- Author:
- Catherine Lloyd <c.lloyd@auckland.ac.nz>
- Date:
- 2010-05-26 19:58:38+12:00
- Desc:
- Fixed model metadata and added meaningful names to the different model versions. Although this has been checked and the metadata is correct, because the metadata set is "incomplete" (as far as PMR2 is concerned) it may not display properly.
- Permanent Source URI:
- http://models.cellml.org/workspace/electrecoblu/rawfile/716bd4229b78591bca8526e8059c7ac7ba1c67e4/ElectrEcoBluModel.cellml
<?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 xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqs="http://www.cellml.org/bqs/1.0#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#">
<rdf:Description rdf:about="">
<dc:title>ElectEcoBluModel: including a positive feedback loop</dc:title>
<dc:creator rdf:parseType="Resource">
<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>The University of Auckland</vCard:Orgname>
<vCard:Orgunit>Auckland Bioengineering Institute</vCard:Orgunit>
</vCard:ORG>
</dc:creator>
</rdf:Description>
<rdf:Description rdf:about="#ElectrEcoBluModel_SVBM">
<bqs:reference rdf:parseType="Resource">
<dc:subject rdf:parseType="Resource">
<bqs:subject_type>keyword</bqs:subject_type>
<rdf:value>
<rdf:Bag>
<rdf:li>synthetic biology</rdf:li>
<rdf:li>gene regulation</rdf:li>
</rdf:Bag>
</rdf:value>
</dc:subject>
</bqs:reference>
</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>
