Rendering of the source text

<?xml version="1.0"?>
<model xmlns="http://www.cellml.org/cellml/1.1#" xmlns:cmeta="http://www.cellml.org/metadata/1.0#" 
xmlns:cellml="http://www.cellml.org/cellml/1.1#"
cmeta:id="VirtualBacterialPhotography" name="VirtualBacterialPhotography"
xmlns:dcterms="http://purl.org/dc/terms/"
xmlns:foaf="http://xmlns.com/foaf/0.1/"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
>

<rdf:RDF>
<foaf:Person rdf:nodeID="mike_cooling">	  
	<foaf:givenName>Mike</foaf:givenName> 
	<foaf:familyName>Cooling</foaf:familyName> 
</foaf:Person>
<foaf:Person rdf:nodeID="xiaoming_wang">	  
	<foaf:givenName>Xiaoming</foaf:givenName> 
	<foaf:familyName>Wang</foaf:familyName> 
</foaf:Person>
<foaf:Group>
	<foaf:name>Auckland Bioengineering Institute</foaf:name>
	<foaf:member rdf:nodeID="mike_cooling"/>
	<foaf:member rdf:nodeID="xiaoming_wang"/>
</foaf:Group>

<rdf:Description rdf:about="#VirtualBacterialPhotography">
	<foaf:maker  rdf:nodeID="mike_cooling"/> 
	<foaf:maker  rdf:nodeID="xiaoming_wang"/> 

	<dcterms:description>
	This model was constructed as a modular teaching tool in the context of the bacterial system described in
	Nature 438, 441-442, doi:10.1038/nature04405
	Synthetic biology: Engineering Escherichia coli to see light
	Anselm Levskaya1, Aaron A. Chevalier, Jeffrey J. Tabor, Zachary Booth Simpson,
	Laura A. Lavery, Matthew Levy, Eric A. Davidson, Alexander Scouras, Andrew D. Ellington, Edward M. Marcotte and Christopher A. Voigt
	</dcterms:description>
</rdf:Description>
</rdf:RDF>

	<component name="SpeciesInitialValues">
		<variable initial_value="0" name="ho1pcyA_mRNA" public_interface="out" units="nM"/>
		<variable initial_value="0" name="Ho1" public_interface="out" units="nM"/>
		<variable initial_value="0" name="BV" public_interface="out" units="nM"/>
		<variable initial_value="0" name="PcyA" public_interface="out" units="nM"/>
		<variable initial_value="0" name="PCB" public_interface="out" units="nM"/>
		<variable initial_value="0" name="Cph8" public_interface="out" units="molecule_per_micrometer2"/>
		<variable initial_value="0" name="Cph8p" public_interface="out" units="molecule_per_micrometer2"/>	
		<variable initial_value="0" name="ompR_mRNA" public_interface="out" units="nM"/>
		<variable initial_value="0" name="OmpR" public_interface="out" units="nM"/>
		<variable initial_value="0" name="OmpRp" public_interface="out" units="nM"/>
		<variable initial_value="0" name="ompC_lacZ_mRNA" public_interface="out" units="nM"/>
		<variable initial_value="0" name="Beta_Galactosidase" public_interface="out" units="nM"/>
		<variable initial_value="0" name="Precipitate" public_interface="out" units="nM"/>
	</component>

	<import xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="Chassis_EColi.cellml">
		<component component_ref="Chassis_EColi" name="E_Coli"/>
	</import>

	<import xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="svp_templates/Time.cellml">
		<component component_ref="Time" name="Time"/>
	</import>

	<import xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="ho1pcyA_Promoter.cellml">
		<component component_ref="ho1pcyA_Promoter" name="ho1pcyA_Promoter"/>
		<units name="nM_per_s" units_ref="nM_per_s"/>
	</import>

	<connection>
		<map_components component_1="ho1pcyA_Promoter" component_2="E_Coli"/>
		<map_variables variable_1="localVolume" variable_2="cellVolume"/>
	</connection>


	<component name="ho1pcyA_mRNA_Interface">
		<variable name="JPlusPromoter" public_interface="in" units="nM_per_s"/>
		<variable name="JGain" public_interface="out" units="nM_per_s"/>
		<variable name="JMinusDegradation" public_interface="in" units="nM_per_s"/>
		<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>

	<connection>
		<map_components component_1="ho1pcyA_mRNA_Interface" component_2="Bioenvironment_Degradation_ho1pcyA_mRNA"/>
		<map_variables variable_1="JMinusDegradation" variable_2="J"/>
	</connection>

	<connection>
		<map_components component_1="ho1pcyA_mRNA_Interface" component_2="ho1pcyA_mRNA"/>
		<map_variables variable_1="JGain" variable_2="JGain"/>
	</connection>

	<connection>
		<map_components component_1="ho1pcyA_mRNA_Interface" component_2="ho1pcyA_Promoter"/>
		<map_variables variable_1="JPlusPromoter" variable_2="JRNA"/>
	</connection>

	<import xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="svp_templates/Template_Species.cellml">
		<component component_ref="Template_Species" name="ho1pcyA_mRNA"/>
		<units name="nM" units_ref="nM"/>
	</import>

	<connection>
		<map_components component_1="ho1pcyA_mRNA" component_2="Time"/>
		<map_variables variable_1="time" variable_2="time"/>
	</connection>

	<connection>
		<map_components component_1="SpeciesInitialValues" component_2="ho1pcyA_mRNA"/>
		<map_variables variable_1="ho1pcyA_mRNA" variable_2="concentrationInitialValue"/>
	</connection>

	<import xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="Bioenvironment_Degradation_ho1pcyA_mRNA.cellml">
		<component component_ref="Bioenvironment_Degradation_ho1pcyA_mRNA" name="Bioenvironment_Degradation_ho1pcyA_mRNA"/>
		<units name="per_s" units_ref="per_s"/>
	</import>

	<connection>
		<map_components component_1="ho1pcyA_mRNA" component_2="Bioenvironment_Degradation_ho1pcyA_mRNA"/>
		<map_variables variable_1="concentration" variable_2="concentration"/>
	</connection>

	<import xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="ho1_RBS.cellml">
		<component component_ref="ho1_RBS" name="ho1_RBS"/>
	</import>

	<connection>
		<map_components component_1="ho1_RBS" component_2="E_Coli"/>
		<map_variables variable_1="localVolume" variable_2="cellVolume"/>
	</connection>

	<connection>
		<map_components component_1="ho1_RBS" component_2="ho1pcyA_mRNA"/>
		<map_variables variable_1="RNA" variable_2="concentration"/>
	</connection>

	<import xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="ho1_CDS.cellml">
		<component component_ref="ho1_CDS" name="ho1_CDS"/>
	</import>

	<connection>
		<map_components component_1="ho1_CDS" component_2="E_Coli"/>
		<map_variables variable_1="localVolume" variable_2="cellVolume"/>
	</connection>

	<connection>
		<map_components component_1="ho1_CDS" component_2="ho1_RBS"/>
		<map_variables variable_1="hostRNARiPs" variable_2="RNARiPs"/>
	</connection>

	<import xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="pcyA_RBS.cellml">
		<component component_ref="pcyA_RBS" name="pcyA_RBS"/>
	</import>

	<connection>
		<map_components component_1="E_Coli" component_2="pcyA_RBS"/>
		<map_variables variable_1="cellVolume" variable_2="localVolume"/>
	</connection>

	<connection>
		<map_components component_1="pcyA_RBS" component_2="ho1pcyA_mRNA"/>
		<map_variables variable_1="RNA" variable_2="concentration"/>
	</connection>

	<import xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="pcyA_CDS.cellml">
		<component component_ref="pcyA_CDS" name="pcyA_CDS"/>
	</import>

	<connection>
		<map_components component_1="E_Coli" component_2="pcyA_CDS"/>
		<map_variables variable_1="cellVolume" variable_2="localVolume"/>
	</connection>

	<connection>
		<map_components component_1="pcyA_RBS" component_2="pcyA_CDS"/>
		<map_variables variable_1="RNARiPs" variable_2="hostRNARiPs"/>
	</connection>

	<component name="Ho1_Interface">
		<variable name="JPlusProduction" public_interface="in" units="nM_per_s"/>
		<variable name="JGain" public_interface="out" units="nM_per_s"/>
		<variable name="JMinusDegradation" public_interface="in" units="nM_per_s"/>
		<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>

	<connection>
		<map_components component_1="Ho1_Interface" component_2="ho1_CDS"/>
		<map_variables variable_1="JPlusProduction" variable_2="J"/>
	</connection>

	<connection>
		<map_components component_1="Ho1_Interface" component_2="Bioenvironment_Degradation_Ho1"/>
		<map_variables variable_1="JMinusDegradation" variable_2="J"/>
	</connection>



	<import xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="svp_templates/Template_Species.cellml">
		<component component_ref="Template_Species" name="Ho1"/>
	</import>

	<connection>
		<map_components component_1="Ho1" component_2="Time"/>
		<map_variables variable_1="time" variable_2="time"/>
	</connection>

	<connection>
		<map_components component_1="Ho1" component_2="Ho1_Interface"/>
		<map_variables variable_1="JGain" variable_2="JGain"/>
	</connection>

	<connection>
		<map_components component_1="Ho1" component_2="SpeciesInitialValues"/>
		<map_variables variable_1="concentrationInitialValue" variable_2="Ho1"/>
	</connection>

	<import xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="Bioenvironment_Degradation_Ho1.cellml">
		<component component_ref="Bioenvironment_Degradation_Ho1" name="Bioenvironment_Degradation_Ho1"/>
	</import>

	<connection>
		<map_components component_1="Ho1" component_2="Bioenvironment_Degradation_Ho1"/>
		<map_variables variable_1="concentration" variable_2="concentration"/>
	</connection>

	<component name="PcyA_Interface">
		<variable name="JPlusProduction" public_interface="in" units="nM_per_s"/>
		<variable name="JGain" public_interface="out" units="nM_per_s"/>
		<variable name="JMinusDegradation" public_interface="in" units="nM_per_s"/>
		<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>

	<connection>
		<map_components component_1="PcyA_Interface" component_2="Bioenvironment_Degradation_PcyA"/>
		<map_variables variable_1="JMinusDegradation" variable_2="J"/>
	</connection>

	<connection>
		<map_components component_1="PcyA_Interface" component_2="pcyA_CDS"/>
		<map_variables variable_1="JPlusProduction" variable_2="J"/>
	</connection>

	<import xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="svp_templates/Template_Species.cellml">
		<component component_ref="Template_Species" name="PcyA"/>
	</import>

	<connection>
		<map_components component_1="PcyA" component_2="Time"/>
		<map_variables variable_1="time" variable_2="time"/>
	</connection>

	<connection>
		<map_components component_1="PcyA" component_2="PcyA_Interface"/>
		<map_variables variable_1="JGain" variable_2="JGain"/>
	</connection>

	<connection>
		<map_components component_1="PcyA" component_2="SpeciesInitialValues"/>
		<map_variables variable_1="concentrationInitialValue" variable_2="PcyA"/>
	</connection>

	<import xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="Bioenvironment_Degradation_PcyA.cellml">
		<component component_ref="Bioenvironment_Degradation_PcyA" name="Bioenvironment_Degradation_PcyA"/>
	</import>

	<connection>
		<map_components component_1="PcyA" component_2="Bioenvironment_Degradation_PcyA"/>
		<map_variables variable_1="concentration" variable_2="concentration"/>
	</connection>

	<component name="BV_Interface">
		<variable name="JPlusProduction" public_interface="in" units="nM_per_s"/>
		<variable name="JGain" public_interface="out" units="nM_per_s"/>
		<variable name="JMinusDegradation" public_interface="in" units="nM_per_s"/>
		<variable name="JMinusPCBFormation" public_interface="in" units="nM_per_s"/>
		<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>JMinusPCBFormation</ci>
				</apply>
			</apply>
		</math>
	</component>

	<connection>
		<map_components component_1="BV_Interface" component_2="Bioenvironment_Degradation_BV"/>
		<map_variables variable_1="JMinusDegradation" variable_2="J"/>
	</connection>

	<connection>
		<map_components component_1="BV_Interface" component_2="Bioenvironment_BVFormation"/>
		<map_variables variable_1="JPlusProduction" variable_2="J"/>
	</connection>

	<connection>
		<map_components component_1="BV_Interface" component_2="Bioenvironment_PCBFormation"/>
		<map_variables variable_1="JMinusPCBFormation" variable_2="J"/>
	</connection>

	<import xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="svp_templates/Template_Species.cellml">
		<component component_ref="Template_Species" name="BV"/>
	</import>

	<connection>
		<map_components component_1="BV" component_2="SpeciesInitialValues"/>
		<map_variables variable_1="concentrationInitialValue" variable_2="BV"/>
	</connection>

	<connection>
		<map_components component_1="BV" component_2="Time"/>
		<map_variables variable_1="time" variable_2="time"/>
	</connection>

	<connection>
		<map_components component_1="BV" component_2="BV_Interface"/>
		<map_variables variable_1="JGain" variable_2="JGain"/>
	</connection>

	<import xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="Bioenvironment_Degradation_BV.cellml">
		<component component_ref="Bioenvironment_Degradation_BV" name="Bioenvironment_Degradation_BV"/>
	</import>

	<connection>
		<map_components component_1="Bioenvironment_Degradation_BV" component_2="BV"/>
		<map_variables variable_1="concentration" variable_2="concentration"/>
	</connection>
	
	<import xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="Bioenvironment_Haem.cellml">
		<component component_ref="Bioenvironment_Haem" name="Haem"/>
	</import>

	<import xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="Bioenvironment_BVFormation.cellml">
		<component component_ref="Bioenvironment_BVFormation" name="Bioenvironment_BVFormation"/>
	</import>

	<connection>
		<map_components component_1="Bioenvironment_BVFormation" component_2="Haem"/>
		<map_variables variable_1="reactant" variable_2="concentration"/>
	</connection>

	<connection>
		<map_components component_1="Bioenvironment_BVFormation" component_2="Ho1"/>
		<map_variables variable_1="catalyst" variable_2="concentration"/>
	</connection>
	

	<component name="PCB_Interface">
		<variable name="JPlusProduction" public_interface="in" units="nM_per_s"/>
		<variable name="JGain" public_interface="out" units="nM_per_s"/>
		<variable name="JMinusDegradation" public_interface="in" units="nM_per_s"/>
		<variable name="JMinusCph8Addition" public_interface="in" units="nM_per_s"/>
		<math xmlns="http://www.w3.org/1998/Math/MathML">
			<apply>
				<eq/>
				<ci>JGain</ci>
				<apply>
					<minus/>
					<ci>JPlusProduction</ci>
					<apply>
						<plus />
						<ci>JMinusDegradation</ci>
						<ci>JMinusCph8Addition</ci>
					</apply>
				</apply>
			</apply>
		</math>
	</component>
	
	<connection>
		<map_components component_1="PCB_Interface" component_2="Bioenvironment_Cph8Formation"/>
		<map_variables variable_1="JMinusCph8Addition" variable_2="Jconcentration"/>
	</connection>

	<connection>
		<map_components component_1="PCB_Interface" component_2="Bioenvironment_Degradation_PCB"/>
		<map_variables variable_1="JMinusDegradation" variable_2="J"/>
	</connection>

	<connection>
		<map_components component_1="PCB_Interface" component_2="Bioenvironment_PCBFormation"/>
		<map_variables variable_1="JPlusProduction" variable_2="J"/>
	</connection>

	<import xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="svp_templates/Template_Species.cellml">
		<component component_ref="Template_Species" name="PCB"/>
	</import>

	<connection>
		<map_components component_1="PCB" component_2="Time"/>
		<map_variables variable_1="time" variable_2="time"/>
	</connection>

	<connection>
		<map_components component_1="PCB" component_2="PCB_Interface"/>
		<map_variables variable_1="JGain" variable_2="JGain"/>
	</connection>

	<connection>
		<map_components component_1="PCB" component_2="SpeciesInitialValues"/>
		<map_variables variable_1="concentrationInitialValue" variable_2="PCB"/>
	</connection>

	<import xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="Bioenvironment_Degradation_PCB.cellml">
		<component component_ref="Bioenvironment_Degradation_PCB" name="Bioenvironment_Degradation_PCB"/>
	</import>

	<connection>
		<map_components component_1="PCB" component_2="Bioenvironment_Degradation_PCB"/>
		<map_variables variable_1="concentration" variable_2="concentration"/>
	</connection>

	<import xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="Bioenvironment_PCBFormation.cellml">
		<component component_ref="Bioenvironment_PCBFormation" name="Bioenvironment_PCBFormation"/>
	</import>

	<connection>
		<map_components component_1="Bioenvironment_PCBFormation" component_2="BV"/>
		<map_variables variable_1="reactant" variable_2="concentration"/>
	</connection>

	<connection>
		<map_components component_1="Bioenvironment_PCBFormation" component_2="PcyA"/>
		<map_variables variable_1="catalyst" variable_2="concentration"/>
	</connection>

	

	<component name="Cph8_Interface">
		<variable name="JPlusPCBAddition" public_interface="in" units="molecule_per_micrometer2_per_s"/>
		<variable name="JMinusCph8Phosphorylation" public_interface="in" units="molecule_per_micrometer2_per_s"/>
		<variable name="JMinusDegradation" public_interface="in" units="molecule_per_micrometer2_per_s"/>
		<variable name="JPlusOmpRpFormation" public_interface="in" units="molecule_per_micrometer2_per_s"/>
		<variable name="JGain" public_interface="out" units="molecule_per_micrometer2_per_s"/>
		<math xmlns="http://www.w3.org/1998/Math/MathML">
			<apply>
				<eq/>
				<ci>JGain</ci>
				<apply>
					<minus/>
						<apply>
							<plus/>
							<ci>JPlusPCBAddition</ci>
							<ci>JPlusOmpRpFormation</ci>
						</apply>
						<apply>
							<plus/>
							<ci>JMinusDegradation</ci>
							<ci>JMinusCph8Phosphorylation</ci>
						</apply>
				</apply>
			</apply>
		</math>
	</component>
	
	<connection>
		<map_components component_1="Cph8_Interface" component_2="Bioenvironment_OmpRpFormation"/>
		<map_variables variable_1="JPlusOmpRpFormation" variable_2="Jdensity"/>
	</connection>
	
	<connection>
		<map_components component_1="Cph8_Interface" component_2="Bioenvironment_LightDependentPhosphorylation_Cph8"/>
		<map_variables variable_1="JMinusCph8Phosphorylation" variable_2="J"/>
	</connection>

	<connection>
		<map_components component_1="Cph8_Interface" component_2="Bioenvironment_Degradation_Cph8"/>
		<map_variables variable_1="JMinusDegradation" variable_2="J"/>
	</connection>

	<connection>
		<map_components component_1="Cph8_Interface" component_2="Bioenvironment_Cph8Formation"/>
		<map_variables variable_1="JPlusPCBAddition" variable_2="Jdensity"/>
	</connection>

	<import xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="svp_templates/Template_BoundSpecies.cellml">
		<component component_ref="Template_BoundSpecies" name="Cph8"/>
		<units name="molecule_per_micrometer2" units_ref="molecule_per_micrometer2"/>
		<units name="molecule_per_micrometer2_per_s" units_ref="molecule_per_micrometer2_per_s"/>
	</import>

	<connection>
		<map_components component_1="Cph8" component_2="Time"/>
		<map_variables variable_1="time" variable_2="time"/>
	</connection>

	<connection>
		<map_components component_1="SpeciesInitialValues" component_2="Cph8"/>
		<map_variables variable_1="Cph8" variable_2="densityInitialValue"/>
	</connection>

	<connection>
		<map_components component_1="Cph8" component_2="Cph8_Interface"/>
		<map_variables variable_1="JGain" variable_2="JGain"/>
	</connection>

	<import xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="Bioenvironment_Degradation_Cph8.cellml">
		<component component_ref="Bioenvironment_Degradation_Cph8" name="Bioenvironment_Degradation_Cph8"/>
	</import>

	<connection>
		<map_components component_1="Cph8" component_2="Bioenvironment_Degradation_Cph8"/>
		<map_variables variable_1="density" variable_2="density"/>
	</connection>	
	
	<import xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="Bioenvironment_Cph8_no_PCB.cellml">
		<component component_ref="Bioenvironment_Cph8_no_PCB" name="Bioenvironment_Cph8_no_PCB"/>
	</import>

	<import xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="Bioenvironment_Cph8Formation.cellml">
		<component component_ref="Bioenvironment_Cph8Formation" name="Bioenvironment_Cph8Formation"/>
	</import>

	<connection>
		<map_components component_1="Bioenvironment_Cph8_no_PCB" component_2="Bioenvironment_Cph8Formation"/>
		<map_variables variable_1="density" variable_2="Cph8_no_PCB"/>
	</connection>

	<connection>
		<map_components component_1="Bioenvironment_Cph8Formation" component_2="PCB"/>
		<map_variables variable_1="PCB" variable_2="concentration"/>
	</connection>	
	
	<connection>
		<map_components component_1="Bioenvironment_Cph8Formation" component_2="E_Coli"/>
		<map_variables variable_1="Ccm" variable_2="Ccm"/>
	</connection>

	<connection>
		<map_components component_1="Cph8" component_2="Bioenvironment_Cph8Formation"/>
		<map_variables variable_1="density" variable_2="Cph8"/>
	</connection>

	
	<import xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="Bioenvironment_PeriodicLightSource.cellml">
		<component component_ref="Bioenvironment_PeriodicLightSource" name="Bioenvironment_PeriodicLightSource"/>
	</import>

	<connection>
		<map_components component_1="Bioenvironment_PeriodicLightSource" component_2="Time"/>
		<map_variables variable_1="time" variable_2="time"/>
	</connection>
	
	<component name="Cph8p_Interface">
		<variable name="JPlusCph8Phosphorylation" public_interface="in" units="molecule_per_micrometer2_per_s"/>
		<variable name="JGain" public_interface="out" units="molecule_per_micrometer2_per_s"/>
		<variable name="JMinusOmpRpFormation" public_interface="in" units="molecule_per_micrometer2_per_s"/>
		<math xmlns="http://www.w3.org/1998/Math/MathML">
			<apply>
				<eq/>
				<ci>JGain</ci>
					<apply>
					<minus/>
					<ci>JPlusCph8Phosphorylation</ci>
					<ci>JMinusOmpRpFormation</ci>
					</apply>
			</apply>
		</math>
	</component>
	
	<connection>
		<map_components component_1="Cph8p_Interface" component_2="Bioenvironment_OmpRpFormation"/>
		<map_variables variable_1="JMinusOmpRpFormation" variable_2="Jdensity"/>
	</connection>
	
	<connection>
		<map_components component_1="Cph8p_Interface" component_2="Bioenvironment_LightDependentPhosphorylation_Cph8"/>
		<map_variables variable_1="JPlusCph8Phosphorylation" variable_2="J"/>
	</connection>

	<import xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="svp_templates/Template_BoundSpecies.cellml">
		<component component_ref="Template_BoundSpecies" name="Cph8p"/>
	</import>

	<connection>
		<map_components component_1="Cph8p" component_2="Time"/>
		<map_variables variable_1="time" variable_2="time"/>
	</connection>

	<connection>
		<map_components component_1="SpeciesInitialValues" component_2="Cph8p"/>
		<map_variables variable_1="Cph8p" variable_2="densityInitialValue"/>
	</connection>

	<connection>
		<map_components component_1="Cph8p" component_2="Cph8p_Interface"/>
		<map_variables variable_1="JGain" variable_2="JGain"/>
	</connection>
	

	<import xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="Bioenvironment_LightDependentPhosphorylation_Cph8.cellml">
		<component component_ref="Bioenvironment_LightDependentPhosphorylation_Cph8" name="Bioenvironment_LightDependentPhosphorylation_Cph8"/>
	</import>
	
	<connection>
		<map_components component_1="Bioenvironment_LightDependentPhosphorylation_Cph8" component_2="Cph8"/>
		<map_variables variable_1="density" variable_2="density"/>
	</connection>
	
	<connection>
		<map_components component_1="Bioenvironment_LightDependentPhosphorylation_Cph8" component_2="Bioenvironment_PeriodicLightSource"/>
		<map_variables variable_1="lightIntensity" variable_2="lightIntensity"/>
	</connection>
	
	
	<import xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="ompR_Promoter.cellml">
		<component component_ref="ompR_Promoter" name="ompR_Promoter"/>
	</import>

	<connection>
		<map_components component_1="ompR_Promoter" component_2="E_Coli"/>
		<map_variables variable_1="localVolume" variable_2="cellVolume"/>
	</connection>
	
	<component name="ompR_mRNA_Interface">
		<variable name="JPlusPromoter" public_interface="in" units="nM_per_s"/>
		<variable name="JGain" public_interface="out" units="nM_per_s"/>
		<variable name="JMinusDegradation" public_interface="in" units="nM_per_s"/>
		<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>

	<connection>
		<map_components component_1="ompR_mRNA_Interface" component_2="Bioenvironment_Degradation_ompR_mRNA"/>
		<map_variables variable_1="JMinusDegradation" variable_2="J"/>
	</connection>

	<connection>
		<map_components component_1="ompR_mRNA_Interface" component_2="ompR_mRNA"/>
		<map_variables variable_1="JGain" variable_2="JGain"/>
	</connection>

	<connection>
		<map_components component_1="ompR_mRNA_Interface" component_2="ompR_Promoter"/>
		<map_variables variable_1="JPlusPromoter" variable_2="JRNA"/>
	</connection>
	
	<import xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="svp_templates/Template_Species.cellml">
		<component component_ref="Template_Species" name="ompR_mRNA"/>
		<units name="nM" units_ref="nM"/>
	</import>

	<connection>
		<map_components component_1="ompR_mRNA" component_2="Time"/>
		<map_variables variable_1="time" variable_2="time"/>
	</connection>

	<connection>
		<map_components component_1="SpeciesInitialValues" component_2="ompR_mRNA"/>
		<map_variables variable_1="ompR_mRNA" variable_2="concentrationInitialValue"/>
	</connection>
	
	<import xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="Bioenvironment_Degradation_ompR_mRNA.cellml">
		<component component_ref="Bioenvironment_Degradation_ompR_mRNA" name="Bioenvironment_Degradation_ompR_mRNA"/>
		<units name="per_s" units_ref="per_s"/>
	</import>

	<connection>
		<map_components component_1="ompR_mRNA" component_2="Bioenvironment_Degradation_ompR_mRNA"/>
		<map_variables variable_1="concentration" variable_2="concentration"/>
	</connection>
	
	<import xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="ompR_RBS.cellml">
		<component component_ref="ompR_RBS" name="ompR_RBS"/>
	</import>

	<connection>
		<map_components component_1="ompR_RBS" component_2="E_Coli"/>
		<map_variables variable_1="localVolume" variable_2="cellVolume"/>
	</connection>

	<connection>
		<map_components component_1="ompR_RBS" component_2="ompR_mRNA"/>
		<map_variables variable_1="RNA" variable_2="concentration"/>
	</connection>

	<import xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="ompR_CDS.cellml">
		<component component_ref="ompR_CDS" name="ompR_CDS"/>
	</import>

	<connection>
		<map_components component_1="ompR_CDS" component_2="E_Coli"/>
		<map_variables variable_1="localVolume" variable_2="cellVolume"/>
	</connection>

	<connection>
		<map_components component_1="ompR_CDS" component_2="ompR_RBS"/>
		<map_variables variable_1="hostRNARiPs" variable_2="RNARiPs"/>
	</connection>
	
	<component name="OmpR_Interface">
		<variable name="JPlusProduction" public_interface="in" units="nM_per_s"/>
		<variable name="JGain" public_interface="out" units="nM_per_s"/>
		<variable name="JMinusDegradation" public_interface="in" units="nM_per_s"/>
		<variable name="JMinusOmpRpFormation" public_interface="in" units="nM_per_s"/>
		<math xmlns="http://www.w3.org/1998/Math/MathML">
			<apply>
				<eq/>
				<ci>JGain</ci>
				<apply>
					<minus/>
					<ci>JPlusProduction</ci>
						<apply>
						<plus/>
						<ci>JMinusDegradation</ci>
						<ci>JMinusOmpRpFormation</ci>
						</apply>
				</apply>
			</apply>
		</math>
	</component>
	
	<connection>
		<map_components component_1="OmpR_Interface" component_2="Bioenvironment_OmpRpFormation"/>
		<map_variables variable_1="JMinusOmpRpFormation" variable_2="Jconcentration"/>
	</connection>

	<connection>
		<map_components component_1="OmpR_Interface" component_2="ompR_CDS"/>
		<map_variables variable_1="JPlusProduction" variable_2="J"/>
	</connection>

	<connection>
		<map_components component_1="OmpR_Interface" component_2="Bioenvironment_Degradation_OmpR"/>
		<map_variables variable_1="JMinusDegradation" variable_2="J"/>
	</connection>



	<import xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="svp_templates/Template_Species.cellml">
		<component component_ref="Template_Species" name="OmpR"/>
	</import>

	<connection>
		<map_components component_1="OmpR" component_2="Time"/>
		<map_variables variable_1="time" variable_2="time"/>
	</connection>

	<connection>
		<map_components component_1="OmpR" component_2="OmpR_Interface"/>
		<map_variables variable_1="JGain" variable_2="JGain"/>
	</connection>

	<connection>
		<map_components component_1="OmpR" component_2="SpeciesInitialValues"/>
		<map_variables variable_1="concentrationInitialValue" variable_2="OmpR"/>
	</connection>

	<import xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="Bioenvironment_Degradation_OmpR.cellml">
		<component component_ref="Bioenvironment_Degradation_OmpR" name="Bioenvironment_Degradation_OmpR"/>
	</import>

	<connection>
		<map_components component_1="OmpR" component_2="Bioenvironment_Degradation_OmpR"/>
		<map_variables variable_1="concentration" variable_2="concentration"/>
	</connection>
		
	<import xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="Bioenvironment_OmpRpFormation.cellml">
		<component component_ref="Bioenvironment_OmpRpFormation" name="Bioenvironment_OmpRpFormation"/>
	</import>
	
	<connection>
		<map_components component_1="Bioenvironment_OmpRpFormation" component_2="E_Coli"/>
		<map_variables variable_1="Ccm" variable_2="Ccm"/>
	</connection>
	
	<connection>
		<map_components component_1="Bioenvironment_OmpRpFormation" component_2="Cph8"/>
		<map_variables variable_1="Cph8" variable_2="density"/>
	</connection>
	
	<connection>
		<map_components component_1="Bioenvironment_OmpRpFormation" component_2="Cph8p"/>
		<map_variables variable_1="Cph8p" variable_2="density"/>
	</connection>
	
	<connection>
		<map_components component_1="Bioenvironment_OmpRpFormation" component_2="OmpR"/>
		<map_variables variable_1="OmpR" variable_2="concentration"/>
	</connection>
	
	<connection>
		<map_components component_1="Bioenvironment_OmpRpFormation" component_2="OmpRp"/>
		<map_variables variable_1="OmpRp" variable_2="concentration"/>
	</connection>
	
	<component name="OmpRp_Interface">
		<variable name="JPlusFormation" public_interface="in" units="nM_per_s"/>
		<variable name="JGain" public_interface="out" units="nM_per_s"/>
		<variable name="JMinusDegradation" public_interface="in" units="nM_per_s"/>
		<math xmlns="http://www.w3.org/1998/Math/MathML">
			<apply>
				<eq/>
				<ci>JGain</ci>
				<apply>
					<minus/>
					<ci>JPlusFormation</ci>
					<ci>JMinusDegradation</ci>
				</apply>
			</apply>
		</math>
	</component>

	<connection>
		<map_components component_1="OmpRp_Interface" component_2="Bioenvironment_OmpRpFormation"/>
		<map_variables variable_1="JPlusFormation" variable_2="Jconcentration"/>
	</connection>

	<connection>
		<map_components component_1="OmpRp_Interface" component_2="Bioenvironment_Degradation_OmpRp"/>
		<map_variables variable_1="JMinusDegradation" variable_2="J"/>
	</connection>
	
	<import xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="svp_templates/Template_Species.cellml">
		<component component_ref="Template_Species" name="OmpRp"/>
	</import>

	<connection>
		<map_components component_1="OmpRp" component_2="Time"/>
		<map_variables variable_1="time" variable_2="time"/>
	</connection>

	<connection>
		<map_components component_1="OmpRp" component_2="OmpRp_Interface"/>
		<map_variables variable_1="JGain" variable_2="JGain"/>
	</connection>
	
	<connection>
		<map_components component_1="OmpRp" component_2="SpeciesInitialValues"/>
		<map_variables variable_1="concentrationInitialValue" variable_2="OmpRp"/>
	</connection>
	
	<import xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="Bioenvironment_Degradation_OmpRp.cellml">
		<component component_ref="Bioenvironment_Degradation_OmpRp" name="Bioenvironment_Degradation_OmpRp"/>
	</import>

	<connection>
		<map_components component_1="OmpRp" component_2="Bioenvironment_Degradation_OmpRp"/>
		<map_variables variable_1="concentration" variable_2="concentration"/>
	</connection>

	
	<import xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="ompC_lacZ_Promoter.cellml">
		<component component_ref="ompC_lacZ_Promoter" name="ompC_lacZ_Promoter"/>
	</import>
	
	<connection>
		<map_components component_1="OmpRp" component_2="ompC_lacZ_Promoter"/>
		<map_variables variable_1="concentration" variable_2="tFactor"/>
	</connection>
	
	<connection>
		<map_components component_1="E_Coli" component_2="ompC_lacZ_Promoter"/>
		<map_variables variable_1="cellVolume" variable_2="localVolume"/>
	</connection>
	
	<component name="ompC_lacZ_mRNA_Interface">
		<variable name="JPlusPromoter" public_interface="in" units="nM_per_s"/>
		<variable name="JGain" public_interface="out" units="nM_per_s"/>
		<variable name="JMinusDegradation" public_interface="in" units="nM_per_s"/>
		<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>

	<connection>
		<map_components component_1="ompC_lacZ_mRNA_Interface" component_2="Bioenvironment_Degradation_ompC_lacZ_mRNA"/>
		<map_variables variable_1="JMinusDegradation" variable_2="J"/>
	</connection>

	<connection>
		<map_components component_1="ompC_lacZ_mRNA_Interface" component_2="ompC_lacZ_mRNA"/>
		<map_variables variable_1="JGain" variable_2="JGain"/>
	</connection>

	<connection>
		<map_components component_1="ompC_lacZ_mRNA_Interface" component_2="ompC_lacZ_Promoter"/>
		<map_variables variable_1="JPlusPromoter" variable_2="JRNA"/>
	</connection>

	<import xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="svp_templates/Template_Species.cellml">
		<component component_ref="Template_Species" name="ompC_lacZ_mRNA"/>
		<units name="nM" units_ref="nM"/>
	</import>

	<connection>
		<map_components component_1="ompC_lacZ_mRNA" component_2="Time"/>
		<map_variables variable_1="time" variable_2="time"/>
	</connection>

	<connection>
		<map_components component_1="SpeciesInitialValues" component_2="ompC_lacZ_mRNA"/>
		<map_variables variable_1="ompC_lacZ_mRNA" variable_2="concentrationInitialValue"/>
	</connection>

	<import xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="Bioenvironment_Degradation_ompC_lacZ_mRNA.cellml">
		<component component_ref="Bioenvironment_Degradation_ompC_lacZ_mRNA" name="Bioenvironment_Degradation_ompC_lacZ_mRNA"/>
		<units name="per_s" units_ref="per_s"/>
	</import>

	<connection>
		<map_components component_1="ompC_lacZ_mRNA" component_2="Bioenvironment_Degradation_ompC_lacZ_mRNA"/>
		<map_variables variable_1="concentration" variable_2="concentration"/>
	</connection>

	<import xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="beta_galactosidase_RBS.cellml">
		<component component_ref="beta_galactosidase_RBS" name="beta_galactosidase_RBS"/>
	</import>

	<connection>
		<map_components component_1="beta_galactosidase_RBS" component_2="E_Coli"/>
		<map_variables variable_1="localVolume" variable_2="cellVolume"/>
	</connection>

	<connection>
		<map_components component_1="beta_galactosidase_RBS" component_2="ompC_lacZ_mRNA"/>
		<map_variables variable_1="RNA" variable_2="concentration"/>
	</connection>

	<import xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="beta_galactosidase_CDS.cellml">
		<component component_ref="beta_galactosidase_CDS" name="beta_galactosidase_CDS"/>
	</import>

	<connection>
		<map_components component_1="beta_galactosidase_CDS" component_2="E_Coli"/>
		<map_variables variable_1="localVolume" variable_2="cellVolume"/>
	</connection>

	<connection>
		<map_components component_1="beta_galactosidase_CDS" component_2="beta_galactosidase_RBS"/>
		<map_variables variable_1="hostRNARiPs" variable_2="RNARiPs"/>
	</connection>
	
	<component name="Beta_Galactosidase_Interface">
		<variable name="JPlusProduction" public_interface="in" units="nM_per_s"/>
		<variable name="JGain" public_interface="out" units="nM_per_s"/>
		<variable name="JMinusDegradation" public_interface="in" units="nM_per_s"/>
		<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>

	<connection>
		<map_components component_1="Beta_Galactosidase_Interface" component_2="beta_galactosidase_CDS"/>
		<map_variables variable_1="JPlusProduction" variable_2="J"/>
	</connection>

	<connection>
		<map_components component_1="Beta_Galactosidase_Interface" component_2="Bioenvironment_Degradation_Beta_Galactosidase"/>
		<map_variables variable_1="JMinusDegradation" variable_2="J"/>
	</connection>

	<import xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="svp_templates/Template_Species.cellml">
		<component component_ref="Template_Species" name="Beta_Galactosidase"/>
	</import>

	<connection>
		<map_components component_1="Beta_Galactosidase" component_2="Time"/>
		<map_variables variable_1="time" variable_2="time"/>
	</connection>

	<connection>
		<map_components component_1="Beta_Galactosidase" component_2="Beta_Galactosidase_Interface"/>
		<map_variables variable_1="JGain" variable_2="JGain"/>
	</connection>

	<connection>
		<map_components component_1="Beta_Galactosidase" component_2="SpeciesInitialValues"/>
		<map_variables variable_1="concentrationInitialValue" variable_2="Beta_Galactosidase"/>
	</connection>

	<import xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="Bioenvironment_Degradation_Beta_Galactosidase.cellml">
		<component component_ref="Bioenvironment_Degradation_Beta_Galactosidase" name="Bioenvironment_Degradation_Beta_Galactosidase"/>
	</import>

	<connection>
		<map_components component_1="Beta_Galactosidase" component_2="Bioenvironment_Degradation_Beta_Galactosidase"/>
		<map_variables variable_1="concentration" variable_2="concentration"/>
	</connection>
	
	<import xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="Bioenvironment_S_Galactosidase.cellml">
		<component component_ref="Bioenvironment_S_Galactosidase" name="S_Galactosidase"/>
	</import>
	
	<component name="Precipitate_Interface">
		<variable name="JPlusProduction" public_interface="in" units="nM_per_s"/>
		<variable name="JGain" public_interface="out" units="nM_per_s"/>
		<math xmlns="http://www.w3.org/1998/Math/MathML">
			<apply>
				<eq/>
				<ci>JGain</ci>
				<ci>JPlusProduction</ci>
			</apply>
		</math>
	</component>

	<connection>
		<map_components component_1="Precipitate_Interface" component_2="Bioenvironment_PrecipitateFormation"/>
		<map_variables variable_1="JPlusProduction" variable_2="J"/>
	</connection>


	<import xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="svp_templates/Template_Species.cellml">
		<component component_ref="Template_Species" name="Precipitate"/>
	</import>

	<connection>
		<map_components component_1="Precipitate" component_2="SpeciesInitialValues"/>
		<map_variables variable_1="concentrationInitialValue" variable_2="Precipitate"/>
	</connection>

	<connection>
		<map_components component_1="Precipitate" component_2="Time"/>
		<map_variables variable_1="time" variable_2="time"/>
	</connection>

	<connection>
		<map_components component_1="Precipitate" component_2="Precipitate_Interface"/>
		<map_variables variable_1="JGain" variable_2="JGain"/>
	</connection>

	<import xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="Bioenvironment_PrecipitateFormation.cellml">
		<component component_ref="Bioenvironment_PrecipitateFormation" name="Bioenvironment_PrecipitateFormation"/>
	</import>

	<connection>
		<map_components component_1="Bioenvironment_PrecipitateFormation" component_2="S_Galactosidase"/>
		<map_variables variable_1="reactant" variable_2="concentration"/>
	</connection>

	<connection>
		<map_components component_1="Bioenvironment_PrecipitateFormation" component_2="Beta_Galactosidase"/>
		<map_variables variable_1="catalyst" variable_2="concentration"/>
	</connection>
</model>
Source
Derived from workspace Virtual Bacterial Photography at changeset fb8422a520b9.
Collaboration
To begin collaborating on this work, please use your git client and issue this command:
License

This work is licensed under a Creative Commons Attribution 3.0 Unported License.