Registry of Standard Biological Models/Basic Component Models/Constitutive Promoter

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>