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

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Activated Promoter Architecture

  • Description: Promoter activated by an activator molecule
  • Hypothesis:
    • Binding of the activator on the promoter (Hill-function-type equation)
    • Continuous transcription rate with an existing maximum rate of transcription
    • Transcription rate depends on number of gene copies
  • Inputs:
    • activator
    • nb-gene-copies
  • Outputs:
    • PoPs_OUT
  • Internal parameters:
    • max-transcription-rate-per-gene
    • dissociation-constant
    • Hill-coefficient
Activated Promoter Brick Architecture

CellML structure (CellML 1.1 spec)

  • Component: ActivatedPromoter
  • Units:
    • Imported from Environment component
  • Variables:
    • nbGeneCopies (public interface = in / init value = 1.0)
    • maxTranscriptionRate (public interface = none / init value = XXX)
    • K (dissociation-constant) (public interface = none / init value = XXX)
    • n (Hill-coefficient) (public interface = none / init value = XXX)
    • activator (public interface = in )
    • PoPsOUT (public interface = out / init value = 0.)
  • MathML
    • <amsmath>PoPsOUT = \frac{nbGenesCopies*maxTranscriptionRate*[activator]^{n}}{K^{n} + [activator]^{n}}</amsmath>

CellML File

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

<model xmlns=""


<component name="activated_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"/> <variable name="dissociation_constant" initial_value="1" public_interface="none" units="dimensionless"/> <variable name="hill_coefficient" initial_value="2" public_interface="none" units="dimensionless"/> <variable name="nb_activator" initial_value="" public_interface="in" units="mole"/>

[math] \lt apply id="mRNAsynthesisRate"\gt \lt eq/\gt \lt ci\gt mRNAsynthesisRate\lt /ci\gt \lt apply\gt \lt divide/\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 power/\gt \lt ci\gt nb_activator\lt /ci\gt \lt ci\gt hill_coefficient\lt /ci\gt \lt /apply\gt \lt /apply\gt \lt apply\gt \lt plus/\gt \lt apply\gt \lt power/\gt \lt ci\gt dissociation_constant\lt /ci\gt \lt ci\gt hill_coefficient\lt /ci\gt \lt /apply\gt \lt apply\gt \lt power/\gt \lt ci\gt nb_activator\lt /ci\gt \lt ci\gt hill_coefficient\lt /ci\gt \lt /apply\gt \lt /apply\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>