Location: Core Domains Principled Model Example @ e8b0e5d10f56 / ExampleDevice.cellml

Author:
Michael Cooling <mcoo001@UoA.auckland.ac.nz>
Date:
2016-04-11 11:48:36+12:00
Desc:
Initial Commit
Permanent Source URI:
https://models.cellml.org/workspace/2c5/rawfile/e8b0e5d10f563c9a997626435bace472ab5f7f34/ExampleDevice.cellml

<?xml version="1.0" encoding="utf-8"?>

<model xmlns:xlink="http://www.w3.org/1999/xlink" name="ExampleDevice" cmeta:id="ExampleDevice"
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#">


	<import xlink:href="Principled_Base/Units_Cellular_Systems.cellml">
		<units name="nM" units_ref="nM"/>
		<units name="nM_per_s" units_ref="nM_per_s"/>
		<units name="per_nM_per_s" units_ref="per_nM_per_s"/>
	</import>
	
	<import xlink:href="Principled_Base/Time.cellml">
		<component name="Time" component_ref="Time"/>
	</import>
	
	<group>
	<relationship_ref relationship="encapsulation" />
		<component_ref component="ExampleDevice">  
			<component_ref component="Chassis" />
			<component_ref component="Promoter" />
			<component_ref component="RNA_n" />
			<component_ref component="RNA_n_delta" />
			<component_ref component="RNA_Transport" />
			<component_ref component="RNA_c" />
			<component_ref component="RNA_c_delta" />
			<component_ref component="RNA_c_Degradation" />
			<component_ref component="RBS_GFP" />
			<component_ref component="CDS_GFP" />
			<component_ref component="GFP" />
			<component_ref component="GFP_delta" />
			<component_ref component="GFP_Degradation" />
		</component_ref>
	</group>
	
    <import xlink:href="Principled_Base/mohr_taylor_newell_2008_subset.cellml">
    	<component name="codata_2006_physicochemical" component_ref="codata_2006_physicochemical_subset" />
    	<units name="per_mole" units_ref="per_mole" />
    </import>
    
   <connection>
   	 <map_components component_1="ExampleDevice" component_2="codata_2006_physicochemical"/>
   	 <map_variables variable_1="avogadrosConstant" variable_2="Avogadro_constant"/>
   </connection> 
	
	<component name="ExampleDevice_Parameters">
		<variable name="transcriptionFactor" units="nM" initial_value="100" public_interface="out" />
		<variable name="RNA_n_init" units="nM" initial_value="0" public_interface="out" />
		<variable name="J_RNA_n_External" units="nM_per_s" initial_value="0" public_interface="out" />
		<variable name="RNA_c_init" units="nM" initial_value="0" public_interface="out" />
		<variable name="J_RNA_c_External" units="nM_per_s" initial_value="0" public_interface="out" />
		<variable name="GFP_init" units="nM" initial_value="0" public_interface="out" />
		<variable name="J_GFP_External" units="nM_per_s" initial_value="0" public_interface="out" />
	</component>	
	
	<import xlink:href="ExampleDevice_Promoter.cellml">
		<units name="PoPs" units_ref="PoPs"/>
		<component name="Promoter_Parameters" component_ref="ExampleDevice_Promoter_Parameters"/>
	</import>
	
	<import xlink:href="Chassis_CoreModelCell.cellml">
		<units name="femtoliter" units_ref="femtoliter"/>
		<component name="Chassis_Parameters" component_ref="Chassis_CoreModelCell_Parameters"/>
	</import>
	
	<import  xlink:href="Bioenvironment_Degradation_ExampleDeviceRNA.cellml">
		<component name="RNA_Degradation_Parameters" component_ref="Bioenvironment_Degradation_ExampleDeviceRNA_Parameters"/>
	</import> 
	
	<import  xlink:href="Bioenvironment_Transport_RNA.cellml">
		<component name="RNA_Transport_Parameters" component_ref="Bioenvironment_Transport_RNA_Parameters"/>
	</import> 
	
	<import  xlink:href="ExampleDevice_RBS_GFP.cellml">
		<component name="ExampleDevice_RBS_GFP_Parameters" component_ref="ExampleDevice_RBS_GFP_Parameters"/>
	</import>
	
	<import  xlink:href="ExampleDevice_RBS_GFP.cellml">
		<component name="RBS_Parameters" component_ref="ExampleDevice_RBS_GFP_Parameters"/>
	</import> 
	
	<import  xlink:href="Bioenvironment_Degradation_GFP.cellml">
		<component name="GFP_Degradation_Parameters" component_ref="Bioenvironment_Degradation_GFP_Parameters"/>
	</import> 

   <component name="ExampleDevice">
	<variable name="time"   units="second" public_interface="in" private_interface="out"/>
	<variable name="k" units="PoPs" public_interface="in" private_interface="out" />
	<variable name="n" units="dimensionless" public_interface="in" private_interface="out"/>
	<variable name="Km" units="nM" public_interface="in" private_interface="out"/>
	<variable name="transcriptionFactor" units="nM" public_interface="in" private_interface="out"/>
	<variable name="transcriptionalVolume_init" units="femtoliter" public_interface="in" private_interface="out"/>
	<variable name="translationalVolume_init" units="femtoliter" public_interface="in" private_interface="out"/>
	<variable name="RNA_n_init" units="nM" public_interface="in" private_interface="out" />
	<variable name="J_RNA_n_External" units="nM_per_s" public_interface="in" private_interface="out" />
	<variable name="RNA_c_init" units="nM" public_interface="in" private_interface="out" />
	<variable name="J_RNA_c_External" units="nM_per_s" public_interface="in" private_interface="out" />
	<variable name="GFP_init" units="nM" public_interface="in" private_interface="out" />
	<variable name="J_GFP_External" units="nM_per_s" public_interface="in" private_interface="out" />
	<variable name="RNA_kDecay" units="per_s" public_interface="in" private_interface="out" />
	<variable name="RNA_Transport_k" units="per_s" public_interface="in" private_interface="out" />
	<variable name="RBS_k" units="RiPs" public_interface="in" private_interface="out" />
	<variable name="GFP_kDecay" units="per_s" public_interface="in" private_interface="out" />
        <variable name="avogadrosConstant" units="per_mole" public_interface="in" private_interface="out"/>
        
        <variable name="J_RNA_n" units="nM_per_s" public_interface="out" private_interface="in" />
	<variable name="RNA_n" units="nM" public_interface="out" private_interface="in"/>
	<variable name="J_RNA_c" units="nM_per_s" public_interface="out" private_interface="in" />
	<variable name="RNA_c" units="nM" public_interface="out" private_interface="in"/>
	<variable name="transcriptionalVolume" units="femtoliter" public_interface="out" private_interface="in"/>
	<variable name="translationalVolume" units="femtoliter" public_interface="out" private_interface="in"/>
	<variable name="J_GFP" units="nM_per_s" public_interface="out" private_interface="in" />
	<variable name="GFP" units="nM" public_interface="out" private_interface="in"/>
    </component>  

     <connection>
      <map_components component_1="Time" component_2="ExampleDevice"/>
		<map_variables variable_1="time" variable_2="time"/>
     </connection>  
     
     <connection>
      <map_components component_1="Promoter_Parameters" component_2="ExampleDevice"/>
		<map_variables variable_1="k" variable_2="k"/>
		<map_variables variable_1="n" variable_2="n"/>
		<map_variables variable_1="Km" variable_2="Km"/>
     </connection>  
     
     <connection>
      <map_components component_1="ExampleDevice_Parameters" component_2="ExampleDevice"/>
		<map_variables variable_1="transcriptionFactor" variable_2="transcriptionFactor"/>
		<map_variables variable_1="RNA_n_init" variable_2="RNA_n_init"/>
		<map_variables variable_1="J_RNA_n_External" variable_2="J_RNA_n_External"/>
		<map_variables variable_1="RNA_c_init" variable_2="RNA_c_init"/>
		<map_variables variable_1="J_RNA_c_External" variable_2="J_RNA_c_External"/>
		<map_variables variable_1="GFP_init" variable_2="GFP_init"/>
		<map_variables variable_1="J_GFP_External" variable_2="J_GFP_External"/>
     </connection>  
     
     <connection>
          <map_components component_1="Chassis_Parameters" component_2="ExampleDevice"/>
    		<map_variables variable_1="transcriptionalVolume_initialValue" variable_2="transcriptionalVolume_init"/>
    		<map_variables variable_1="translationalVolume_initialValue" variable_2="translationalVolume_init"/>
     </connection> 
     
     <connection>
          <map_components component_1="RBS_Parameters" component_2="ExampleDevice"/>
    		<map_variables variable_1="k" variable_2="RBS_k"/>
     </connection> 
     
     <connection>
          <map_components component_1="RNA_Transport_Parameters" component_2="ExampleDevice"/>
    		<map_variables variable_1="k" variable_2="RNA_Transport_k"/>
     </connection> 
     
  	<connection>
  	<map_components component_1="RNA_Degradation_Parameters" component_2="ExampleDevice"/>
  		<map_variables variable_1="kDecay" variable_2="RNA_kDecay"/>
  	</connection>
  	
   	<connection>
   	<map_components component_1="GFP_Degradation_Parameters" component_2="ExampleDevice"/>
   		<map_variables variable_1="kDecay" variable_2="GFP_kDecay"/>
  	</connection>
     
     
     <connection>
      <map_components component_1="Chassis" component_2="ExampleDevice"/>
		<map_variables variable_1="transcriptionalVolume" variable_2="transcriptionalVolume"/>
		<map_variables variable_1="transcriptionalVolume_initialValue" variable_2="transcriptionalVolume_init"/>
		<map_variables variable_1="translationalVolume" variable_2="translationalVolume"/>
		<map_variables variable_1="translationalVolume_initialValue" variable_2="translationalVolume_init"/>
     </connection>  
     
  
	<import  xlink:href="Chassis_CoreModelCell.cellml">
		<component name="Chassis" component_ref="Chassis_CoreModelCell"/>
	</import>

 
	<import xlink:href="ExampleDevice_Promoter.cellml">
		<component name="Promoter" component_ref="ExampleDevice_Promoter"/>
	</import>

     <connection>
      <map_components component_1="Promoter" component_2="ExampleDevice"/>
		<map_variables variable_1="k" variable_2="k"/>
		<map_variables variable_1="n" variable_2="n"/>
		<map_variables variable_1="Km" variable_2="Km"/>
		<map_variables variable_1="tFactor" variable_2="transcriptionFactor"/>
		<map_variables variable_1="avogadrosConstant" variable_2="avogadrosConstant"/>
     </connection>  
     
        <connection>
      <map_components component_1="Chassis" component_2="Promoter"/>  
     	<map_variables variable_1="transcriptionalVolume" variable_2="localVolume"/>
       </connection>  
  
	<import  xlink:href="Principled_Base/Template_Species_uM.cellml">
		<component name="RNA_n" component_ref="Template_Species_uM"/>
	</import> 
	
     <connection>
      <map_components component_1="RNA_n" component_2="ExampleDevice"/>
		<map_variables variable_1="concentrationInitialValue" variable_2="RNA_n_init"/>
		<map_variables variable_1="time" variable_2="time"/>
		<map_variables variable_1="concentration" variable_2="RNA_n"/>
     </connection>  
     

     
	<connection>
	<map_components component_1="RNA_n" component_2="RNA_n_delta"/>
		<map_variables variable_1="JGain" variable_2="JNet"/>
	</connection>
  	   
  	<connection>
  	<map_components component_1="ExampleDevice" component_2="RNA_n_delta"/>
  		<map_variables variable_1="J_RNA_n_External" variable_2="JPlusExternal"/>
  		<map_variables variable_1="J_RNA_n" variable_2="JNet"/>
  	</connection>
  	
  	<connection>
  	<map_components component_1="Promoter" component_2="RNA_n_delta"/>
  		<map_variables variable_1="JRNA" variable_2="JPlusPromoter"/>
  	</connection>
  	   
  	<component name="RNA_n_delta">
		<variable name="JNet"  units="nM_per_s" public_interface="out" />
		<variable name="JPlusPromoter" units="nM_per_s" public_interface="in" />
		<variable name="JPlusExternal" units="nM_per_s" public_interface="in" />
		<variable name="JMinusTransport" units="nM_per_s" public_interface="in" />
		<math xmlns="http://www.w3.org/1998/Math/MathML">
			<apply>
				<eq/>
				<ci>JNet</ci>
				<apply>
					<minus/>
					<apply>
						<plus/>
						<ci>JPlusExternal</ci>
						<ci>JPlusPromoter</ci>
					</apply>
					<ci>JMinusTransport</ci>
				</apply>
			</apply>
		</math>
  	</component>
  	
  	<import  xlink:href="Bioenvironment_Transport_RNA.cellml">
		<component name="RNA_Transport" component_ref="Bioenvironment_Transport_RNA"/>
	</import> 
	
  	<connection>
  	<map_components component_1="RNA_Transport" component_2="ExampleDevice"/>
  		<map_variables variable_1="k" variable_2="RNA_Transport_k"/>
  	</connection>
  	
  	<connection>
  	<map_components component_1="RNA_Transport" component_2="Chassis"/>
  		<map_variables variable_1="fromVolume" variable_2="transcriptionalVolume"/>
  		<map_variables variable_1="toVolume" variable_2="translationalVolume"/>
  	</connection>

  	
    	<connection>
    	<map_components component_1="RNA_Transport" component_2="RNA_n"/>
    		<map_variables variable_1="concentration" variable_2="concentration"/>
  	</connection>
  	
     	<connection>
     	<map_components component_1="RNA_Transport" component_2="RNA_c_delta"/>
     		<map_variables variable_1="J_toVolume" variable_2="JPlusTransport"/>
  	</connection>	
  	
       	<connection>
       	<map_components component_1="RNA_Transport" component_2="RNA_n_delta"/>
       		<map_variables variable_1="J_fromVolume" variable_2="JMinusTransport"/>
  	</connection>	
  	
 	<import  xlink:href="Principled_Base/Template_Species_uM.cellml">
 		<component name="RNA_c" component_ref="Template_Species_uM"/>
 	</import> 
 	
      <connection>
       <map_components component_1="RNA_c" component_2="ExampleDevice"/>
 		<map_variables variable_1="concentrationInitialValue" variable_2="RNA_c_init"/>
 		<map_variables variable_1="time" variable_2="time"/>
 		<map_variables variable_1="concentration" variable_2="RNA_c"/>
      </connection>  

 	<connection>
 	<map_components component_1="RNA_c" component_2="RNA_c_delta"/>
 		<map_variables variable_1="JGain" variable_2="JNet"/>
 	</connection>
   	   
   	<connection>
   	<map_components component_1="ExampleDevice" component_2="RNA_c_delta"/>
   		<map_variables variable_1="J_RNA_c_External" variable_2="JPlusExternal"/>
   		<map_variables variable_1="J_RNA_c" variable_2="JNet"/>
   	</connection>
   	
  	<component name="RNA_c_delta">
			<variable name="JNet"  units="nM_per_s" public_interface="out" />
			<variable name="JPlusTransport" units="nM_per_s" public_interface="in" />
			<variable name="JPlusExternal" units="nM_per_s" public_interface="in" />
			<variable name="JMinusDegradation" units="nM_per_s" public_interface="in" />
			<math xmlns="http://www.w3.org/1998/Math/MathML">
				<apply>
					<eq/>
					<ci>JNet</ci>
					<apply>
						<minus/>
						<apply>
							<plus/>
							<ci>JPlusExternal</ci>
							<ci>JPlusTransport</ci>
						</apply>
						<ci>JMinusDegradation</ci>
					</apply>
				</apply>
			</math>
  	</component>
  	
	<import  xlink:href="Bioenvironment_Degradation_ExampleDeviceRNA.cellml">
		<units name="per_s" units_ref="per_s"/>
		<component name="RNA_c_Degradation" component_ref="Bioenvironment_Degradation_ExampleDeviceRNA"/>
	</import> 
	
  	<connection>
  	<map_components component_1="RNA_c_Degradation" component_2="ExampleDevice"/>
  		<map_variables variable_1="kDecay" variable_2="RNA_kDecay"/>
  	</connection>

  	
    	<connection>
    	<map_components component_1="RNA_c_Degradation" component_2="RNA_c"/>
    		<map_variables variable_1="concentration" variable_2="concentration"/>
  	</connection>
  	
     	<connection>
     	<map_components component_1="RNA_c_Degradation" component_2="RNA_c_delta"/>
     		<map_variables variable_1="J" variable_2="JMinusDegradation"/>
  	</connection>
  	
	<import  xlink:href="ExampleDevice_RBS_GFP.cellml">
		<units name="RiPs" units_ref="RiPs"/>
		<component name="RBS_GFP" component_ref="ExampleDevice_RBS_GFP"/>
	</import> 
	
     	<connection>
     	<map_components component_1="RBS_GFP" component_2="ExampleDevice"/>
     		<map_variables variable_1="k" variable_2="RBS_k"/>
  	</connection>
  	
      	<connection>
      	<map_components component_1="RBS_GFP" component_2="Chassis"/>
      		<map_variables variable_1="localVolume" variable_2="translationalVolume"/>
  	</connection>
  	
      	<connection>
      	<map_components component_1="RBS_GFP" component_2="RNA_c"/>
      		<map_variables variable_1="RNA" variable_2="concentration"/>
  	</connection>
  	
	<import  xlink:href="ExampleDevice_ProteinCDS_GFP.cellml">
		<component name="CDS_GFP" component_ref="ExampleDevice_ProteinCDS_GFP"/>
	</import> 
	
     	<connection>
     	<map_components component_1="CDS_GFP" component_2="Chassis"/>
     		<map_variables variable_1="localVolume" variable_2="translationalVolume"/>
  	</connection>
  	
      	<connection>
      	<map_components component_1="CDS_GFP" component_2="RBS_GFP"/>
      		<map_variables variable_1="hostRNARiPs" variable_2="RNARiPs"/>
  	</connection>
  	
	<import  xlink:href="Principled_Base/Template_Species_uM.cellml">
		<component name="GFP" component_ref="Template_Species_uM"/>
	</import> 
	
     <connection>
      <map_components component_1="GFP" component_2="ExampleDevice"/>
		<map_variables variable_1="concentrationInitialValue" variable_2="GFP_init"/>
		<map_variables variable_1="time" variable_2="time"/>
		<map_variables variable_1="concentration" variable_2="GFP"/>
     </connection>  
     
	<connection>
	<map_components component_1="GFP" component_2="GFP_delta"/>
		<map_variables variable_1="JGain" variable_2="JNet"/>
	</connection>
  	   
  	<connection>
  	<map_components component_1="ExampleDevice" component_2="GFP_delta"/>
  		<map_variables variable_1="J_GFP_External" variable_2="JPlusExternal"/>
  		<map_variables variable_1="J_GFP" variable_2="JNet"/>
  	</connection>
  	
  	<connection>
  	<map_components component_1="CDS_GFP" component_2="GFP_delta"/>
  		<map_variables variable_1="J" variable_2="JPlusCDS"/>
  	</connection>
  	   
  	<component name="GFP_delta">
		<variable name="JNet"  units="nM_per_s" public_interface="out" />
		<variable name="JPlusCDS" units="nM_per_s" public_interface="in" />
		<variable name="JPlusExternal" units="nM_per_s" public_interface="in" />
		<variable name="JMinusDegradation" units="nM_per_s" public_interface="in" /> 
		<math xmlns="http://www.w3.org/1998/Math/MathML">
			<apply>
				<eq/>
				<ci>JNet</ci>
				<apply>
					<minus/> 
					<apply>
						<plus/>
						<ci>JPlusExternal</ci>
						<ci>JPlusCDS</ci>
					</apply>
					<ci>JMinusDegradation</ci>
				</apply> 
			</apply>
		</math>
  	</component>
	
	<import  xlink:href="Bioenvironment_Degradation_GFP.cellml">
		<component name="GFP_Degradation" component_ref="Bioenvironment_Degradation_GFP"/>
	</import> 
	
	<connection>
	    	<map_components component_1="GFP_Degradation" component_2="GFP"/>
	    		<map_variables variable_1="concentration" variable_2="concentration"/>
	 </connection>
	 
	<connection>
	    	<map_components component_1="GFP_Degradation" component_2="ExampleDevice"/>
	    		<map_variables variable_1="kDecay" variable_2="GFP_kDecay"/>
	 </connection>
	  	
	<connection>
	     	<map_components component_1="GFP_Degradation" component_2="GFP_delta"/>
	     		<map_variables variable_1="J" variable_2="JMinusDegradation"/>
  	</connection>

</model>