Registry of Standard Biological Models/Basic Component Models/Constitutive Promoter: Difference between revisions

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**TBD
**TBD
*'''Variables''':
*'''Variables''':
**nb-gene-copies (public interface = in / init value = 1.0)
**nbGeneCopies (public interface = in / init value = 1.0)
**transcription-rate (public interface = none / init value = XXX)
**transcriptionRatePerGene (public interface = none / init value = XXX)
**PoPs-OUT (public interface = out / init value = 0.)
**PoPs_OUT (public interface = out / init value = 0.)
*'''MathML'''
*'''MathML'''
**<amsmath>PoPs-OUT = transcription-rate*nb-genes-copies</amsmath>
**<amsmath>PoPsOUT = nbGenesCopies*transcriptionRatePerGene</amsmath>
 
==CellML File==
 
<syntax type='xml'>
<?xml version="1.0"?>
 
<model xmlns="http://www.cellml.org/cellml/1.0#"
      xmlns:cmeta="http://www.cellml.org/metadata/1.0#"
      xml:base="file:///C:/CellML_models/constitutive_promoter.cml"
      cmeta:id="constitutive_promoter"
      name="constitutive_promoter">
 
<!-- LIST OF COMPONENTS -->
 
<component name="constitutive_promoter">
 
<variable name="mRNAsynthesisRate"        initial_value=""  public_interface="out"  units="moles_per_second"/>
<variable name="nb_gene"                  initial_value="1"  public_interface="none" units="dimensionless"/>
<variable name="mRNAsynthesisRatePerGene" initial_value="1"  public_interface="none" units="moles_per_second"/>
<math xmlns="http://www.w3.org/1998/Math/MathML" id="mRNA synthesis rate">
 
  <apply id="mRNAsynthesisRate">
  <eq/>
  <ci>mRNAsynthesisRate</ci>
  <apply>
  <times/>
  <ci>mRNAsynthesisRatePerGene</ci>
  <ci>nb_gene</ci>
  </apply>
  </apply>
</math>
 
</component>
 
 
<!-- END LIST OF COMPONENTS -->
 
 
 
<!-- LIST OF IMPORTS -->
 
<import xmlns:xlink="http://www.w3.org/1999/xlink"
        xlink:href="file://C:\CellML_models\units.cml">
 
      <units name="moles_per_second" units_ref="moles_per_second"/>
      <units name="per_second"      units_ref="per_second"/>
</import>
 
<!-- END LIST OF IMPORTS -->
 
 
<!-- LIST OF CONNECTIONS -->
 
 
<!-- END LIST OF CONNECTIONS -->
 
</model>
</syntax>
 
 




==Comments==
==Comments==

Latest revision as of 03:45, 18 January 2008

Constitutive Promoter Architecture

  • Description: Promoter with constant transcription rate at a given number of gene copies
  • Hypothesis:
    • Constant and continuous transcription rate
    • Transcription rate depends on the number of gene copies
    • unlimited resources for transcription (excess in polymerase ...)
    • No effect from activators or repressors
  • Inputs:
    • nb-gene-copies
  • Outputs:
    • PoPs_out
  • Characteristic parameters:
    • transcription-rate-per-gene
Constitutive Promoter Brick Architecture

CellML structure (CellML 1.1 spec)

  • Component: ConstitutivePromoter
  • Units:
    • TBD
  • Variables:
    • nbGeneCopies (public interface = in / init value = 1.0)
    • transcriptionRatePerGene (public interface = none / init value = XXX)
    • PoPs_OUT (public interface = out / init value = 0.)
  • MathML
    • <amsmath>PoPsOUT = nbGenesCopies*transcriptionRatePerGene</amsmath>

CellML File

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

<model xmlns="http://www.cellml.org/cellml/1.0#" 

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

<component name="constitutive_promoter">

<variable name="mRNAsynthesisRate" initial_value="" public_interface="out" units="moles_per_second"/> <variable name="nb_gene" initial_value="1" public_interface="none" units="dimensionless"/> <variable name="mRNAsynthesisRatePerGene" initial_value="1" public_interface="none" units="moles_per_second"/>

[math]\displaystyle{ \lt apply id="mRNAsynthesisRate"\gt \lt eq/\gt \lt ci\gt mRNAsynthesisRate\lt /ci\gt \lt apply\gt \lt times/\gt \lt ci\gt mRNAsynthesisRatePerGene\lt /ci\gt \lt ci\gt nb_gene\lt /ci\gt \lt /apply\gt \lt /apply\gt }[/math]

</component>




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

       xlink:href="file://C:\CellML_models\units.cml">

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

</import>




</model> </syntax>



Comments

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