Location: ElectrEcoBlu Standard Virtual Biological Machine @ f9c750111270 / ElectrEcoBluModel.cellml

Author:
mcoo001 <devnull@localhost>
Date:
2009-07-01 17:24:40+12:00
Desc:
Initial Commit.
Permanent Source URI:
http://models.cellml.org/workspace/electrecoblu/rawfile/f9c750111270e5ffae4ebc27e4104b44b2a9f295/ElectrEcoBluModel.cellml
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<?xml version="1.0" encoding="utf-8"?>
<model name="ElectrEcoBluModel_SVBM" cmeta:id="ElectrEcoBluModel_SVBM"
xmlns="http://www.cellml.org/cellml/1.1#"
    xmlns:cellml="http://www.cellml.org/cellml/1.1#"
    xmlns:cmeta="http://www.cellml.org/metadata/1.0#"
    xmlns:xlink="http://www.w3.org/1999/xlink"
    xmlns:dc="http://purl.org/dc/elements/1.0/"
    xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
    xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#">

    <rdf:RDF>
    <rdf:Description rdf:about="#ElectrEcoBluModel_SVBM">
    <dc:creator>
    <vCard:N rdf:parseType="Resource">
        <vCard:Family>Cooling</vCard:Family>
        <vCard:Given>Mike</vCard:Given>
    </vCard:N>
    <vCard:EMAIL rdf:parseType="Resource">
        <rdf:value>m.cooling@auckland.ac.nz</rdf:value>
        <rdf:type rdf:resource="http://imc.org/vCard/3.0#internet"/>
    </vCard:EMAIL>
    <vCard:ORG rdf:parseType="Resource">
        <vCard:Orgname>Auckland Bioengineering Institute</vCard:Orgname>
        <vCard:Orgunit>University of Auckland</vCard:Orgunit>
    </vCard:ORG>
    </dc:creator>
    </rdf:Description>
    </rdf:RDF>
    
   <import xlink:href="http://models.cellml.org/workspace/SVP_00000032/@@rawfile/b30fd8b7c4da0f9642f678cb5d59c1dcea7f7822/Chassis_EColi.cellml">
       <component name="eColiCell" component_ref="Chassis_EColi" />
   </import>
   
   <import xlink:href="http://models.cellml.org/workspace/SVP_Templates200906/@@rawfile/b1e53aaa6bb9f958b4ddb2412bb1ae417c45e250/Time.cellml">
       <component name="Time" component_ref="Time" />
   </import>  
          
  <component name="SpeciesInitialConcentrations">
        <variable name="RNA_Device1" units="nM" initial_value="0" public_interface="out" />
        <variable name="TF" units="nM" initial_value="8621" public_interface="out" />
        <variable name="TFS" units="nM" initial_value="0" public_interface="out" />
        <variable name="RNA_Device2" units="nM" initial_value="0" public_interface="out" />
        <variable name="IC" units="nM" initial_value="0" public_interface="out" />
        <variable name="PhzS" units="nM" initial_value="0" public_interface="out" />
        <variable name="PhzM" units="nM" initial_value="0" public_interface="out" />
        <variable name="PYO" units="nM" initial_value="0" public_interface="out" />
  </component>
    
  <import xlink:href="http://models.cellml.org/workspace/SVP_00000033/@@rawfile/6e852a8be81ef8340fcdcd24e6c5a8831525c438/ElectrEcoBluDevice1_Promoter.cellml">
        <units name="nM_per_s" units_ref="nM_per_s" />
        <component name="ElectrEcoBluDevice1_Promoter" component_ref="ElectrEcoBluDevice1_Promoter" />
  </import>
     
  <import xlink:href="http://models.cellml.org/workspace/SVP_Templates200906/@@rawfile/b1e53aaa6bb9f958b4ddb2412bb1ae417c45e250/Template_Species.cellml">
     <units name="nM" units_ref="nM" />
    <component name="RNA_Device1" component_ref="Template_Species" />
  </import>

  <component name="RNA_Device1_interface">
           <variable name="JPlusPromoter" units="nM_per_s" public_interface="in"/>
           <variable name="JGain" units="nM_per_s" public_interface="out"/>
           <variable name="JMinusDegradation" units="nM_per_s" public_interface="in"/>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
              <apply>
                 <eq/>
                 <ci>JGain</ci>
                 <apply>
                    <minus/>
                    <ci>JPlusPromoter</ci>
                    <ci>JMinusDegradation</ci>
                 </apply>
              </apply>
           </math>
  </component>
  
  <import xlink:href="http://models.cellml.org/workspace/SVP_00000003/@@rawfile/c375eed99c5d750a41b8ca4cfcee8acaa62a740e/Bioenvironment_Degradation_ElectrEcoBluDevice1RNA.cellml">
         <units name="per_s" units_ref="per_s" />
         <component name="Bioenvironment_Degradation_Device1RNA" component_ref="Bioenvironment_Degradation_ElectrEcoBluDevice1RNA" />
  </import>
  
  <import xlink:href="http://models.cellml.org/workspace/SVP_00000035/@@rawfile/399039e4f33c884465be73a65c261755ca9b0fe7/ElectrEcoBluDevice1_RBS.cellml">
          <component name="ElectrEcoBluDevice1_RBS" component_ref="ElectrEcoBluDevice1_RBS" />
  </import>
  
  <import xlink:href="http://models.cellml.org/workspace/SVP_00000039/@@rawfile/6226c68bd09bef205848357006466a0115a4585e/ElectrEcoBluDevice1_ProteinCDS_TF.cellml">
              <component name="ElectrEcoBluDevice1_ProteinCDS_TF" component_ref="ElectrEcoBluDevice1_ProteinCDS_TF" />
  </import>
  
  <import xlink:href="http://models.cellml.org/workspace/SVP_Templates200906/@@rawfile/b1e53aaa6bb9f958b4ddb2412bb1ae417c45e250/Template_Species.cellml">
             <component name="TF" component_ref="Template_Species" />
  </import> 
  
  <component name="TF_interface">
        <variable name="JPlusProductionDevice1" units="nM_per_s" public_interface="in"/>
        <variable name="JPlusProductionDevice2" units="nM_per_s" public_interface="in"/>
        <variable name="JMinusDegradation" units="nM_per_s" public_interface="in"/>
        <variable name="JMinusTFSFormation" units="nM_per_s" public_interface="in"/>
        <variable name="JGain" units="nM_per_s" public_interface="out"/>
        <math xmlns="http://www.w3.org/1998/Math/MathML">
           <apply>
              <eq/>
              <ci>JGain</ci>
              <apply>
                 <minus/>
                 <apply>
                    <minus/>
                    <apply>
                       <plus/>
                       <ci>JPlusProductionDevice1</ci>
                       <ci>JPlusProductionDevice2</ci>
                    </apply>
                    <ci>JMinusDegradation</ci>
                 </apply>
                 <ci>JMinusTFSFormation</ci>
              </apply>
           </apply>
        </math>
   </component>
  
   <import xlink:href="http://models.cellml.org/workspace/SVP_00000014/@@rawfile/f53a81550e6738a9258d1c7f3d0531fc8662f572/Bioenvironment_Degradation_TF.cellml">
               <component name="Bioenvironment_Degradation_TF" component_ref="Bioenvironment_Degradation_TF" />
   </import>
   
   <component name="S">
      <variable name="concentration" units="nM" initial_value="5000" public_interface="out"/>
   </component>   
   
  <import xlink:href="http://models.cellml.org/workspace/SVP_00000022/@@rawfile/bb7c8980f3a2b0492f843a8b030d855e0869f69b/Bioenvironment_RxR2P1Rev_TFSFormation.cellml">
         <component name="RxR2P1_TFSformation" component_ref="Bioenvironment_RxR2P1Rev_TFSFormation" />
  </import>
  
  <import xlink:href="http://models.cellml.org/workspace/SVP_Templates200906/@@rawfile/b1e53aaa6bb9f958b4ddb2412bb1ae417c45e250/Template_Species.cellml">
             <component name="TFS" component_ref="Template_Species" />
  </import>  
  
   <component name="TFS_interface">
      <variable name="JPlusProduction" units="nM_per_s" public_interface="in"/>
      <variable name="JGain" units="nM_per_s" public_interface="out"/>
      <variable name="JMinusDegradation" units="nM_per_s" public_interface="in"/>
      <math xmlns="http://www.w3.org/1998/Math/MathML">
         <apply>
            <eq/>
            <ci>JGain</ci>
            <apply>
               <minus/>
               <ci>JPlusProduction</ci>
               <ci>JMinusDegradation</ci>
            </apply>
         </apply>
      </math>
   </component>
   
  <import xlink:href="http://models.cellml.org/workspace/SVP_00000015/@@rawfile/91e0b2507c26ce16d5ec6116bc926e22704af0cc/Bioenvironment_Degradation_TFS.cellml">
         <component name="Bioenvironment_Degradation_TFS" component_ref="Bioenvironment_Degradation_TFS" />
  </import>
  
  <import xlink:href="http://models.cellml.org/workspace/SVP_00000034/@@rawfile/e85eec07c615aea7cdb28b311f94e748b462a349/ElectrEcoBluDevice2_Promoter.cellml">
         <component name="ElectrEcoBluDevice2_Promoter" component_ref="ElectrEcoBluDevice2_Promoter" />
  </import>  
  
  <import xlink:href="http://models.cellml.org/workspace/SVP_Templates200906/@@rawfile/b1e53aaa6bb9f958b4ddb2412bb1ae417c45e250/Template_Species.cellml">
             <component name="RNA_Device2" component_ref="Template_Species" />
  </import>
  
   <component name="RNA_Device2_interface">
      <variable name="JPlusPromoter" units="nM_per_s" public_interface="in"/>
      <variable name="JGain" units="nM_per_s" public_interface="out"/>
      <variable name="JMinusDegradation" units="nM_per_s" public_interface="in"/>
      <math xmlns="http://www.w3.org/1998/Math/MathML">
         <apply>
            <eq/>
            <ci>JGain</ci>
            <apply>
               <minus/>
               <ci>JPlusPromoter</ci>
               <ci>JMinusDegradation</ci>
            </apply>
         </apply>
      </math>
   </component>
   
   <import xlink:href="http://models.cellml.org/workspace/SVP_00000004/@@rawfile/4473bb00253c1d40cc6346c87230f369d6b34806/Bioenvironment_Degradation_ElectrEcoBluDevice2RNA.cellml">
         <component name="Bioenvironment_Degradation_Device2RNA" component_ref="Bioenvironment_Degradation_ElectrEcoBluDevice2RNA" />
   </import>   
  
    <import xlink:href="http://models.cellml.org/workspace/SVP_00000036/@@rawfile/8f17d1edfef8da8928a849d3e51f1f230ec8fe9e/ElectrEcoBluDevice2_RBS_PhzM.cellml">
               <component name="ElectrEcoBluDevice2_RBS_PhzM" component_ref="ElectrEcoBluDevice2_RBS_PhzM" />
    </import>
    
    <import xlink:href="http://models.cellml.org/workspace/SVP_00000040/@@rawfile/ffa84b1d02969c255bdce176f32852a82a1e318a/ElectrEcoBluDevice2_ProteinCDS_PhzM.cellml">
                  <component name="ElectrEcoBluDevice2_ProteinCDS_PhzM" component_ref="ElectrEcoBluDevice2_ProteinCDS_PhzM" />
    </import>

    <import xlink:href="http://models.cellml.org/workspace/SVP_00000037/@@rawfile/65efca7374cd0805adea6dca292ed8d4498f1ef9/ElectrEcoBluDevice2_RBS_PhzS.cellml">
               <component name="ElectrEcoBluDevice2_RBS_PhzS" component_ref="ElectrEcoBluDevice2_RBS_PhzS" />
    </import>
    
    <import xlink:href="http://models.cellml.org/workspace/SVP_00000041/@@rawfile/6fa5bb789c4c47889ed053faa8afc3182b53111e/ElectrEcoBluDevice2_ProteinCDS_PhzS.cellml">
                  <component name="ElectrEcoBluDevice2_ProteinCDS_PhzS" component_ref="ElectrEcoBluDevice2_ProteinCDS_PhzS" />
    </import>
    
    <import xlink:href="http://models.cellml.org/workspace/SVP_00000038/@@rawfile/b54b03e8b0c7fc6a7cfab960b6a216509195f420/ElectrEcoBluDevice2_RBS_TF.cellml">
                   <component name="ElectrEcoBluDevice2_RBS_TF" component_ref="ElectrEcoBluDevice2_RBS_TF" />
    </import>
    
    <import xlink:href="http://models.cellml.org/workspace/SVP_00000042/@@rawfile/f936840e1d88795caa7351bc2da1487819dafbcf/ElectrEcoBluDevice2_ProteinCDS_TF.cellml">
                  <component name="ElectrEcoBluDevice2_ProteinCDS_TF" component_ref="ElectrEcoBluDevice2_ProteinCDS_TF" />
    </import>  
  
    <import xlink:href="http://models.cellml.org/workspace/SVP_Templates200906/@@rawfile/b1e53aaa6bb9f958b4ddb2412bb1ae417c45e250/Template_Species.cellml">
             <component name="PhzM" component_ref="Template_Species" />
    </import>  
    
   <component name="PhzM_interface">
      <variable name="JPlusProduction" units="nM_per_s" public_interface="in"/>
      <variable name="JGain" units="nM_per_s" public_interface="out"/>
      <variable name="JMinusDegradation" units="nM_per_s" public_interface="in"/>
      <math xmlns="http://www.w3.org/1998/Math/MathML">
         <apply>
            <eq/>
            <ci>JGain</ci>
            <apply>
               <minus/>
               <ci>JPlusProduction</ci>
               <ci>JMinusDegradation</ci>
            </apply>
         </apply>
      </math>
   </component>
   
  <import xlink:href="http://models.cellml.org/workspace/SVP_00000007/@@rawfile/b16bb1d30c3ae6d0f304223c80bed86bf19c55e7/Bioenvironment_Degradation_PhzM.cellml">
                  <component name="Bioenvironment_Degradation_PhzM" component_ref="Bioenvironment_Degradation_PhzM" />
  </import>
  
  <component name="PCA">
          <variable name="concentration" units="nM" initial_value="2" public_interface="out"/>
  </component>
  
  <import xlink:href="http://models.cellml.org/workspace/SVP_00000018/@@rawfile/db93705913efb3c62bcde923ca62dba76850368a/Bioenvironment_RxR1P1MM_ICFormation.cellml">
             <component name="RxR1P1MM_ICformation" component_ref="Bioenvironment_RxR1P1MM_ICFormation" />
  </import>
  
  <import xlink:href="http://models.cellml.org/workspace/SVP_Templates200906/@@rawfile/b1e53aaa6bb9f958b4ddb2412bb1ae417c45e250/Template_Species.cellml">
             <component name="IC" component_ref="Template_Species" />
  </import>
  
  <component name="IC_interface">
      <variable name="JPlusProduction" units="nM_per_s" public_interface="in"/>
      <variable name="JGain" units="nM_per_s" public_interface="out"/>
      <variable name="JMinusDegradation" units="nM_per_s" public_interface="in"/>
      <variable name="JMinusPYOFormation" units="nM_per_s" public_interface="in"/>
      <math xmlns="http://www.w3.org/1998/Math/MathML">
         <apply>
            <eq/>
            <ci>JGain</ci>
            <apply>
               <minus/>
               <apply>
                  <minus/>
                  <ci>JPlusProduction</ci>
                  <ci>JMinusDegradation</ci>
               </apply>
               <ci>JMinusPYOFormation</ci>
            </apply>
         </apply>
      </math>
   </component>
  
  <import xlink:href="http://models.cellml.org/workspace/SVP_00000006/@@rawfile/07c66e9a83811d6ee92a7069053b8e7a85a3dc40/Bioenvironment_Degradation_IC.cellml">
                     <component name="Bioenvironment_Degradation_IC" component_ref="Bioenvironment_Degradation_IC" />
  </import>
  
  <import xlink:href="http://models.cellml.org/workspace/SVP_Templates200906/@@rawfile/b1e53aaa6bb9f958b4ddb2412bb1ae417c45e250/Template_Species.cellml">
             <component name="PhzS" component_ref="Template_Species" />
  </import>
  
  <component name="PhzS_interface">
      <variable name="JPlusProduction" units="nM_per_s" public_interface="in"/>
      <variable name="JGain" units="nM_per_s" public_interface="out"/>
      <variable name="JMinusDegradation" units="nM_per_s" public_interface="in"/>
      <math xmlns="http://www.w3.org/1998/Math/MathML">
         <apply>
            <eq/>
            <ci>JGain</ci>
            <apply>
               <minus/>
               <ci>JPlusProduction</ci>
               <ci>JMinusDegradation</ci>
            </apply>
         </apply>
      </math>
   </component>  
  
  <import xlink:href="http://models.cellml.org/workspace/SVP_00000008/@@rawfile/bb696f40cbaa3f7afc8b0adf82be27da296c55f8/Bioenvironment_Degradation_PhzS.cellml">
          <component name="Bioenvironment_Degradation_PhzS" component_ref="Bioenvironment_Degradation_PhzS" />
  </import>  
  
  <import xlink:href="http://models.cellml.org/workspace/SVP_00000019/@@rawfile/12561c856efc2538d19edc1e66bc2b51c18d3924/Bioenvironment_RxR1P1MM_PYOFormation.cellml">
            <component name="RxR1P1MM_PYOformation" component_ref="Bioenvironment_RxR1P1MM_PYOFormation" />
  </import>  
  
  <import xlink:href="http://models.cellml.org/workspace/SVP_Templates200906/@@rawfile/b1e53aaa6bb9f958b4ddb2412bb1ae417c45e250/Template_Species.cellml">
             <component name="PYO" component_ref="Template_Species" />
  </import>

   <component name="PYO_interface">
      <variable name="JPlusProduction" units="nM_per_s" public_interface="in"/>
      <variable name="JGain" units="nM_per_s" public_interface="out"/>
      <variable name="JMinusDegradation" units="nM_per_s" public_interface="in"/>
      <math xmlns="http://www.w3.org/1998/Math/MathML">
         <apply>
            <eq/>
            <ci>JGain</ci>
            <apply>
               <minus/>
               <ci>JPlusProduction</ci>
               <ci>JMinusDegradation</ci>
            </apply>
         </apply>
      </math>
   </component>
   
  <import xlink:href="http://models.cellml.org/workspace/SVP_00000009/@@rawfile/daca30aa00cdb9cf860873ef04af99930c74f883/Bioenvironment_Degradation_PYO.cellml">
             <component name="Bioenvironment_Degradation_PYO" component_ref="Bioenvironment_Degradation_PYO" />
  </import>
  
   <connection>
      <map_components component_1="ElectrEcoBluDevice1_Promoter" component_2="eColiCell"/>
      <map_variables variable_1="localVolume" variable_2="cellVolume"/>
   </connection>
   
   <connection>
      <map_components component_1="RNA_Device1" component_2="Time"/>
      <map_variables variable_1="time" variable_2="time"/>
   </connection>
   
   <connection>
      <map_components component_1="RNA_Device1" component_2="SpeciesInitialConcentrations"/>
      <map_variables variable_1="concentrationInitialValue" variable_2="RNA_Device1"/>
   </connection>
   
   <connection>
      <map_components component_1="RNA_Device1_interface" component_2="Bioenvironment_Degradation_Device1RNA"/>
      <map_variables variable_1="JMinusDegradation" variable_2="J"/>
   </connection>
   
   <connection>
      <map_components component_1="RNA_Device1" component_2="RNA_Device1_interface"/>
      <map_variables variable_1="JGain" variable_2="JGain"/>
   </connection>
   
   <connection>
      <map_components component_1="RNA_Device1_interface" component_2="ElectrEcoBluDevice1_Promoter"/>
      <map_variables variable_1="JPlusPromoter" variable_2="JRNA"/>
   </connection>
   
   <connection>
      <map_components component_1="Bioenvironment_Degradation_Device1RNA" component_2="RNA_Device1"/>
      <map_variables variable_1="concentration" variable_2="concentration"/>
   </connection>
   
   <connection>
      <map_components component_1="ElectrEcoBluDevice1_RBS" component_2="eColiCell"/>
      <map_variables variable_1="localVolume" variable_2="cellVolume"/>
   </connection>
   
   <connection>
      <map_components component_1="ElectrEcoBluDevice1_RBS" component_2="RNA_Device1"/>
      <map_variables variable_1="RNA" variable_2="concentration"/>
   </connection>
   
   <connection>
      <map_components component_1="ElectrEcoBluDevice1_ProteinCDS_TF" component_2="eColiCell"/>
      <map_variables variable_1="localVolume" variable_2="cellVolume"/>
   </connection>
   
   <connection>
      <map_components component_1="ElectrEcoBluDevice1_ProteinCDS_TF" component_2="ElectrEcoBluDevice1_RBS"/>
      <map_variables variable_1="hostRNARiPs" variable_2="RNARiPs"/>
   </connection>
  
   <connection>
      <map_components component_1="TF" component_2="Time"/>
      <map_variables variable_1="time" variable_2="time"/>
   </connection>
   
   <connection>
      <map_components component_1="TF" component_2="TF_interface"/>
      <map_variables variable_1="JGain" variable_2="JGain"/>
   </connection>
   
   <connection>
         <map_components component_1="TF" component_2="SpeciesInitialConcentrations"/>
         <map_variables variable_1="concentrationInitialValue" variable_2="TF"/>
   </connection>
  
   <connection>
      <map_components component_1="TF_interface" component_2="ElectrEcoBluDevice1_ProteinCDS_TF"/>
      <map_variables variable_1="JPlusProductionDevice1" variable_2="J"/>
   </connection>
   
   <connection>
      <map_components component_1="TF_interface" component_2="ElectrEcoBluDevice2_ProteinCDS_TF"/>
      <map_variables variable_1="JPlusProductionDevice2" variable_2="J"/>
   </connection>
   
   <connection>
      <map_components component_1="TF_interface" component_2="Bioenvironment_Degradation_TF"/>
      <map_variables variable_1="JMinusDegradation" variable_2="J"/>
   </connection>
   
   <connection>
      <map_components component_1="TF_interface" component_2="RxR2P1_TFSformation"/>
      <map_variables variable_1="JMinusTFSFormation" variable_2="J"/>
   </connection>
   
   <connection>
       <map_components component_1="Bioenvironment_Degradation_TF" component_2="TF"/>
       <map_variables variable_1="concentration" variable_2="concentration"/>
   </connection>
   
   <connection>
       <map_components component_1="RxR2P1_TFSformation" component_2="TF"/>
       <map_variables variable_1="reactant1" variable_2="concentration"/>
   </connection>
   
   <connection>
      <map_components component_1="RxR2P1_TFSformation" component_2="S"/>
      <map_variables variable_1="reactant2" variable_2="concentration"/>
   </connection>
   
   <connection>
      <map_components component_1="RxR2P1_TFSformation" component_2="TFS"/>
      <map_variables variable_1="product" variable_2="concentration"/>
   </connection>
   
   <connection>
      <map_components component_1="TFS" component_2="Time"/>
      <map_variables variable_1="time" variable_2="time"/>
   </connection>
   
   <connection>
      <map_components component_1="TFS" component_2="TFS_interface"/>
      <map_variables variable_1="JGain" variable_2="JGain"/>
   </connection>
   
   <connection>
      <map_components component_1="TFS_interface" component_2="RxR2P1_TFSformation"/>
      <map_variables variable_1="JPlusProduction" variable_2="J"/>
   </connection>
   
   <connection>
      <map_components component_1="TFS" component_2="SpeciesInitialConcentrations"/>
      <map_variables variable_1="concentrationInitialValue" variable_2="TFS"/>
   </connection>
   
   <connection>
      <map_components component_1="TFS_interface" component_2="Bioenvironment_Degradation_TFS"/>
      <map_variables variable_1="JMinusDegradation" variable_2="J"/>
   </connection>
   
   <connection>
      <map_components component_1="Bioenvironment_Degradation_TFS" component_2="TFS"/>
      <map_variables variable_1="concentration" variable_2="concentration"/>
   </connection>
   
   <connection>
      <map_components component_1="ElectrEcoBluDevice2_Promoter" component_2="eColiCell"/>
      <map_variables variable_1="localVolume" variable_2="cellVolume"/>
   </connection>
   
   <connection>
      <map_components component_1="ElectrEcoBluDevice2_Promoter" component_2="TFS"/>
      <map_variables variable_1="tFactor" variable_2="concentration"/>
   </connection>
   
   <connection>
      <map_components component_1="RNA_Device2_interface" component_2="ElectrEcoBluDevice2_Promoter"/>
      <map_variables variable_1="JPlusPromoter" variable_2="JRNA"/>
   </connection>
   
   <connection>
      <map_components component_1="RNA_Device2_interface" component_2="Bioenvironment_Degradation_Device2RNA"/>
      <map_variables variable_1="JMinusDegradation" variable_2="J"/>
   </connection>
  
   <connection>
      <map_components component_1="RNA_Device2" component_2="RNA_Device2_interface"/>
      <map_variables variable_1="JGain" variable_2="JGain"/>
   </connection>
   
   <connection>
      <map_components component_1="RNA_Device2" component_2="Time"/>
      <map_variables variable_1="time" variable_2="time"/>
   </connection>
   
   <connection>
       <map_components component_1="RNA_Device2" component_2="SpeciesInitialConcentrations"/>
       <map_variables variable_1="concentrationInitialValue" variable_2="RNA_Device2"/>
   </connection>
   
   <connection>
      <map_components component_1="Bioenvironment_Degradation_Device2RNA" component_2="RNA_Device2"/>
      <map_variables variable_1="concentration" variable_2="concentration"/>
   </connection>
   
   <connection>
      <map_components component_1="ElectrEcoBluDevice2_RBS_PhzM" component_2="eColiCell"/>
      <map_variables variable_1="localVolume" variable_2="cellVolume"/>
   </connection>
   
   <connection>
      <map_components component_1="ElectrEcoBluDevice2_RBS_PhzM" component_2="RNA_Device2"/>
      <map_variables variable_1="RNA" variable_2="concentration"/>
   </connection>
   
   <connection>
      <map_components component_1="ElectrEcoBluDevice2_ProteinCDS_PhzM" component_2="eColiCell"/>
      <map_variables variable_1="localVolume" variable_2="cellVolume"/>
   </connection>
   
   <connection>
      <map_components component_1="ElectrEcoBluDevice2_ProteinCDS_PhzM" component_2="ElectrEcoBluDevice2_RBS_PhzM"/>
      <map_variables variable_1="hostRNARiPs" variable_2="RNARiPs"/>
   </connection>
   
   <connection>
      <map_components component_1="ElectrEcoBluDevice2_RBS_PhzS" component_2="eColiCell"/>
      <map_variables variable_1="localVolume" variable_2="cellVolume"/>
   </connection>
   
   <connection>
      <map_components component_1="ElectrEcoBluDevice2_RBS_PhzS" component_2="RNA_Device2"/>
      <map_variables variable_1="RNA" variable_2="concentration"/>
   </connection>
   
   <connection>
      <map_components component_1="ElectrEcoBluDevice2_ProteinCDS_PhzS" component_2="eColiCell"/>
      <map_variables variable_1="localVolume" variable_2="cellVolume"/>
   </connection>
   
   <connection>
      <map_components component_1="ElectrEcoBluDevice2_ProteinCDS_PhzS" component_2="ElectrEcoBluDevice2_RBS_PhzS"/>
      <map_variables variable_1="hostRNARiPs" variable_2="RNARiPs"/>
   </connection>
   
   <connection>
      <map_components component_1="ElectrEcoBluDevice2_RBS_TF" component_2="eColiCell"/>
      <map_variables variable_1="localVolume" variable_2="cellVolume"/>
   </connection>
   
   <connection>
      <map_components component_1="ElectrEcoBluDevice2_RBS_TF" component_2="RNA_Device2"/>
      <map_variables variable_1="RNA" variable_2="concentration"/>
   </connection>
   
   <connection>
      <map_components component_1="ElectrEcoBluDevice2_ProteinCDS_TF" component_2="eColiCell"/>
      <map_variables variable_1="localVolume" variable_2="cellVolume"/>
   </connection>
   
   <connection>
      <map_components component_1="ElectrEcoBluDevice2_ProteinCDS_TF" component_2="ElectrEcoBluDevice2_RBS_TF"/>
      <map_variables variable_1="hostRNARiPs" variable_2="RNARiPs"/>
   </connection>
   
   <connection>
      <map_components component_1="PhzM" component_2="Time"/>
      <map_variables variable_1="time" variable_2="time"/>
   </connection>
   
   <connection>
      <map_components component_1="PhzM" component_2="PhzM_interface"/>
      <map_variables variable_1="JGain" variable_2="JGain"/>
   </connection>
   
   <connection>
    <map_components component_1="PhzM" component_2="SpeciesInitialConcentrations"/>
    <map_variables variable_1="concentrationInitialValue" variable_2="PhzM"/>
   </connection> 
   
   <connection>
      <map_components component_1="PhzM_interface" component_2="ElectrEcoBluDevice2_ProteinCDS_PhzM"/>
      <map_variables variable_1="JPlusProduction" variable_2="J"/>
   </connection>
   
   <connection>
      <map_components component_1="PhzM_interface" component_2="Bioenvironment_Degradation_PhzM"/>
      <map_variables variable_1="JMinusDegradation" variable_2="J"/>
   </connection>
   
   <connection>
       <map_components component_1="Bioenvironment_Degradation_PhzM" component_2="PhzM"/>
       <map_variables variable_1="concentration" variable_2="concentration"/>
   </connection>

   <connection>
      <map_components component_1="RxR1P1MM_ICformation" component_2="PCA"/>
      <map_variables variable_1="reactant" variable_2="concentration"/>
   </connection> 

   <connection>
      <map_components component_1="RxR1P1MM_ICformation" component_2="PhzM"/>
      <map_variables variable_1="catalyst" variable_2="concentration"/>
   </connection>
   
   <connection>
    <map_components component_1="IC" component_2="SpeciesInitialConcentrations"/>
    <map_variables variable_1="concentrationInitialValue" variable_2="IC"/>
   </connection>
   
   <connection>
      <map_components component_1="IC" component_2="Time"/>
      <map_variables variable_1="time" variable_2="time"/>
   </connection>
   
   <connection>
      <map_components component_1="IC" component_2="IC_interface"/>
      <map_variables variable_1="JGain" variable_2="JGain"/>
   </connection>  
   
   <connection>
      <map_components component_1="IC_interface" component_2="Bioenvironment_Degradation_IC"/>
      <map_variables variable_1="JMinusDegradation" variable_2="J"/>
   </connection>
   
   <connection>
      <map_components component_1="IC_interface" component_2="RxR1P1MM_ICformation"/>
      <map_variables variable_1="JPlusProduction" variable_2="J"/>
   </connection>
   
   <connection>
      <map_components component_1="IC_interface" component_2="RxR1P1MM_PYOformation"/>
      <map_variables variable_1="JMinusPYOFormation" variable_2="J"/>
   </connection>
   
   <connection>
      <map_components component_1="Bioenvironment_Degradation_IC" component_2="IC"/>
      <map_variables variable_1="concentration" variable_2="concentration"/>
   </connection>
   
   <connection>
      <map_components component_1="PhzS" component_2="Time"/>
      <map_variables variable_1="time" variable_2="time"/>
   </connection>
   
   <connection>
      <map_components component_1="PhzS" component_2="PhzS_interface"/>
      <map_variables variable_1="JGain" variable_2="JGain"/>
   </connection>
   
   <connection>
    <map_components component_1="PhzS" component_2="SpeciesInitialConcentrations"/>
    <map_variables variable_1="concentrationInitialValue" variable_2="PhzS"/>
   </connection>
   
   <connection>
      <map_components component_1="PhzS_interface" component_2="Bioenvironment_Degradation_PhzS"/>
      <map_variables variable_1="JMinusDegradation" variable_2="J"/>
   </connection>
   
   <connection>
      <map_components component_1="PhzS_interface" component_2="ElectrEcoBluDevice2_ProteinCDS_PhzS"/>
      <map_variables variable_1="JPlusProduction" variable_2="J"/>
   </connection>
   
   <connection>
      <map_components component_1="Bioenvironment_Degradation_PhzS" component_2="PhzS"/>
      <map_variables variable_1="concentration" variable_2="concentration"/>
   </connection>
   
   <connection>
      <map_components component_1="RxR1P1MM_PYOformation" component_2="IC"/>
      <map_variables variable_1="reactant" variable_2="concentration"/>
   </connection>
   
   <connection>
      <map_components component_1="RxR1P1MM_PYOformation" component_2="PhzS"/>
      <map_variables variable_1="catalyst" variable_2="concentration"/>
   </connection>
   
   <connection>
      <map_components component_1="PYO" component_2="Time"/>
      <map_variables variable_1="time" variable_2="time"/>
   </connection>
   
   <connection>
      <map_components component_1="PYO" component_2="PYO_interface"/>
      <map_variables variable_1="JGain" variable_2="JGain"/>
   </connection>
   
   <connection>
       <map_components component_1="PYO" component_2="SpeciesInitialConcentrations"/>
       <map_variables variable_1="concentrationInitialValue" variable_2="PYO"/>
   </connection>
      
   <connection>
      <map_components component_1="PYO_interface" component_2="Bioenvironment_Degradation_PYO"/>
      <map_variables variable_1="JMinusDegradation" variable_2="J"/>
   </connection>
   
   <connection>
      <map_components component_1="PYO_interface" component_2="RxR1P1MM_PYOformation"/>
      <map_variables variable_1="JPlusProduction" variable_2="J"/>
   </connection>
   
   <connection>
      <map_components component_1="Bioenvironment_Degradation_PYO" component_2="PYO"/>
      <map_variables variable_1="concentration" variable_2="concentration"/>
   </connection>
   
</model>