate_constant"/>
      <variable initial_value="1.6e-5" name="koff_M9T1_star" public_interface="out" units="first_order_rate_constant"/>
	  <variable initial_value="6.3e-4" name="kon_M9T1" public_interface="out" units="first_order_rate_constant"/>
      <variable initial_value="2.5e-4" name="koff_M9T1" public_interface="out" units="first_order_rate_constant"/>
	  <variable initial_value="1.9e6" name="kon_M3_pM9T1" public_interface="out" units="second_order_rate_constant"/>
      <variable initial_value="1.26e-4" name="koff_M3_pM9T1" public_interface="out" units="first_order_rate_constant"/>
	  <variable initial_value="1e4" name="kon_TrpM9" public_interface="out" units="second_order_rate_constant"/>
      <variable initial_value="0.007" name="koff_TrpM9" public_interface="out" units="first_order_rate_constant"/>
	  <variable initial_value="1e4" name="kon_TrpM9T1" public_interface="out" units="second_order_rate_constant"/>
	  <variable initial_value="0.007" name="koff_TrpM9T1" public_interface="out" units="first_order_rate_constant"/>
      <variable initial_value="1e4" name="kon_TrpM9T1M3" public_interface="out" units="second_order_rate_constant"/>
      <variable initial_value="0.007" name="koff_TrpM9T1M3" public_interface="out" units="first_order_rate_constant"/>
      <variable initial_value="7.48e-5" name="kon_M9_M3T1" public_interface="out" units="first_order_rate_constant"/>
      <variable initial_value="3.4e4" name="koff_M9_M3T1" public_interface="out" units="second_order_rate_constant"/>
	  <variable initial_value="0.00057" name="kact_M3pM9T1" public_interface="out" units="first_order_rate_constant"/>
	  <variable initial_value="0.00057" name="kact_M3pM9T1M3" public_interface="out" units="first_order_rate_constant"/>
      <variable initial_value="1.26e-4" name="kact_M9T1M3" public_interface="out" units="first_order_rate_constant"/>
      <variable initial_value="0.002" name="kact_TrpM9" public_interface="out" units="first_order_rate_constant"/>
	  <variable initial_value="0.0006" name="kact_TrpM9T1" public_interface="out" units="first_order_rate_constant"/>
	  <variable initial_value="0.0006" name="kact_TrpM9T1M3" public_interface="out" units="first_order_rate_constant"/>
	  <variable initial_value="0.0019" name="kact_M3pM9" public_interface="out" units="first_order_rate_constant"/>  
   </component>
   <connection>
      <map_components component_1="pM9" component_2="v1"/>
      <map_variables variable_1="pM9" variable_2="pM9"/>
      <map_variables variable_1="v1" variable_2="v1"/>
   </connection>
   <connection>
      <map_components component_1="pM9" component_2="v4"/>
      <map_variables variable_1="pM9" variable_2="pM9"/>
      <map_variables variable_1="v4" variable_2="v4"/>
   </connection>
   <connection>
      <map_components component_1="pM9" component_2="v11"/>
      <map_variables variable_1="pM9" variable_2="pM9"/>
      <map_variables variable_1="v11" variable_2="v11"/>
   </connection>
   <connection>
      <map_components component_1="pM9" component_2="v15"/>
      <map_variables variable_1="pM9" variable_2="pM9"/>
      <map_variables variable_1="v15" variable_2="v15"/>
   </connection>
   <connection>
      <map_components component_1="M3" component_2="v1"/>
      <map_variables variable_1="M3" variable_2="M3"/>
      <map_variables variable_1="v1" variable_2="v1"/>
   </connection>
   <connection>
      <map_components component_1="M3" component_2="v2"/>
      <map_variables variable_1="v2" variable_2="v2"/>
   </connection>
   <connection>
      <map_components component_1="M3" component_2="v3"/>
      <map_variables variable_1="M3" variable_2="M3"/>
      <map_variables variable_1="v3" variable_2="v3"/>
   </connection>
   <connection>
      <map_components component_1="M3" component_2="v5"/>
      <map_variables variable_1="M3" variable_2="M3"/>
      <map_variables variable_1="v5" variable_2="v5"/>
   </connection>
   <connection>
      <map_components component_1="M3" component_2="v6"/>
      <map_variables variable_1="v6" variable_2="v6"/>
   </connection>
   <connection>
      <map_components component_1="M3" component_2="v10"/>
      <map_variables variable_1="M3" variable_2="M3"/>
      <map_variables variable_1="v10" variable_2="v10"/>
   </connection>
   <connection>
      <map_components component_1="M3" component_2="v12"/>
      <map_variables variable_1="M3" variable_2="M3"/>
      <map_variables variable_1="v12" variable_2="v12"/>
   </connection>
   <connection>
      <map_components component_1="M3" component_2="v13"/>
      <map_variables variable_1="v13" variable_2="v13"/>
   </connection>
   <connection>
      <map_components component_1="M3" component_2="v14"/>
      <map_variables variable_1="v14" variable_2="v14"/>
   </connection>
   <connection>
      <map_components component_1="M3_pM9" component_2="v1"/>
      <map_variables variable_1="M3_pM9" variable_2="M3_pM9"/>
      <map_variables variable_1="v1" variable_2="v1"/>
   </connection>
   <connection>
      <map_components component_1="M3_pM9" component_2="v2"/>
      <map_variables variable_1="M3_pM9" variable_2="M3_pM9"/>
      <map_variables variable_1="v2" variable_2="v2"/>
   </connection>
   <connection>
      <map_components component_1="T1" component_2="v3"/>
      <map_variables variable_1="T1" variable_2="T1"/>
      <map_variables variable_1="v3" variable_2="v3"/>
   </connection>
   <connection>
      <map_components component_1="T1" component_2="v4"/>
      <map_variables variable_1="T1" variable_2="T1"/>
      <map_variables variable_1="v4" variable_2="v4"/>
   </connection>
   <connection>
      <map_components component_1="T1" component_2="v7"/>
      <map_variables variable_1="T1" variable_2="T1"/>
      <map_variables variable_1="v7" variable_2="v7"/>
   </connection>
   <connection>
      <map_components component_1="M3_T1" component_2="v3"/>
      <map_variables variable_1="M3_T1" variable_2="M3_T1"/>
      <map_variables variable_1="v3" variable_2="v3"/>
   </connection>
   <connection>
      <map_components component_1="M3_T1" component_2="v11"/>
      <map_variables variable_1="M3_T1" variable_2="M3_T1"/>
      <map_variables variable_1="v11" variable_2="v11"/>
   </connection>
   <connection>
      <map_components component_1="pM9_T1" component_2="v4"/>
      <map_variables variable_1="pM9_T1" variable_2="pM9_T1"/>
      <map_variables variable_1="v4" variable_2="v4"/>
   </connection>
   <connection>
      <map_components component_1="pM9_T1" component_2="v5"/>
      <map_variables variable_1="pM9_T1" variable_2="pM9_T1"/>
      <map_variables variable_1="v5" variable_2="v5"/>
   </connection>
   <connection>
      <map_components component_1="pM9_T1" component_2="v10"/>
      <map_variables variable_1="pM9_T1" variable_2="pM9_T1"/>
      <map_variables variable_1="v10" variable_2="v10"/>
   </connection>
   <connection>
      <map_components component_1="pM9_T1" component_2="v17"/>
      <map_variables variable_1="pM9_T1" variable_2="pM9_T1"/>
      <map_variables variable_1="v17" variable_2="v17"/>
   </connection>
   <connection>
      <map_components component_1="M3_pM9_T1" component_2="v5"/>
      <map_variables variable_1="M3_pM9_T1" variable_2="M3_pM9_T1"/>
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<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"><rdf:Description rdf:nodeID="n1"><boundIntervals xmlns="http://www.cellml.org/metadata/simulation/1.0#"><rdf:Description rdf:nodeID="n2"/></boundIntervals></rdf:Description><rdf:Description rdf:about="#Tr_pM9_T1"><alternative xmlns="http://purl.org/dc/terms/" xml:lang="en">trypsin-proMMP9-TIMP1</alternative><title xmlns="http://purl.org/dc/elements/1.1/" xml:lang="en">Tr_pM9_T1</title></rdf:Description><rdf:Description rdf:about="rdf:#37cd525f-07bb-4e1e-85a4-485c3ab63962"><W3CDTF xmlns="http://purl.org/dc/terms/" xml:lang="en">2007-12-28</W3CDTF></rdf:Description><rdf:Description rdf:about="#M3_pM9"><alternative xmlns="http://purl.org/dc/terms/" xml:lang="en">matrix metalloproteinase-3-promatrix metalloproteinase-9 complex</alternative><alternative xmlns="http://purl.org/dc/terms/" xml:lang="en">MMP3-proMMP9</alternative><title xmlns="http://purl.org/dc/elements/1.1/" xml:lang="en">M3_pM9</title></rdf:Description><rdf:Description rdf:about="#Tr_pM9"><alternative xmlns="http://purl.org/dc/terms/" xml:lang="en">trypsin-proMMP9</alternative><title xmlns="http://purl.org/dc/elements/1.1/" xml:lang="en">Tr_pM9</title></rdf:Description><rdf:Description rdf:about=""><publisher xmlns="http://purl.org/dc/elements/1.1/" xml:lang="en">The University of Auckland, Bioengineering Institute</publisher><cmeta:comment><rdf:Description rdf:about="rdf:#e5c86249-1568-46a8-9278-522f42e31787"/></cmeta:comment><created xmlns="http://purl.org/dc/terms/"><rdf:Description rdf:about="rdf:#6a95ebdc-836e-49e1-9d4e-ba254a9746ae"/></created><creator xmlns="http://purl.org/dc/elements/1.1/"><rdf:Description rdf:about="rdf:#46126a1b-26da-4940-9104-db0dae978bfa"/></creator></rdf:Description><rdf:Description rdf:about="rdf:#93c4590b-3a63-4a59-88f9-f4d7bb0d489a"><subject xmlns="http://purl.org/dc/elements/1.1/"><rdf:Description rdf:about="rdf:#9685a5af-b02a-47e9-990d-8089718a022e"/></subject></rdf:Description><rdf:Description rdf:about="#M9"><alternative xmlns="http://purl.org/dc/terms/" xml:lang="en">matrix metalloproteinase-9</alternative><alternative xmlns="http://purl.org/dc/terms/" xml:lang="en">MMP9</alternative><title xmlns="http://purl.org/dc/elements/1.1/" xml:lang="en">M9</title></rdf:Description><rdf:Description rdf:about="#pM9_T1"><alternative xmlns="http://purl.org/dc/terms/" xml:lang="en">promatrix metalloproteinase-9-tissue inhibitor of metalloproteinase-1 complex</alternative><alternative xmlns="http://purl.org/dc/terms/" xml:lang="en">proMMP9-TIMP1</alternative><title xmlns="http://purl.org/dc/elements/1.1/" xml:lang="en">pM9_T1</title></rdf:Description><rdf:Description rdf:about="rdf:#46126a1b-26da-4940-9104-db0dae978bfa"><ORG xmlns="http://www.w3.org/2001/vcard-rdf/3.0#"><rdf:Description rdf:about="rdf:#b7821ec9-cc87-4023-a0b8-1173ecb7658b"/></ORG><EMAIL xmlns="http://www.w3.org/2001/vcard-rdf/3.0#"><rdf:Description rdf:about="rdf:#8f95675c-5980-4216-9d87-d7c02a32e53e"/></EMAIL><N xmlns="http://www.w3.org/2001/vcard-rdf/3.0#"><rdf:Description rdf:about="rdf:#34fd54d2-3217-4412-be5a-76251117c684"/></N></rdf:Description><rdf:Description rdf:about="rdf:#e5c86249-1568-46a8-9278-522f42e31787"><rdf:value xml:lang="en">This cellML model is known to run in both PCEnv and COR to recreate the results in the published paper.  The units have been checked and they are consistent. Please note that many of the figures in the paper are complex and requite special simulation conditions. This particular CellMl model represents the basic core model presented in the paper. Initial conditions can be modified to generate more complex results.  We thank the model author Prakash Vempati for his assistance in getting this CellML model to run.</rdf:value><creator xmlns="http://purl.org/dc/elements/1.1/"><rdf:Description rdf:about="rdf:#10b253a6-ce0e-4703-aa30-926f86e59cda"/></creator></rdf:Description><rdf:Description rdf:about="#M3"><alternative xmlns="http://purl.org/dc/terms/" xml:lang="en">matrix metalloproteinase-3</alternative><alternative xmlns="http://purl.org/dc/terms/" xml:lang="en">MMP3</alternative><title xmlns="http://purl.org/dc/elements/1.1/" xml:lang="en">M3</title></rdf:Description><rdf:Description rdf:about="#M9_T1_M3"><alternative xmlns="http://purl.org/dc/terms/" xml:lang="en">MMP9-TIMP1-MMP3</alternative><title xmlns="http://purl.org/dc/elements/1.1/" xml:lang="en">M9_T1_M3</title></rdf:Description><rdf:Description rdf:about="#vempati_model_2007"><simulation xmlns="http://www.cellml.org/metadata/simulation/1.0#"><rdf:Description rdf:nodeID="n1"/></simulation><reference xmlns="http://www.cellml.org/bqs/1.0#"><rdf:Description rdf:about="rdf:#7962016d-39d0-43e8-a1f9-c67f5257bf89"/></reference><reference xmlns="http://www.cellml.org/bqs/1.0#"><rdf:Description rdf:about="rdf:#93c4590b-3a63-4a59-88f9-f4d7bb0d489a"/></reference><cmeta:comment><rdf:Description rdf:about="rdf:#4db5e780-313c-48d1-a7dd-361b8e006fa2"/></cmeta:comment><title xmlns="http://purl.org/dc/elements/1.1/" xml:lang="en">
        Vempati et al.'s 2007 biochemical model of the matrix metalloproteinase 9 activation and inhibition.
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