Location: Bugbuster Standard Virtual Biological Machine @ 3fca39c2d2b5 / BugbusterModel.cellml

Author:
mcoo001
Date:
2010-01-11 13:58 +1300
Desc:
Added a title to description index.html
Permanent Source URI:
http://models.cellml.org/workspace/bugbuster/rawfile/3fca39c2d2b58137a15310ec7df42421fceea028/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#">
    
    <rdf:RDF>
    <rdf:Description rdf:about="#BugbusterModel_SVBM">
    <dc:creator>
        <rdf:Seq>
        <rdf:li rdf:parseType="Resource">
            <vCard:N rdf:parseType="Resource">
            <vCard:Family>Misirli</vCard:Family>
            <vCard:Given>Goksel</vCard:Given>
            </vCard:N>
            <vCard:EMAIL rdf:parseType="Resource">
            <rdf:value>goksel.misirli@ncl.ac.uk</rdf:value>
            <rdf:type rdf:resource="http://imc.org/vCard/3.0#internet"/>
            </vCard:EMAIL>
            <vCard:ORG rdf:parseType="Resource">
            <vCard:Orgname>School of Computing Science</vCard:Orgname>
            <vCard:Orgunit>Newcastle University</vCard:Orgunit>
            </vCard:ORG>
            <vCard:ADR rdf:parseType="Resource">
            <vCard:Locality>Newcastle upon Tyne</vCard:Locality>
            <vCard:Pcode>NE1 7RU</vCard:Pcode>
            <vCard:Country>UK</vCard:Country>
            </vCard:ADR>
        </rdf:li>
        <rdf:li rdf:parseType="Resource">
            <vCard:N rdf:parseType="Resource">
            <vCard:Family>Hallinan</vCard:Family>
            <vCard:Given>Jennifer</vCard:Given>
            </vCard:N>
            <vCard:EMAIL rdf:parseType="Resource">
            <rdf:value>j.s.hallinan@ncl.ac.uk</rdf:value>
            <rdf:type rdf:resource="http://imc.org/vCard/3.0#internet"/>
            </vCard:EMAIL>
            <vCard:ORG rdf:parseType="Resource">
            <vCard:Orgname>School of Computing Science</vCard:Orgname>
            <vCard:Orgunit>Newcastle University</vCard:Orgunit>
            </vCard:ORG>
            <vCard:ADR rdf:parseType="Resource">
            <vCard:Locality>Newcastle upon Tyne</vCard:Locality>
            <vCard:Pcode>NE1 7RU</vCard:Pcode>
            <vCard:Country>UK</vCard:Country>
            </vCard:ADR>
        </rdf:li>
        <rdf:li rdf:parseType="Resource">
            <vCard:N rdf:parseType="Resource">
            <vCard:Family>Wipat</vCard:Family>
            <vCard:Given>Anil</vCard:Given>
            </vCard:N>
            <vCard:EMAIL rdf:parseType="Resource">
            <rdf:value>anil.wipat@ncl.ac.uk</rdf:value>
            <rdf:type rdf:resource="http://imc.org/vCard/3.0#internet"/>
            </vCard:EMAIL>
            <vCard:ORG rdf:parseType="Resource">
            <vCard:Orgname>School of Computing Science</vCard:Orgname>
            <vCard:Orgunit>Newcastle University</vCard:Orgunit>
            </vCard:ORG>
            <vCard:ADR rdf:parseType="Resource">
            <vCard:Locality>Newcastle upon Tyne</vCard:Locality>
            <vCard:Pcode>NE1 7RU</vCard:Pcode>
            <vCard:Country>UK</vCard:Country>
            </vCard:ADR>
        </rdf:li>
        <rdf:li>
            <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:Seq>  
    </dc:creator>
    </rdf:Description>
    </rdf:RDF>

    <import xlink:href="http://models.cellml.org/workspace/SVP_00000031/@@rawfile/ebb93757f49dccd7146fbc49440406779a910a7e/Chassis_Bacillus.cellml">
        <component name="ChassisBacillus" component_ref="Chassis_Bacillus" />
    </import>

    <import xlink:href="http://models.cellml.org/workspace/SVP_Templates200906/@@rawfile/b1e53aaa6bb9f958b4ddb2412bb1ae417c45e250/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="http://models.cellml.org/workspace/SVP_00000023/@@rawfile/271c4f54224324ce5f47385a04a9834f1453f603/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="http://models.cellml.org/workspace/SVP_Templates200906/@@rawfile/b1e53aaa6bb9f958b4ddb2412bb1ae417c45e250/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="http://models.cellml.org/workspace/SVP_00000001/@@rawfile/b5917ffecc75470c0a81f5439c4548234c8ff75f/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="http://models.cellml.org/workspace/SVP_00000030/@@rawfile/fd6a6147ebab120864a06cdbe30a1476937c2c79/Bugbuster_RBS_spaR.cellml">
            <component name="Bugbuster_RBS_spaR" component_ref="Bugbuster_RBS_spaR" />
        </import>
        
        <import xlink:href="http://models.cellml.org/workspace/SVP_00000027/@@rawfile/520c5b4cf12f2c781043b232c852d63f8f6dadf7/Bugbuster_ProteinCDS_spaR.cellml">
            <component name="Bugbuster_ProteinCDS_spaR" component_ref="Bugbuster_ProteinCDS_spaR" />
        </import>
    
        <import xlink:href="http://models.cellml.org/workspace/SVP_00000029/@@rawfile/ada06f0cc50cf16594079706bb7b8592cc0ecc43/Bugbuster_RBS_spaK.cellml">
                <component name="Bugbuster_RBS_spaK" component_ref="Bugbuster_RBS_spaK" />
        </import>
        
        <import xlink:href="http://models.cellml.org/workspace/SVP_00000026/@@rawfile/ff3b2fc31554c7b583e07bec0f99c9e8c89426e9/Bugbuster_ProteinCDS_spaK.cellml">
                <component name="Bugbuster_ProteinCDS_spaK" component_ref="Bugbuster_ProteinCDS_spaK" />
        </import>
            
       <import xlink:href="http://models.cellml.org/workspace/SVP_Templates200906/@@rawfile/b1e53aaa6bb9f958b4ddb2412bb1ae417c45e250/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="http://models.cellml.org/workspace/SVP_00000010/@@rawfile/58ab9569b25f2f93f91e6f57617e8a17cfb9a32e/Bioenvironment_Degradation_spaK.cellml">
               <component name="Bioenvironment_Degradation_spaK" component_ref="Bioenvironment_Degradation_spaK" />
       </import>
       
         <import xlink:href="http://models.cellml.org/workspace/SVP_00000020/@@rawfile/e98205f457c4cdce2c7e1a0e72f7a0a3215e965f/Bioenvironment_RxR2P1_spaKActivation.cellml">
               <component name="spaKActivation" component_ref="Bioenvironment_RxR2P1_spaKActivation" />
    </import>
    
    <import xlink:href="http://models.cellml.org/workspace/SVP_Templates200906/@@rawfile/b1e53aaa6bb9f958b4ddb2412bb1ae417c45e250/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="http://models.cellml.org/workspace/SVP_00000016/@@rawfile/39b60e0d6f1decbbd95843e19f752ffc185ac899/Bioenvironment_Dephosphorylation_spaKactive.cellml">
                <component name="Bioenvironment_Dephosphorylation_spaKactive" component_ref="Bioenvironment_Dephosphorylation_spaKactive" />
    </import>
    
      <import xlink:href="http://models.cellml.org/workspace/SVP_00000011/@@rawfile/35ba0f03c929f5c6756d29fa9d3386eefed4f5a3/Bioenvironment_Degradation_spaKactive.cellml">
                <component name="Bioenvironment_Degradation_spaKactive" component_ref="Bioenvironment_Degradation_spaKactive" />
    </import>
    
     <import xlink:href="http://models.cellml.org/workspace/SVP_Templates200906/@@rawfile/b1e53aaa6bb9f958b4ddb2412bb1ae417c45e250/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="http://models.cellml.org/workspace/SVP_00000012/@@rawfile/581927e80ec03f8b242b4f9e8c03f77b55faf1da/Bioenvironment_Degradation_spaR.cellml">
	            <component name="Bioenvironment_Degradation_spaR" component_ref="Bioenvironment_Degradation_spaR" />
	    </import>
    
    
    <import xlink:href="http://models.cellml.org/workspace/SVP_00000021/@@rawfile/f25ed7150be1bfbc137acce59c51745c9ef52496/Bioenvironment_RxR2P1_spaRActivation.cellml">
            <component name="spaRActivation" component_ref="Bioenvironment_RxR2P1_spaRActivation" />
        </import>
        
        <import xlink:href="http://models.cellml.org/workspace/SVP_Templates200906/@@rawfile/b1e53aaa6bb9f958b4ddb2412bb1ae417c45e250/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="http://models.cellml.org/workspace/SVP_00000017/@@rawfile/eb77e5d18b115d9fecca7a71f5ca01f5b5755ba7/Bioenvironment_Dephosphorylation_spaRactive.cellml">
                <component name="Bioenvironment_Dephosphorylation_spaRactive" component_ref="Bioenvironment_Dephosphorylation_spaRactive" />
    </import>
    
        <import xlink:href="http://models.cellml.org/workspace/SVP_00000013/@@rawfile/6e4e06a837d3a7978e73a041a98cde338dccf1ce/Bioenvironment_Degradation_spaRactive.cellml">
                <component name="Bioenvironment_Degradation_spaRactive" component_ref="Bioenvironment_Degradation_spaRactive" />
    </import>
    
      <import xlink:href="http://models.cellml.org/workspace/SVP_00000024/@@rawfile/e21465457b0e0f6dd562f5eda6d24dd409d3a1b9/Bugbuster_Promoter2.cellml">
                 <component name="Bugbuster_Promoter2" component_ref="Bugbuster_Promoter2" />
        </import>  
        
        <import xlink:href="http://models.cellml.org/workspace/SVP_Templates200906/@@rawfile/b1e53aaa6bb9f958b4ddb2412bb1ae417c45e250/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="http://models.cellml.org/workspace/SVP_00000002/@@rawfile/97067e21d62e6ce6b4be54307980b4bed49629d5/Bioenvironment_Degradation_BugbusterRNA2.cellml">
        <component name="Bioenvironment_Degradation_RNA2" component_ref="Bioenvironment_Degradation_BugbusterRNA2" />
    </import>
    
        <import xlink:href="http://models.cellml.org/workspace/SVP_00000028/@@rawfile/ecffc7bb36e2f00c79d1cb757c911753f4d85964/Bugbuster_RBS_GFP.cellml">
                    <component name="Bugbuster_RBS_GFP" component_ref="Bugbuster_RBS_GFP" />
        </import>
        
        <import xlink:href="http://models.cellml.org/workspace/SVP_00000025/@@rawfile/5e36f31003ffd4598175fc08d1f1fa87272c0c05/Bugbuster_ProteinCDS_GFP.cellml">
                <component name="Bugbuster_ProteinCDS_GFP" component_ref="Bugbuster_ProteinCDS_GFP" />
        </import>
        
        <import xlink:href="http://models.cellml.org/workspace/SVP_Templates200906/@@rawfile/b1e53aaa6bb9f958b4ddb2412bb1ae417c45e250/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="http://models.cellml.org/workspace/SVP_00000005/@@rawfile/0e90a0e2a269fd9c28059752f4af690ba21bcba4/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>