- Author:
- Mike Cooling <m.cooling@auckland.ac.nz>
- Date:
- 2010-12-03 16:39:16+13:00
- Desc:
- updated SVPs 12,13 and 16 to include their Templates...
- Permanent Source URI:
- http://models.cellml.org/workspace/bugbuster/rawfile/8071102781e2ced9ca3c68e48b8f0f5fbad97459/BugbusterModel.cellml
<?xml version="1.0" encoding="utf-8"?>
<model name="BugbusterModel_SVBM" cmeta:id="BugbusterModel_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#"
xmlns:bqs="http://www.cellml.org/bqs/1.0#"
xmlns:dcterms="http://purl.org/dc/terms/">
<rdf:RDF>
<rdf:Description rdf:about="">
<!--
The Model Builder Metadata. The Dublin Core "creator" element is used
to indicate the person who translated the model into CellML.
The rdf:about of the Description has to remain blank for PMR2 to pick this up properly....
-->
<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="#BugbusterModel_SVBM">
<bqs:reference rdf:parseType="Resource">
<bqs:JournalArticle rdf:parseType="Resource">
<dc:creator>
<rdf:Seq>
<rdf:li 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>Auckland Bioengineering Institute</vCard:Orgname>
<vCard:Orgunit>University of Auckland</vCard:Orgunit>
</vCard:ORG>
</rdf:li>
<rdf:li rdf:parseType="Resource">
<vCard:N rdf:parseType="Resource">
<vCard:Family>Rouilly</vCard:Family>
<vCard:Given>Vincent</vCard:Given>
</vCard:N>
</rdf:li>
<rdf:li rdf:parseType="Resource">
<vCard:N rdf:parseType="Resource">
<vCard:Family>Misirli</vCard:Family>
<vCard:Given>Goksel</vCard:Given>
</vCard:N>
</rdf:li>
<rdf:li rdf:parseType="Resource">
<vCard:N rdf:parseType="Resource">
<vCard:Family>Lawson</vCard:Family>
<vCard:Given>James</vCard:Given>
</vCard:N>
</rdf:li>
<rdf:li rdf:parseType="Resource">
<vCard:N rdf:parseType="Resource">
<vCard:Family>Yu</vCard:Family>
<vCard:Given>Tommy</vCard:Given>
</vCard:N>
</rdf:li>
<rdf:li rdf:parseType="Resource">
<vCard:N rdf:parseType="Resource">
<vCard:Family>Hallinan</vCard:Family>
<vCard:Given>Jennifer</vCard:Given>
</vCard:N>
</rdf:li>
<rdf:li rdf:parseType="Resource">
<vCard:N rdf:parseType="Resource">
<vCard:Family>Wipat</vCard:Family>
<vCard:Given>Anil</vCard:Given>
</vCard:N>
</rdf:li>
</rdf:Seq>
</dc:creator>
<dc:title>Standard Virtual Biological Parts: A Repository of Modular Modeling Components for Synthetic Biology</dc:title>
<bqs:volume>26</bqs:volume>
<bqs:first_page>925</bqs:first_page>
<bqs:last_page>931</bqs:last_page>
<bqs:Journal rdf:parseType="Resource">
<dc:title>Bioinformatics</dc:title>
</bqs:Journal>
<dcterms:issued rdf:parseType="Resource">
<dcterms:W3CDTF>2010-00-00 00:00</dcterms:W3CDTF>
</dcterms:issued>
</bqs:JournalArticle>
</bqs:reference>
</rdf:Description>
</rdf:RDF>
<import xlink:href="SVP_00000031/Chassis_Bacillus.cellml">
<component name="ChassisBacillus" component_ref="Chassis_Bacillus" />
</import>
<import xlink:href="SVP_Templates200906/Time.cellml">
<component name="Time" component_ref="Time" />
</import>
<component name="Subtilin">
<variable name="concentration" units="nM" initial_value="1000" public_interface="out"/>
</component>
<component name="SpeciesInitialConcentrations">
<variable name="RNA1" units="nM" initial_value="0" public_interface="out" />
<variable name="RNA2" units="nM" initial_value="0" public_interface="out" />
<variable name="spaK" units="nM" initial_value="0" public_interface="out" />
<variable name="spaR" units="nM" initial_value="0" public_interface="out" />
<variable name="spaKactive" units="nM" initial_value="0" public_interface="out" />
<variable name="spaRactive" units="nM" initial_value="0" public_interface="out" />
<variable name="GFP" units="nM" initial_value="0" public_interface="out" />
</component>
<import xlink:href="SVP_00000023/Bugbuster_Promoter1.cellml">
<units name="nM_per_s" units_ref="nM_per_s" />
<component name="Bugbuster_Promoter1" component_ref="Bugbuster_Promoter1" />
</import>
<import xlink:href="SVP_Templates200906/Template_Species.cellml">
<units name="nM" units_ref="nM" />
<component name="RNA1" component_ref="Template_Species" />
</import>
<component name="RNA1_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="SVP_00000001/Bioenvironment_Degradation_BugbusterRNA1.cellml">
<units name="per_s" units_ref="per_s" />
<component name="Bioenvironment_Degradation_RNA1" component_ref="Bioenvironment_Degradation_BugbusterRNA1" />
</import>
<import xlink:href="SVP_00000030/Bugbuster_RBS_spaR.cellml">
<component name="Bugbuster_RBS_spaR" component_ref="Bugbuster_RBS_spaR" />
</import>
<import xlink:href="SVP_00000027/Bugbuster_ProteinCDS_spaR.cellml">
<component name="Bugbuster_ProteinCDS_spaR" component_ref="Bugbuster_ProteinCDS_spaR" />
</import>
<import xlink:href="SVP_00000029/Bugbuster_RBS_spaK.cellml">
<component name="Bugbuster_RBS_spaK" component_ref="Bugbuster_RBS_spaK" />
</import>
<import xlink:href="SVP_00000026/Bugbuster_ProteinCDS_spaK.cellml">
<component name="Bugbuster_ProteinCDS_spaK" component_ref="Bugbuster_ProteinCDS_spaK" />
</import>
<import xlink:href="SVP_Templates200906/Template_Species.cellml">
<component name="spaK" component_ref="Template_Species" />
</import>
<component name="spaK_interface">
<variable name="JPlusProduction" units="nM_per_s" public_interface="in"/>
<variable name="JPlusspaRActivation" units="nM_per_s" public_interface="in"/>
<variable name="JPlusspaKActiveDephosphorylation" units="nM_per_s" public_interface="in"/>
<variable name="JMinusDegradation" units="nM_per_s" public_interface="in"/>
<variable name="JMinusspaKActivation" 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>
<plus/>
<ci>JPlusProduction</ci>
<ci>JPlusspaRActivation</ci>
<ci>JPlusspaKActiveDephosphorylation</ci>
</apply>
<apply>
<plus/>
<ci>JMinusspaKActivation</ci>
<ci>JMinusDegradation</ci>
</apply>
</apply>
</apply>
</math>
</component>
<import xlink:href="SVP_00000010/Bioenvironment_Degradation_spaK.cellml">
<component name="Bioenvironment_Degradation_spaK" component_ref="Bioenvironment_Degradation_spaK" />
</import>
<import xlink:href="SVP_00000020/Bioenvironment_RxR2P1_spaKActivation.cellml">
<component name="spaKActivation" component_ref="Bioenvironment_RxR2P1_spaKActivation" />
</import>
<import xlink:href="SVP_Templates200906/Template_Species.cellml">
<component name="spaKactive" component_ref="Template_Species" />
</import>
<component name="spaKactive_interface">
<variable name="JPlusspaKActivation" units="nM_per_s" public_interface="in"/>
<variable name="JMinusDegradation" units="nM_per_s" public_interface="in"/>
<variable name="JMinusDephosphorylation" units="nM_per_s" public_interface="in"/>
<variable name="JMinusspaRActivation" 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/>
<ci>JPlusspaKActivation</ci>
<apply>
<plus />
<ci>JMinusDegradation</ci>
<ci>JMinusDephosphorylation</ci>
<ci>JMinusspaRActivation</ci>
</apply>
</apply>
</apply>
</math>
</component>
<import xlink:href="SVP_00000016/Bioenvironment_Dephosphorylation_spaKactive.cellml">
<component name="Bioenvironment_Dephosphorylation_spaKactive" component_ref="Bioenvironment_Dephosphorylation_spaKactive" />
</import>
<import xlink:href="SVP_00000011/Bioenvironment_Degradation_spaKactive.cellml">
<component name="Bioenvironment_Degradation_spaKactive" component_ref="Bioenvironment_Degradation_spaKactive" />
</import>
<import xlink:href="SVP_Templates200906/Template_Species.cellml">
<component name="spaR" component_ref="Template_Species" />
</import>
<component name="spaR_interface">
<variable name="JPlusProduction" units="nM_per_s" public_interface="in"/>
<variable name="JMinusDegradation" units="nM_per_s" public_interface="in"/>
<variable name="JMinusspaRActivation" units="nM_per_s" public_interface="in"/>
<variable name="JPlusspaRActiveDephosphorylation" 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>
<plus/>
<ci>JPlusProduction</ci>
<ci>JPlusspaRActiveDephosphorylation</ci>
</apply>
<apply>
<plus/>
<ci>JMinusDegradation</ci>
<ci>JMinusspaRActivation</ci>
</apply>
</apply>
</apply>
</math>
</component>
<import xlink:href="SVP_00000012/Bioenvironment_Degradation_spaR.cellml">
<component name="Bioenvironment_Degradation_spaR" component_ref="Bioenvironment_Degradation_spaR" />
</import>
<import xlink:href="SVP_00000021/Bioenvironment_RxR2P1_spaRActivation.cellml">
<component name="spaRActivation" component_ref="Bioenvironment_RxR2P1_spaRActivation" />
</import>
<import xlink:href="SVP_Templates200906/Template_Species.cellml">
<component name="spaRactive" component_ref="Template_Species" />
</import>
<component name="spaRactive_interface">
<variable name="JMinusDegradation" units="nM_per_s" public_interface="in"/>
<variable name="JMinusDephosphorylation" units="nM_per_s" public_interface="in"/>
<variable name="JPlusspaRActivation" 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/>
<ci>JPlusspaRActivation</ci>
<apply>
<plus />
<ci>JMinusDegradation</ci>
<ci>JMinusDephosphorylation</ci>
</apply>
</apply>
</apply>
</math>
</component>
<import xlink:href="SVP_00000017/Bioenvironment_Dephosphorylation_spaRactive.cellml">
<component name="Bioenvironment_Dephosphorylation_spaRactive" component_ref="Bioenvironment_Dephosphorylation_spaRactive" />
</import>
<import xlink:href="SVP_00000013/Bioenvironment_Degradation_spaRactive.cellml">
<component name="Bioenvironment_Degradation_spaRactive" component_ref="Bioenvironment_Degradation_spaRactive" />
</import>
<import xlink:href="SVP_00000024/Bugbuster_Promoter2.cellml">
<component name="Bugbuster_Promoter2" component_ref="Bugbuster_Promoter2" />
</import>
<import xlink:href="SVP_Templates200906/Template_Species.cellml">
<component name="RNA2" component_ref="Template_Species" />
</import>
<component name="RNA2_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="SVP_00000002/Bioenvironment_Degradation_BugbusterRNA2.cellml">
<component name="Bioenvironment_Degradation_RNA2" component_ref="Bioenvironment_Degradation_BugbusterRNA2" />
</import>
<import xlink:href="SVP_00000028/Bugbuster_RBS_GFP.cellml">
<component name="Bugbuster_RBS_GFP" component_ref="Bugbuster_RBS_GFP" />
</import>
<import xlink:href="SVP_00000025/Bugbuster_ProteinCDS_GFP.cellml">
<component name="Bugbuster_ProteinCDS_GFP" component_ref="Bugbuster_ProteinCDS_GFP" />
</import>
<import xlink:href="SVP_Templates200906/Template_Species.cellml">
<component name="GFP" component_ref="Template_Species" />
</import>
<component name="GFP_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="SVP_00000005/Bioenvironment_Degradation_GFP.cellml">
<component name="Bioenvironment_Degradation_GFP" component_ref="Bioenvironment_Degradation_GFP" />
</import>
<connection>
<map_components component_1="Bugbuster_Promoter1" component_2="ChassisBacillus"/>
<map_variables variable_1="localVolume" variable_2="cellVolume"/>
</connection>
<connection>
<map_components component_1="RNA1" component_2="Time"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<connection>
<map_components component_1="RNA1" component_2="SpeciesInitialConcentrations"/>
<map_variables variable_1="concentrationInitialValue" variable_2="RNA1"/>
</connection>
<connection>
<map_components component_1="RNA1" component_2="RNA1_interface"/>
<map_variables variable_1="JGain" variable_2="JGain"/>
</connection>
<connection>
<map_components component_1="RNA1_interface" component_2="Bugbuster_Promoter1"/>
<map_variables variable_1="JPlusProduction" variable_2="JRNA"/>
</connection>
<connection>
<map_components component_1="RNA1_interface" component_2="Bioenvironment_Degradation_RNA1"/>
<map_variables variable_1="JMinusDegradation" variable_2="J"/>
</connection>
<connection>
<map_components component_1="Bioenvironment_Degradation_RNA1" component_2="RNA1"/>
<map_variables variable_1="concentration" variable_2="concentration"/>
</connection>
<connection>
<map_components component_1="Bugbuster_RBS_spaR" component_2="ChassisBacillus"/>
<map_variables variable_1="localVolume" variable_2="cellVolume"/>
</connection>
<connection>
<map_components component_1="Bugbuster_RBS_spaR" component_2="RNA1"/>
<map_variables variable_1="RNA" variable_2="concentration"/>
</connection>
<connection>
<map_components component_1="Bugbuster_ProteinCDS_spaR" component_2="ChassisBacillus"/>
<map_variables variable_1="localVolume" variable_2="cellVolume"/>
</connection>
<connection>
<map_components component_1="Bugbuster_ProteinCDS_spaR" component_2="Bugbuster_RBS_spaR"/>
<map_variables variable_1="hostRNARiPs" variable_2="RNARiPs"/>
</connection>
<connection>
<map_components component_1="Bugbuster_RBS_spaK" component_2="RNA1"/>
<map_variables variable_1="RNA" variable_2="concentration"/>
</connection>
<connection>
<map_components component_1="Bugbuster_RBS_spaK" component_2="ChassisBacillus"/>
<map_variables variable_1="localVolume" variable_2="cellVolume"/>
</connection>
<connection>
<map_components component_1="Bugbuster_ProteinCDS_spaK" component_2="ChassisBacillus"/>
<map_variables variable_1="localVolume" variable_2="cellVolume"/>
</connection>
<connection>
<map_components component_1="Bugbuster_ProteinCDS_spaK" component_2="Bugbuster_RBS_spaK"/>
<map_variables variable_1="hostRNARiPs" variable_2="RNARiPs"/>
</connection>
<connection>
<map_components component_1="spaK" component_2="spaK_interface"/>
<map_variables variable_1="JGain" variable_2="JGain"/>
</connection>
<connection>
<map_components component_1="spaK" component_2="Time"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<connection>
<map_components component_1="spaK" component_2="SpeciesInitialConcentrations"/>
<map_variables variable_1="concentrationInitialValue" variable_2="spaK"/>
</connection>
<connection>
<map_components component_1="spaK_interface" component_2="Bugbuster_ProteinCDS_spaK"/>
<map_variables variable_1="JPlusProduction" variable_2="J"/>
</connection>
<connection>
<map_components component_1="spaK_interface" component_2="Bioenvironment_Degradation_spaK"/>
<map_variables variable_1="JMinusDegradation" variable_2="J"/>
</connection>
<connection>
<map_components component_1="spaK_interface" component_2="spaKActivation"/>
<map_variables variable_1="JMinusspaKActivation" variable_2="J"/>
</connection>
<connection>
<map_components component_1="spaK_interface" component_2="Bioenvironment_Dephosphorylation_spaKactive"/>
<map_variables variable_1="JPlusspaKActiveDephosphorylation" variable_2="J"/>
</connection>
<connection>
<map_components component_1="spaK_interface" component_2="spaRActivation"/>
<map_variables variable_1="JPlusspaRActivation" variable_2="J"/>
</connection>
<connection>
<map_components component_1="Bioenvironment_Degradation_spaK" component_2="spaK"/>
<map_variables variable_1="concentration" variable_2="concentration"/>
</connection>
<connection>
<map_components component_1="spaKActivation" component_2="Subtilin"/>
<map_variables variable_1="reactant1" variable_2="concentration"/>
</connection>
<connection>
<map_components component_1="spaKActivation" component_2="spaK"/>
<map_variables variable_1="reactant2" variable_2="concentration"/>
</connection>
<connection>
<map_components component_1="spaKactive" component_2="spaKactive_interface"/>
<map_variables variable_1="JGain" variable_2="JGain"/>
</connection>
<connection>
<map_components component_1="spaKactive" component_2="Time"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<connection>
<map_components component_1="spaKactive" component_2="SpeciesInitialConcentrations"/>
<map_variables variable_1="concentrationInitialValue" variable_2="spaKactive"/>
</connection>
<connection>
<map_components component_1="spaKactive_interface" component_2="spaKActivation"/>
<map_variables variable_1="JPlusspaKActivation" variable_2="J"/>
</connection>
<connection>
<map_components component_1="spaKactive_interface" component_2="Bioenvironment_Dephosphorylation_spaKactive"/>
<map_variables variable_1="JMinusDephosphorylation" variable_2="J"/>
</connection>
<connection>
<map_components component_1="spaKactive_interface" component_2="Bioenvironment_Degradation_spaKactive"/>
<map_variables variable_1="JMinusDegradation" variable_2="J"/>
</connection>
<connection>
<map_components component_1="spaKactive_interface" component_2="spaRActivation"/>
<map_variables variable_1="JMinusspaRActivation" variable_2="J"/>
</connection>
<connection>
<map_components component_1="Bioenvironment_Dephosphorylation_spaKactive" component_2="spaKactive"/>
<map_variables variable_1="concentration" variable_2="concentration"/>
</connection>
<connection>
<map_components component_1="Bioenvironment_Degradation_spaKactive" component_2="spaKactive"/>
<map_variables variable_1="concentration" variable_2="concentration"/>
</connection>
<connection>
<map_components component_1="spaR" component_2="spaR_interface"/>
<map_variables variable_1="JGain" variable_2="JGain"/>
</connection>
<connection>
<map_components component_1="spaR" component_2="Time"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<connection>
<map_components component_1="spaR" component_2="SpeciesInitialConcentrations"/>
<map_variables variable_1="concentrationInitialValue" variable_2="spaR"/>
</connection>
<connection>
<map_components component_1="spaR_interface" component_2="Bugbuster_ProteinCDS_spaR"/>
<map_variables variable_1="JPlusProduction" variable_2="J"/>
</connection>
<connection>
<map_components component_1="spaR_interface" component_2="Bioenvironment_Degradation_spaR"/>
<map_variables variable_1="JMinusDegradation" variable_2="J"/>
</connection>
<connection>
<map_components component_1="spaR_interface" component_2="spaRActivation"/>
<map_variables variable_1="JMinusspaRActivation" variable_2="J"/>
</connection>
<connection>
<map_components component_1="spaR_interface" component_2="Bioenvironment_Dephosphorylation_spaRactive"/>
<map_variables variable_1="JPlusspaRActiveDephosphorylation" variable_2="J"/>
</connection>
<connection>
<map_components component_1="Bioenvironment_Degradation_spaR" component_2="spaR"/>
<map_variables variable_1="concentration" variable_2="concentration"/>
</connection>
<connection>
<map_components component_1="spaRActivation" component_2="spaKactive"/>
<map_variables variable_1="reactant1" variable_2="concentration"/>
</connection>
<connection>
<map_components component_1="spaRActivation" component_2="spaR"/>
<map_variables variable_1="reactant2" variable_2="concentration"/>
</connection>
<connection>
<map_components component_1="spaRactive" component_2="spaRactive_interface"/>
<map_variables variable_1="JGain" variable_2="JGain"/>
</connection>
<connection>
<map_components component_1="spaRactive" component_2="Time"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<connection>
<map_components component_1="spaRactive" component_2="SpeciesInitialConcentrations"/>
<map_variables variable_1="concentrationInitialValue" variable_2="spaRactive"/>
</connection>
<connection>
<map_components component_1="spaRactive_interface" component_2="spaRActivation"/>
<map_variables variable_1="JPlusspaRActivation" variable_2="J"/>
</connection>
<connection>
<map_components component_1="spaRactive_interface" component_2="Bioenvironment_Dephosphorylation_spaRactive"/>
<map_variables variable_1="JMinusDephosphorylation" variable_2="J"/>
</connection>
<connection>
<map_components component_1="spaRactive_interface" component_2="Bioenvironment_Degradation_spaRactive"/>
<map_variables variable_1="JMinusDegradation" variable_2="J"/>
</connection>
<connection>
<map_components component_1="Bioenvironment_Dephosphorylation_spaRactive" component_2="spaRactive"/>
<map_variables variable_1="concentration" variable_2="concentration"/>
</connection>
<connection>
<map_components component_1="Bioenvironment_Degradation_spaRactive" component_2="spaRactive"/>
<map_variables variable_1="concentration" variable_2="concentration"/>
</connection>
<connection>
<map_components component_1="Bugbuster_Promoter2" component_2="ChassisBacillus"/>
<map_variables variable_1="localVolume" variable_2="cellVolume"/>
</connection>
<connection>
<map_components component_1="Bugbuster_Promoter2" component_2="spaRactive"/>
<map_variables variable_1="tFactor" variable_2="concentration"/>
</connection>
<connection>
<map_components component_1="RNA2" component_2="Time"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<connection>
<map_components component_1="RNA2" component_2="SpeciesInitialConcentrations"/>
<map_variables variable_1="concentrationInitialValue" variable_2="RNA2"/>
</connection>
<connection>
<map_components component_1="RNA2" component_2="RNA2_interface"/>
<map_variables variable_1="JGain" variable_2="JGain"/>
</connection>
<connection>
<map_components component_1="RNA2_interface" component_2="Bugbuster_Promoter2"/>
<map_variables variable_1="JPlusProduction" variable_2="JRNA"/>
</connection>
<connection>
<map_components component_1="RNA2_interface" component_2="Bioenvironment_Degradation_RNA2"/>
<map_variables variable_1="JMinusDegradation" variable_2="J"/>
</connection>
<connection>
<map_components component_1="Bioenvironment_Degradation_RNA2" component_2="RNA2"/>
<map_variables variable_1="concentration" variable_2="concentration"/>
</connection>
<connection>
<map_components component_1="Bugbuster_RBS_GFP" component_2="ChassisBacillus"/>
<map_variables variable_1="localVolume" variable_2="cellVolume"/>
</connection>
<connection>
<map_components component_1="Bugbuster_RBS_GFP" component_2="RNA2"/>
<map_variables variable_1="RNA" variable_2="concentration"/>
</connection>
<connection>
<map_components component_1="Bugbuster_ProteinCDS_GFP" component_2="ChassisBacillus"/>
<map_variables variable_1="localVolume" variable_2="cellVolume"/>
</connection>
<connection>
<map_components component_1="Bugbuster_ProteinCDS_GFP" component_2="Bugbuster_RBS_GFP"/>
<map_variables variable_1="hostRNARiPs" variable_2="RNARiPs"/>
</connection>
<connection>
<map_components component_1="GFP" component_2="GFP_interface"/>
<map_variables variable_1="JGain" variable_2="JGain"/>
</connection>
<connection>
<map_components component_1="GFP" component_2="Time"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<connection>
<map_components component_1="GFP" component_2="SpeciesInitialConcentrations"/>
<map_variables variable_1="concentrationInitialValue" variable_2="GFP"/>
</connection>
<connection>
<map_components component_1="GFP_interface" component_2="Bugbuster_ProteinCDS_GFP"/>
<map_variables variable_1="JPlusProduction" variable_2="J"/>
</connection>
<connection>
<map_components component_1="GFP_interface" component_2="Bioenvironment_Degradation_GFP"/>
<map_variables variable_1="JMinusDegradation" variable_2="J"/>
</connection>
<connection>
<map_components component_1="Bioenvironment_Degradation_GFP" component_2="GFP"/>
<map_variables variable_1="concentration" variable_2="concentration"/>
</connection>
</model>
