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

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="http://www.cellml.org/cellml/1.0#"

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

<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]\displaystyle{ \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]

</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>