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

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Contents

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
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


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"/>


Failed to parse (Missing texvc executable; please see math/README to configure.): <apply id="mRNAsynthesisRate"> <eq/> <ci>mRNAsynthesisRate</ci> <apply> <divide/> <apply> <times/> <ci>mRNAsynthesisRatePerGene</ci> <ci>nb_gene</ci> <apply> <power/> <ci>nb_activator</ci> <ci>hill_coefficient</ci> </apply> </apply><apply><plus/> <apply> <power/> <ci>dissociation_constant</ci> <ci>hill_coefficient</ci> </apply> <apply> <power/> <ci>nb_activator</ci> <ci>hill_coefficient</ci> </apply> </apply> </apply> </apply>


</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>


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