Registry of Standard Biological Models/Basic Component Models/mRNA

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]\displaystyle{ <apply id="rate of change of mRNA"> <eq/> <apply> <diff/> <bvar> <ci>time</ci> </bvar> <ci>nb_mRNA</ci> </apply> <apply> <minus/> <ci>mRNAsynthesisRate</ci> <apply> <times/> <ci>mRNAdegradationRate</ci> <ci>nb_mRNA</ci> </apply> </apply> </apply> }[/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.