Attachment 'mySBMLmodel.xml'

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   1 <?xml version="1.0" encoding="UTF-8"?>
   2 <!-- Created by libAntimony version v2.5 on 2014-08-15 14:52 with libSBML version 5.9.1. -->
   3 <sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
   4   <model id="__main" name="__main">
   5     <listOfCompartments>
   6       <compartment sboTerm="SBO:0000410" id="default_compartment" spatialDimensions="3" size="1" constant="true"/>
   7     </listOfCompartments>
   8     <listOfSpecies>
   9       <species id="X0" compartment="default_compartment" initialConcentration="10" hasOnlySubstanceUnits="false" boundaryCondition="true" constant="false"/>
  10       <species id="S1" compartment="default_compartment" initialConcentration="20" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
  11       <species id="S4" compartment="default_compartment" initialConcentration="5" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
  12       <species id="S2" compartment="default_compartment" initialConcentration="5" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
  13       <species id="S3" compartment="default_compartment" initialConcentration="5" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
  14       <species id="X1" compartment="default_compartment" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="true" constant="false"/>
  15     </listOfSpecies>
  16     <listOfParameters>
  17       <parameter id="Vm1" value="10" constant="true"/>
  18       <parameter id="Keq1" value="10" constant="true"/>
  19       <parameter id="h" value="6" constant="true"/>
  20       <parameter id="k1" value="0.3" constant="true"/>
  21       <parameter id="k2" value="0.1" constant="true"/>
  22       <parameter id="k3" value="0.1" constant="true"/>
  23       <parameter id="Vm2" value="2.5" constant="true"/>
  24       <parameter id="Km" value="0.8" constant="true"/>
  25     </listOfParameters>
  26     <listOfReactions>
  27       <reaction id="J0" reversible="true" fast="false">
  28         <listOfReactants>
  29           <speciesReference species="X0" stoichiometry="1" constant="true"/>
  30         </listOfReactants>
  31         <listOfProducts>
  32           <speciesReference species="S1" stoichiometry="1" constant="true"/>
  33         </listOfProducts>
  34         <listOfModifiers>
  35           <modifierSpeciesReference species="S4"/>
  36         </listOfModifiers>
  37         <kineticLaw>
  38           <math xmlns="http://www.w3.org/1998/Math/MathML">
  39             <apply>
  40               <divide/>
  41               <apply>
  42                 <times/>
  43                 <ci> Vm1 </ci>
  44                 <apply>
  45                   <minus/>
  46                   <ci> X0 </ci>
  47                   <apply>
  48                     <divide/>
  49                     <ci> S1 </ci>
  50                     <ci> Keq1 </ci>
  51                   </apply>
  52                 </apply>
  53               </apply>
  54               <apply>
  55                 <plus/>
  56                 <cn type="integer"> 1 </cn>
  57                 <ci> X0 </ci>
  58                 <ci> S1 </ci>
  59                 <apply>
  60                   <power/>
  61                   <ci> S4 </ci>
  62                   <ci> h </ci>
  63                 </apply>
  64               </apply>
  65             </apply>
  66           </math>
  67         </kineticLaw>
  68       </reaction>
  69       <reaction id="J1" reversible="true" fast="false">
  70         <listOfReactants>
  71           <speciesReference species="S1" stoichiometry="1" constant="true"/>
  72         </listOfReactants>
  73         <listOfProducts>
  74           <speciesReference species="S2" stoichiometry="1" constant="true"/>
  75         </listOfProducts>
  76         <kineticLaw>
  77           <math xmlns="http://www.w3.org/1998/Math/MathML">
  78             <apply>
  79               <times/>
  80               <ci> k1 </ci>
  81               <ci> S1 </ci>
  82             </apply>
  83           </math>
  84         </kineticLaw>
  85       </reaction>
  86       <reaction id="J2" reversible="true" fast="false">
  87         <listOfReactants>
  88           <speciesReference species="S2" stoichiometry="1" constant="true"/>
  89         </listOfReactants>
  90         <listOfProducts>
  91           <speciesReference species="S3" stoichiometry="1" constant="true"/>
  92         </listOfProducts>
  93         <kineticLaw>
  94           <math xmlns="http://www.w3.org/1998/Math/MathML">
  95             <apply>
  96               <times/>
  97               <ci> k2 </ci>
  98               <ci> S2 </ci>
  99             </apply>
 100           </math>
 101         </kineticLaw>
 102       </reaction>
 103       <reaction id="J3" reversible="true" fast="false">
 104         <listOfReactants>
 105           <speciesReference species="S3" stoichiometry="1" constant="true"/>
 106         </listOfReactants>
 107         <listOfProducts>
 108           <speciesReference species="S4" stoichiometry="1" constant="true"/>
 109         </listOfProducts>
 110         <kineticLaw>
 111           <math xmlns="http://www.w3.org/1998/Math/MathML">
 112             <apply>
 113               <times/>
 114               <ci> k3 </ci>
 115               <ci> S3 </ci>
 116             </apply>
 117           </math>
 118         </kineticLaw>
 119       </reaction>
 120       <reaction id="J4" reversible="true" fast="false">
 121         <listOfReactants>
 122           <speciesReference species="S4" stoichiometry="1" constant="true"/>
 123         </listOfReactants>
 124         <listOfProducts>
 125           <speciesReference species="X1" stoichiometry="1" constant="true"/>
 126         </listOfProducts>
 127         <kineticLaw>
 128           <math xmlns="http://www.w3.org/1998/Math/MathML">
 129             <apply>
 130               <divide/>
 131               <apply>
 132                 <times/>
 133                 <ci> Vm2 </ci>
 134                 <ci> S4 </ci>
 135               </apply>
 136               <apply>
 137                 <plus/>
 138                 <ci> Km </ci>
 139                 <ci> S4 </ci>
 140               </apply>
 141             </apply>
 142           </math>
 143         </kineticLaw>
 144       </reaction>
 145     </listOfReactions>
 146   </model>
 147 </sbml>

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  • [get | view] (2014-05-26 17:15:22, 119.9 KB) [[attachment:Agenda.pdf]]
  • [get | view] (2014-08-15 15:27:16, 4.0 KB) [[attachment:DiffusionChemotaxExample.zip]]
  • [get | view] (2014-08-05 15:44:24, 119.9 KB) [[attachment:HamnerDirections.pdf]]
  • [get | view] (2014-04-04 17:07:58, 244.7 KB) [[attachment:PosterImage.jpg]]
  • [get | view] (2014-04-10 20:13:49, 246.0 KB) [[attachment:PosterImage_v2.jpg]]
  • [get | view] (2014-08-15 21:44:55, 2.9 KB) [[attachment:VascularTumor_2D.zip]]
  • [get | view] (2014-08-15 18:07:26, 2.9 KB) [[attachment:Vascular_1.zip]]
  • [get | view] (2014-04-04 17:10:08, 610.4 KB) [[attachment:WorkshopPoster_2014_JAG.pdf]]
  • [get | view] (2014-04-10 20:15:17, 647.3 KB) [[attachment:WorkshopPoster_2014_JAG_v2.pdf]]
  • [get | view] (2014-08-16 14:16:48, 5.8 KB) [[attachment:mySBMLmodel.xml]]
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