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

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

<model xmlns:xlink="http://www.w3.org/1999/xlink" name="NFAT_Cycling" cmeta:id="NFAT_Cycling"
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 xmlns="http://www.cellml.org/cellml/1.1#" 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 xmlns="http://www.cellml.org/cellml/1.1#" xlink:href="Principled_Base/Time.cellml">
		<component name="Time" component_ref="Time"/>
	</import>
	
	<group>
	<relationship_ref relationship="encapsulation" />
		<component_ref component="NFAT_Cycling">  
			<component_ref component="NFATp_c" />
			<component_ref component="NFATp_c_delta" />
			<component_ref component="NFATN_c" />
			<component_ref component="NFATN_c_delta" />
			<component_ref component="NFATN_n" />
			<component_ref component="NFATN_n_delta" />
			<component_ref component="NFATp_n" />
			<component_ref component="NFATp_n_delta" />
			<component_ref component="R1" />
			<component_ref component="R3" />
			<component_ref component="R2" />
			<component_ref component="R4" />
		</component_ref>
	</group>
	
	<component name="NFAT_Cycling_Parameters">
		<variable name="Ccn" units="dimensionless" initial_value="50" public_interface="out"/>
		<variable name="act_N" units="dimensionless"  initial_value="0.9" public_interface="out"/>
		<variable name="Ntot" units="nM" initial_value="1000" public_interface="out"/>
		<variable name="k_f1" units="per_nM_per_s" initial_value="7.68934e-6" public_interface="out"/>
		<variable name="k_r1" units="per_s" initial_value="0.019256" public_interface="out"/>
		<variable name="k_f2" units="per_s" initial_value="0.00144192" public_interface="out"/>
		<variable name="k_f3" units="per_s" initial_value="0.000361944" public_interface="out"/>
		<variable name="k_r3" units="per_nM_per_s" initial_value="4.70813e-5" public_interface="out"/>
		<variable name="k_f4" units="per_s" initial_value="0.000444695" public_interface="out"/>
		
		<variable name="NFATp_c_init" units="nM" initial_value="1.0" public_interface="out"/>
		<variable name="NFATN_c_init" units="nM" initial_value="0" public_interface="out"/>
		<variable name="NFATN_n_init" units="nM" initial_value="0" public_interface="out"/>
		<variable name="NFATp_n_init" units="nM" initial_value="0" public_interface="out"/>
		
		<variable name="J_NFATp_c_External" units="nM_per_s" initial_value="0" public_interface="out"/>
		<variable name="J_NFATN_c_External" units="nM_per_s" initial_value="0" public_interface="out"/>
		<variable name="J_NFATN_n_External" units="nM_per_s" initial_value="0" public_interface="out"/>
		<variable name="J_NFATp_n_External" units="nM_per_s" initial_value="0" public_interface="out"/>

	</component>	
	
 
   <component name="NFAT_Cycling">
          <variable name="time"   units="second" public_interface="in" private_interface="out"/>
      	  <variable name="Ntot" units="nM" public_interface="in" private_interface="out"/>
          <variable name="act_N" units="dimensionless" public_interface="in" private_interface="out"/>
      	  <variable name="Ccn" units="dimensionless" public_interface="in" private_interface="out"/>
          <variable name="k_f1" units="per_nM_per_s" public_interface="in" private_interface="out"/>
          <variable name="k_r1" units="per_s" public_interface="in"/>
          <variable name="k_f2" units="per_s" public_interface="in" private_interface="out"/>
          <variable name="k_f3" units="per_s" public_interface="in" />
          <variable name="k_r3" units="per_nM_per_s" public_interface="in" private_interface="out"/>
          <variable name="k_f4" units="per_s" public_interface="in" private_interface="out"/>
	  <variable name="NFATp_c_init" units="nM" private_interface="out" public_interface="in"/>
	  <variable name="NFATN_c_init" units="nM" private_interface="out" public_interface="in"/>
	  <variable name="NFATN_n_init" units="nM" private_interface="out" public_interface="in"/>
	  <variable name="NFATp_n_init" units="nM" private_interface="out" public_interface="in"/>
	  <variable name="J_NFATp_c_External" units="nM_per_s" private_interface="out" public_interface="in"/>
	  <variable name="J_NFATN_c_External" units="nM_per_s" private_interface="out" public_interface="in"/>
	  <variable name="J_NFATN_n_External" units="nM_per_s" private_interface="out" public_interface="in"/>
	  <variable name="J_NFATp_n_External" units="nM_per_s" private_interface="out" public_interface="in"/>
          
          <variable name="N_active" units="nM" public_interface="out" private_interface="out"/>
          <variable name="inact_N" units="dimensionless" />
          
          <variable name="k_r1_scaled" units="per_s" private_interface="out"/>
          <variable name="k_f3_scaled" units="per_s" private_interface="out"/>
          
          <variable name="NFATp_c" units="nM" private_interface="in" public_interface="out"/>
          <variable name="NFATN_c" units="nM" private_interface="in" public_interface="out"/>
          <variable name="NFATN_n" units="nM" private_interface="in" public_interface="out"/>
          <variable name="NFATp_n" units="nM" private_interface="in" public_interface="out"/>
          
	  <variable name="J_NFATp_c" units="nM_per_s" private_interface="in" public_interface="out"/>
	  <variable name="J_NFATN_c" units="nM_per_s" private_interface="in" public_interface="out"/>
	  <variable name="J_NFATN_n" units="nM_per_s" private_interface="in" public_interface="out"/>
	  <variable name="J_NFATp_n" units="nM_per_s" private_interface="in" public_interface="out"/>
     
	<math xmlns="http://www.w3.org/1998/Math/MathML">
	
	<apply>
	<eq/>
	<ci>N_active</ci>
	<apply>
	<times/>
	<ci>Ntot</ci>
	<ci>act_N</ci>
	</apply>
	</apply>
	
	<apply>
	<eq/>
	<ci>inact_N</ci>
	<apply>
	<minus/>
	<cn cellml:units="dimensionless">1</cn>
	<ci>act_N</ci>
	</apply>
	</apply>
	
	<apply>
	<eq/>
	<ci>k_r1_scaled</ci>
	<apply>
	<times/>
	<ci>k_r1</ci>
	<ci>inact_N</ci>
	</apply>
	</apply>
	
	<apply>
	<eq/>
	<ci>k_f3_scaled</ci>
	<apply>
	<times/>
	<ci>k_f3</ci>
	<ci>inact_N</ci>
	</apply>
	</apply>
	</math>
    </component>     

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

       <connection>
         <map_components component_1="NFAT_Cycling_Parameters" component_2="NFAT_Cycling"/>
   		<map_variables variable_1="act_N" variable_2="act_N"/>
   		<map_variables variable_1="Ntot" variable_2="Ntot"/>
   		<map_variables variable_1="k_f1" variable_2="k_f1"/>
   		<map_variables variable_1="k_r1" variable_2="k_r1"/>
   		<map_variables variable_1="k_f2" variable_2="k_f2"/>
   		<map_variables variable_1="k_f3" variable_2="k_f3"/>
   		<map_variables variable_1="k_r3" variable_2="k_r3"/>
   		<map_variables variable_1="k_f4" variable_2="k_f4"/>
   		<map_variables variable_1="Ccn" variable_2="Ccn"/>
   		
   		<map_variables variable_1="NFATp_c_init" variable_2="NFATp_c_init"/>
   		<map_variables variable_1="NFATN_c_init" variable_2="NFATN_c_init"/>
   		<map_variables variable_1="NFATN_n_init" variable_2="NFATN_n_init"/>
   		<map_variables variable_1="NFATp_n_init" variable_2="NFATp_n_init"/>
   		
   		<map_variables variable_1="J_NFATp_c_External" variable_2="J_NFATp_c_External"/>
   		<map_variables variable_1="J_NFATN_c_External" variable_2="J_NFATN_c_External"/>
   		<map_variables variable_1="J_NFATN_n_External" variable_2="J_NFATN_n_External"/>
   		<map_variables variable_1="J_NFATp_n_External" variable_2="J_NFATp_n_External"/>
   	</connection>
   	
  	<import xmlns="http://www.cellml.org/cellml/1.1#" xlink:href="Principled_Base/Template_Species_uM.cellml">
  		<units name="per_s" units_ref="per_s"/>
  		<component name="NFATp_c" component_ref="Template_Species_uM"/>
  	</import>
  	
  	   <connection>
  	      <map_components component_1="NFATp_c" component_2="NFAT_Cycling"/>
  	      <map_variables variable_1="time" variable_2="time"/>
  	      <map_variables variable_1="concentrationInitialValue" variable_2="NFATp_c_init"/>
  	      <map_variables variable_1="concentration" variable_2="NFATp_c"/>
  	   </connection>
  
  	   <connection>
  	      <map_components component_1="NFATp_c" component_2="NFATp_c_delta"/>
  	      <map_variables variable_1="JGain" variable_2="JNet"/>
  	   </connection>
  	   
  	<connection>
  	<map_components component_1="NFAT_Cycling" component_2="NFATp_c_delta"/>
  		<map_variables variable_1="Ccn" variable_2="Ccn"/>
  		<map_variables variable_1="J_NFATp_c_External" variable_2="JPlusExternal"/>
  		<map_variables variable_1="J_NFATp_c" variable_2="JNet"/>
  	</connection>
  	
  	<connection>
  	<map_components component_1="R4" component_2="NFATp_c_delta"/>
  		<map_variables variable_1="J" variable_2="JPlusR4"/>
  	</connection>
  	
  	<connection>
  		<map_components component_1="R1" component_2="NFATp_c_delta"/>
  			<map_variables variable_1="J" variable_2="JMinusR1"/>
  	</connection>
  	   
  	<component name="NFATp_c_delta">
  	<variable name="JNet"  units="nM_per_s" public_interface="out" />
  	<variable name="JPlusR4"  units="nM_per_s" public_interface="in" />
  	<variable name="JMinusR1"  units="nM_per_s" public_interface="in" />
  	<variable name="JPlusExternal"  units="nM_per_s" public_interface="in" />
  	<variable name="Ccn"  units="dimensionless" public_interface="in" />
  	<math xmlns="http://www.w3.org/1998/Math/MathML">
  		<apply>
  			<eq/>
  			<ci>JNet</ci>
  			<apply>
  			    <minus/>
  			    <apply>
  			    	<plus/>
  			    		<ci>JPlusExternal</ci>
					<apply>
					       <divide/>
					       <ci>JPlusR4</ci>
					       <ci>Ccn</ci>
					</apply>
  			    </apply>
  			    <ci>JMinusR1</ci>
                   	</apply>
  		</apply>
  	</math>
  	</component>
  	
  	<import xmlns="http://www.cellml.org/cellml/1.1#" xlink:href="Principled_Base/Template_Species_uM.cellml">
  		<component name="NFATN_c" component_ref="Template_Species_uM"/>
  	</import>
  	
  	   <connection>
  	      <map_components component_1="NFATN_c" component_2="NFAT_Cycling"/>
  	      <map_variables variable_1="time" variable_2="time"/>
  	      <map_variables variable_1="concentrationInitialValue" variable_2="NFATN_c_init"/>
  	      <map_variables variable_1="concentration" variable_2="NFATN_c"/>
  	   </connection>
	<connection>
		<map_components component_1="NFATN_c_delta" component_2="NFAT_Cycling"/> 
		<map_variables variable_1="JPlusExternal" variable_2="J_NFATN_c_External"/>
		<map_variables variable_1="JNet" variable_2="J_NFATN_c"/>
	</connection>
  	   <connection>
  	      <map_components component_1="NFATN_c" component_2="NFATN_c_delta"/>
  	      <map_variables variable_1="JGain" variable_2="JNet"/>
  	   </connection>
  	   
  	<connection>
  	<map_components component_1="R2" component_2="NFATN_c_delta"/>
  		<map_variables variable_1="J" variable_2="JMinusR2"/>
  	</connection>
  	
  	<connection>
  		<map_components component_1="R1" component_2="NFATN_c_delta"/>
  			<map_variables variable_1="J" variable_2="JPlusR1"/>
  	</connection>
  	   
  	<component name="NFATN_c_delta">
  	<variable name="JNet"  units="nM_per_s" public_interface="out" />
  	<variable name="JPlusR1"  units="nM_per_s" public_interface="in" />
  	<variable name="JMinusR2"  units="nM_per_s" public_interface="in" />
  	<variable name="JPlusExternal"  units="nM_per_s" public_interface="in" />
  	<math xmlns="http://www.w3.org/1998/Math/MathML">
  		<apply>
  			<eq/>
  			<ci>JNet</ci>
  			<apply>
  				<plus/>
  				<ci>JPlusExternal</ci>
					<apply>
						<minus/>
						<ci>JPlusR1</ci>
						<ci>JMinusR2</ci>
					</apply>
			</apply>
  		</apply>
  	</math>
  	</component>
  	
  	<import xmlns="http://www.cellml.org/cellml/1.1#" xlink:href="Principled_Base/Template_Species_uM.cellml">
  		<component name="NFATN_n" component_ref="Template_Species_uM"/>
  	</import>
  	
  	   <connection>
  	      <map_components component_1="NFATN_n" component_2="NFAT_Cycling"/>
  	      <map_variables variable_1="time" variable_2="time"/>
  	      <map_variables variable_1="concentrationInitialValue" variable_2="NFATN_n_init"/>
  	      <map_variables variable_1="concentration" variable_2="NFATN_n"/>
  	   </connection>
  
  	   <connection>
  	      <map_components component_1="NFATN_n" component_2="NFATN_n_delta"/>
  	      <map_variables variable_1="JGain" variable_2="JNet"/>
  	   </connection>
  	   
  	<connection>
  	<map_components component_1="NFATN_n_delta" component_2="NFAT_Cycling"/>
  		<map_variables variable_1="Ccn" variable_2="Ccn"/>
  		<map_variables variable_1="JPlusExternal" variable_2="J_NFATN_n_External"/>
  		<map_variables variable_1="JNet" variable_2="J_NFATN_n"/>
  	</connection>
  	
  	<connection>
  	<map_components component_1="NFATN_n_delta" component_2="R2"/>
  			<map_variables variable_1="JPlusR2" variable_2="J"/>
  	</connection>
  	
  	<connection>
  	<map_components component_1="NFATN_n_delta" component_2="R3"/>
  			<map_variables variable_1="JMinusR3" variable_2="J"/>
  	</connection>  
  	   
  	<component name="NFATN_n_delta">
  	<variable name="JNet"  units="nM_per_s" public_interface="out" />
  	<variable name="JPlusR2"  units="nM_per_s" public_interface="in" />
  	<variable name="JMinusR3"  units="nM_per_s" public_interface="in" />
  	<variable name="JPlusExternal"  units="nM_per_s" public_interface="in" />
  	<variable name="Ccn"  units="dimensionless" public_interface="in" />
  	<math xmlns="http://www.w3.org/1998/Math/MathML">
  		<apply>
  			<eq/>
  			<ci>JNet</ci>
			<apply>
				<minus/>
					<apply>	
						<plus/>
						<ci>JPlusExternal</ci>
						<apply>
						<times/>
							<ci>JPlusR2</ci>
							<ci>Ccn</ci>
						</apply>
					</apply>
				<ci>JMinusR3</ci>
			</apply>
  		</apply>
  	</math>
  	</component>
  	
  	<import xmlns="http://www.cellml.org/cellml/1.1#" xlink:href="Principled_Base/Template_Species_uM.cellml">
  		<component name="NFATp_n" component_ref="Template_Species_uM"/>
  	</import>
  	
  	   <connection>
  	      <map_components component_1="NFATp_n" component_2="NFAT_Cycling"/>
  	      <map_variables variable_1="time" variable_2="time"/>
  	      <map_variables variable_1="concentrationInitialValue" variable_2="NFATp_n_init"/>
  	      <map_variables variable_1="concentration" variable_2="NFATp_n"/>
  	   </connection>
  	   
	<connection>
		<map_components component_1="NFATp_n_delta" component_2="NFAT_Cycling"/> 
		<map_variables variable_1="JPlusExternal" variable_2="J_NFATp_n_External"/>
		<map_variables variable_1="JNet" variable_2="J_NFATp_n"/>
	</connection>
  
  	   <connection>
  	      <map_components component_1="NFATp_n" component_2="NFATp_n_delta"/>
  	      <map_variables variable_1="JGain" variable_2="JNet"/>
  	   </connection>
  	   
  	<connection>
  	<map_components component_1="NFATp_n_delta" component_2="R4"/>
  		<map_variables variable_1="JMinusR4" variable_2="J"/>
  	</connection>
  	
  	<connection>
  	<map_components component_1="NFATp_n_delta" component_2="R3"/>
  			<map_variables variable_1="JPlusR3" variable_2="J"/>
  	</connection>   
  	
  	<component name="NFATp_n_delta">
  	<variable name="JNet"  units="nM_per_s" public_interface="out" />
  	<variable name="JPlusR3"  units="nM_per_s" public_interface="in" />
  	<variable name="JMinusR4"  units="nM_per_s" public_interface="in" />
  	<variable name="JPlusExternal"  units="nM_per_s" public_interface="in" />
  	<math xmlns="http://www.w3.org/1998/Math/MathML">
  		<apply>
  			<eq/>
  			<ci>JNet</ci>
  				<apply>
  					<plus/>
  					<ci>JPlusExternal</ci>
						 <apply>
						    <minus/>
						    <ci>JPlusR3</ci>
						    <ci>JMinusR4</ci>
						 </apply>
				</apply>
  		</apply>
  	</math>
	</component>
   	
  <import xmlns="http://www.cellml.org/cellml/1.1#" xlink:href="Principled_Base/Template_RateEqR2P1_uM.cellml">
  		<component name="R1" component_ref="Template_RateEqR2P1_uM"/>
  	</import>
  	
  	   <connection>
  	      <map_components component_1="R1" component_2="NFAT_Cycling"/>
  	      <map_variables variable_1="kf" variable_2="k_f1"/>
  	      <map_variables variable_1="kr" variable_2="k_r1_scaled"/>
  	      <map_variables variable_1="B" variable_2="N_active"/>
  	   </connection>
  	  
  	   <connection>
  	      <map_components component_1="R1" component_2="NFATp_c"/>
  	      <map_variables variable_1="A" variable_2="concentration"/>
  	   </connection>
  	   
  	   <connection>
  	      <map_components component_1="R1" component_2="NFATN_c"/>
  	      <map_variables variable_1="C" variable_2="concentration"/>
  	   </connection>
  	
  	<import xmlns="http://www.cellml.org/cellml/1.1#" xlink:href="Principled_Base/Template_RateEqR1P2_uM.cellml">
  		<component name="R3" component_ref="Template_RateEqR1P2_uM"/>
  	</import>
  	
  	   <connection>
  	      <map_components component_1="R3" component_2="NFAT_Cycling"/>
  	      <map_variables variable_1="kr" variable_2="k_r3"/>
  	      <map_variables variable_1="kf" variable_2="k_f3_scaled"/>
  	      <map_variables variable_1="B" variable_2="N_active"/>
  	   </connection>
  	  
  	   <connection>
  	      <map_components component_1="R3" component_2="NFATN_n"/>
  	      <map_variables variable_1="A" variable_2="concentration"/>
  	   </connection>
  	   
  	   <connection>
  	      <map_components component_1="R3" component_2="NFATp_n"/>
  	      <map_variables variable_1="C" variable_2="concentration"/>
  	   </connection>
  	   
  	<import xmlns="http://www.cellml.org/cellml/1.1#" xlink:href="Principled_Base/Template_RateEqR1_uM.cellml">
  		<component name="R2" component_ref="Template_RateEqR1_uM"/>
  	</import>
  	
  	   <connection>
  	      <map_components component_1="R2" component_2="NFAT_Cycling"/>
  	      <map_variables variable_1="k" variable_2="k_f2"/>
  	   </connection>
  	  
  	   <connection>
  	      <map_components component_1="R2" component_2="NFATN_c"/>
  	      <map_variables variable_1="concentration" variable_2="concentration"/>
  	   </connection>
  	   
  	<import xmlns="http://www.cellml.org/cellml/1.1#" xlink:href="Principled_Base/Template_RateEqR1_uM.cellml">
  		<component name="R4" component_ref="Template_RateEqR1_uM"/>
  	</import>
  	
  	   <connection>
  	      <map_components component_1="R4" component_2="NFAT_Cycling"/>
  	      <map_variables variable_1="k" variable_2="k_f4"/>
  	   </connection>
  	  
  	   <connection>
  	      <map_components component_1="R4" component_2="NFATp_n"/>
  	      <map_variables variable_1="concentration" variable_2="concentration"/>
	   </connection>
  
</model>