Location: Virtual Bacterial Photography @ fb8422a520b9 / Bioenvironment_Cph8Formation.cellml

Author:
Tommy Yu <tommy.yu@auckland.ac.nz>
Date:
2011-06-16 15:08:26+12:00
Desc:
Removed extra <br> in title.
Permanent Source URI:
http://models.cellml.org/w/mcoo001/virtualbacterialphotography/rawfile/fb8422a520b9635b0903bc7595334305ef205e3a/Bioenvironment_Cph8Formation.cellml
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<?xml version="1.0"?>
<model xmlns="http://www.cellml.org/cellml/1.1#" xmlns:cmeta="http://www.cellml.org/metadata/1.0#" cmeta:id="Bioenvironment_Cph8Formation" name="Bioenvironment_Cph8Formation"
 xmlns:cellml="http://www.cellml.org/cellml/1.1#">
            
    <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
            <rdf:Description rdf:about="#Bioenvironment_Cph8Reaction">
            <dc:creator xmlns:dc="http://purl.org/dc/elements/1.0/">
            <vCard:N xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" rdf:parseType="Resource">
                <vCard:Family>Cooling</vCard:Family>
                <vCard:Given>Mike</vCard:Given>
            </vCard:N>
            <vCard:EMAIL xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" 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 xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" rdf:parseType="Resource">
                <vCard:Orgname>Auckland Bioengineering Institute</vCard:Orgname>
                <vCard:Orgunit>University of Auckland</vCard:Orgunit>
            </vCard:ORG>
            </dc:creator>
            </rdf:Description>
   </rdf:RDF>
   
   <units name="nM_per_s">
      <unit units="nM"/>
      <unit units="per_s"/>
   </units>
   
  <import xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="svp_templates/Template_RxBoundR2BoundP1Rev.cellml">
       <units name="molecule_per_micrometer2_per_s" units_ref="molecule_per_micrometer2_per_s"/>
       <units name="molecule_per_micrometer2" units_ref="molecule_per_micrometer2"/>
       <units name="micrometer2_per_molecule_per_s" units_ref="micrometer2_per_molecule_per_s"/>
       <units name="per_s" units_ref="per_s"/>
       <component component_ref="Template_RxBoundR2BoundP1Rev" name="Template_RxBoundR2BoundP1Rev"/>
  </import>
  
  <import xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="svp_templates/Template_ConcentrationToDensityConversion.cellml">
       <component component_ref="Template_ConcentrationToDensityConversion" name="Template_ConcentrationToDensityConversion"/>
       <units name="molecule_per_micrometer2_per_nM" units_ref="molecule_per_micrometer2_per_nM"/>
       <units name="nM" units_ref="nM"/>
  </import>
  
   <import xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="svp_templates/Template_DensityToConcentrationConversion.cellml">
        <component component_ref="Template_DensityToConcentrationConversion" name="Template_DensityToConcentrationConversion"/>
  </import>

   <component name="Bioenvironment_Cph8Formation">
    <variable name="Jdensity" private_interface="in" public_interface="out" units="molecule_per_micrometer2_per_s"/>
    <variable name="Jdensity_timeless" private_interface="out" units="molecule_per_micrometer2"/>
    <variable name="Jconcentration_timeless" private_interface="in" units="nM"/>
    <variable name="Jconcentration" public_interface="out" units="nM_per_s"/>
    <variable name="PCB" private_interface="out" public_interface="in" units="nM"/>
    <variable name="Cph8_no_PCB" private_interface="out" public_interface="in" units="molecule_per_micrometer2"/>
    <variable name="Cph8" private_interface="out" public_interface="in" units="molecule_per_micrometer2"/>
    <variable name="Ccm" private_interface="out" public_interface="in" units="molecule_per_micrometer2_per_nM"/>
    <variable initial_value="1" name="kf" private_interface="out" units="micrometer2_per_molecule_per_s"/>
    <variable initial_value="0.001" name="kb" private_interface="out" units="per_s"/>
    
    <math xmlns="http://www.w3.org/1998/Math/MathML">
    	<apply>
    		<eq/>
    		<ci>Jdensity_timeless</ci>
		<apply>
			<times/>
			<cn cellml:units="second">1</cn>
			<ci>Jdensity</ci>
		</apply>
    	</apply>
	<apply>
		<eq/>
		<ci>Jconcentration</ci>
		<apply>
			<divide/>
			<ci>Jconcentration_timeless</ci>
			<cn cellml:units="second">1</cn>
		</apply>
    	</apply>
    </math>
   </component>
 
   <group>
    <relationship_ref relationship="encapsulation"/>
    <component_ref component="Bioenvironment_Cph8Formation">
      <component_ref component="Template_RxBoundR2BoundP1Rev"/>
      <component_ref component="Template_ConcentrationToDensityConversion"/>
      <component_ref component="Template_DensityToConcentrationConversion"/>
    </component_ref>
   </group> 
  
<connection>
	<map_components component_1="Bioenvironment_Cph8Formation" component_2="Template_RxBoundR2BoundP1Rev"/>
	<map_variables variable_1="Jdensity" variable_2="J"/>
	<map_variables variable_1="kf" variable_2="kf"/>
	<map_variables variable_1="kb" variable_2="kb"/>
	<map_variables variable_1="Cph8_no_PCB" variable_2="reactant2"/>
	<map_variables variable_1="Cph8" variable_2="product"/>
</connection>

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

<connection>
	<map_components component_1="Template_RxBoundR2BoundP1Rev" component_2="Template_ConcentrationToDensityConversion"/>
	<map_variables variable_1="reactant1" variable_2="density"/>
</connection>

<connection>
	<map_components component_1="Template_DensityToConcentrationConversion" component_2="Bioenvironment_Cph8Formation"/>
	<map_variables variable_1="Ccm" variable_2="Ccm"/>
	<map_variables variable_1="density" variable_2="Jdensity_timeless"/>
	<map_variables variable_1="concentration" variable_2="Jconcentration_timeless"/>
</connection>

</model>