Registry of Standard Biological Models/Basic Component Models/mRNA

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mRNA molecule architecture

  • Description: mRNA molecule
  • Hypothesis:
    • mRNA molecules are produced following the binding of a promoter by a polymerase
    • mRNA production is continuous (no stochastic effect)
    • unlimited resources for transcription (excess of polymerases ...)
  • Inputs:
    • PoPs-IN
    • time
  • Outputs:
    • [mRNA]
  • Characteristic parameters:
    • mRNA-degradation-rate
mRNA Brick Architecture


CellML structure (CellML 1.1 spec)

  • Component: mRNA-molecule
  • Units:
    • Imported from Environment component
  • Variables:
    • time (public interface = in)
    • PoPsIN (public interface = in )
    • K_{deg} (mRNADegradationRate) (public interface = none / init value = XXX)
    • mRNA (public interface = out / init value = 0.)
  • MathML
    • <amsmath>\frac{d[mRNA]}{dtime} = PoPsIN - K_{deg}*[mRNA] </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/mRNA.cml"
      cmeta:id="mRNA"
      name="mRNA">
 

<component name="mRNA">

     <variable name="mRNAdegradationRate" initial_value="1"     public_interface="none" units="per_second"/>
     <variable name="nb_mRNA"             initial_value="0"     public_interface="out"  units="mole"/>
     <variable name="mRNAsynthesisRate"   initial_value="none"  public_interface="in"   units="moles_per_second"/>
     <variable name="time"                initial_value="none"  public_interface="in"   units="second"/>

[math] \lt apply id="rate of change of mRNA"\gt \lt eq/\gt \lt apply\gt \lt diff/\gt \lt bvar\gt \lt ci\gt time\lt /ci\gt \lt /bvar\gt \lt ci\gt nb_mRNA\lt /ci\gt \lt /apply\gt \lt apply\gt \lt minus/\gt \lt ci\gt mRNAsynthesisRate\lt /ci\gt \lt apply\gt \lt times/\gt \lt ci\gt mRNAdegradationRate\lt /ci\gt \lt ci\gt nb_mRNA\lt /ci\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>


Comments

  • I feel uneasy with this component design as it is not a 'real' biobrick. I would like to encapsulate it into a higher level component, related to the coded protein.