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

From OpenWetWare
Jump to navigationJump to search

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=""


<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]


<import xmlns:xlink=""

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


</model> </syntax>