Registry of Standard Biological Models/Basic Component Models/Constitutive Protein Expression Dynamic

ID: Constitutive mRNA/Protein expression

• Description: Constitutive Protein expression
• Hypothesis:
  • central dogma: gene -> mRNA -> protein
  • quasi steady state on mRNA expression
  • all hypothesis applicable to sub-parts
• Inputs:
  • nb-gene-copies
• Outputs:
  • [Protein]
• Internal parameters:
  • ???

CellML structure (CellML 1.1 spec)

• Component: ConstitutiveProteinExpression
• Units:
  • TBD
• Imports:
  • Components:
    • ConstituvePromoter_RBS_Coupled
    • Protein

• Variables:
  • time (public interface = in)
  • nbGeneCopies (public interface = in)
  • protein (public interface = out / init value = 0.)
• MathML
  • none

Examples

BioBricks from Registry	CellML file
<bbpart>BBa_I7101</bbpart> ==> GFP protein expression from TetR	Media:BBa_I7101_Model.xml
other part	other file

CellML Code

[http://openwetware.org/index.php?title=Registry_of_Standard_Biological_Models/Basic_Component_Models/Constitutive_Protein_Expression_Dynamic&action=raw"

<syntax type = 'xml'> <?xml version="1.0"?>

<model xmlns="http://www.cellml.org/cellml/1.1#"

      xmlns:cmeta="http://www.cellml.org/metadata/1.0#"
      xml:base="file:///C:/CellML_models/protein-generator.cml"
      cmeta:id="protein-generator"
      name="protein-generator">

<import xmlns:xlink="http://www.w3.org/1999/xlink"

       xlink:href="http://openwetware.org/index.php?title=Registry_of_Standard_Biological_Models/Basic_Component_Models/...&action=raw">
     
     <component component_ref="Protein" name="Protein"/>

</import>

<import xmlns:xlink="http://www.w3.org/1999/xlink"

       xlink:href="http://openwetware.org/index.php?title=Registry_of_Standard_Biological_Models/Basic_Component_Models/...&action=raw">

     <component component_ref="promoter-RBS_constitutive" name="promoter-RBS_constitutive"/>

</import>

<import xmlns:xlink="http://www.w3.org/1999/xlink"

       xlink:href="http://openwetware.org/index.php?title=Registry_of_Standard_Biological_Models/Basic_Component_Models/...&action=raw">

     <component component_ref="Plasmid" name="Plasmid"/>

</import>

<import xmlns:xlink="http://www.w3.org/1999/xlink"

       xlink:href="http://openwetware.org/index.php?title=Registry_of_Standard_Biological_Models/Basic_Component_Models/...&action=raw">

     <units name="moles_per_second" units_ref="moles_per_second"/>
     <units name="per_second" units_ref="per_second"/>

</import>

<group>

<relationship_ref name="protein-generator" relationship="encapsulation"/>

   <component_ref component="protein-generator"> 
      <component_ref component="promoter-RBS_constitutive"/> 
      <component_ref component="Protein"/>
      <component_ref component="Plasmid"/>
   </component_ref> 

</group>

<component name="protein-generator">

     <variable name="time"                 public_interface="in"  private_interface="out" units="second"/>
     <variable name="proteinConcentration" public_interface="out" private_interface="in" units="second"/>

</component>

<connection> <map_components component_1="Plasmid" component_2="promoter-RBS_constitutive"/> <map_variables variable_1="nbGeneCopiesOut" variable_2="nbGeneCopiesIn"/> </connection>

<connection> <map_components component_1="promoter-RBS_constitutive" component_2="Protein"/> <map_variables variable_1="RiPSOut" variable_2="RiPSIn"/> </connection>

<connection>

      <map_components component_1="Protein"  component_2="protein-generator"/>
      <map_variables variable_1="time"       variable_2="time"/>

</connection>

<connection>

      <map_components component_1="Protein"            component_2="protein-generator"/>
      <map_variables variable_1="proteinConcentration" variable_2="proteinConcentration"/>

</connection>

</model> </syntax>

Comments

• No too sure how to connect the components together following the import
• Do I have to declare all the variables I need to use from the imported components ?
• How do I 'trigger' the dynamic behaviour of the sub-components ?