Registry of Standard Biological Models/Basic Component Models/RBS mRNA

Ribosome Binding Site + mRNA architecture

Description: RBS_mRNA Hypothesis: Continuous and constant transcription and translation rate Unlimited resource for transcription and translation Inputs: time PoPs IN Outputs: [mRNA] synthesis-rate Characteristic parameters: mRNA degradation rate translation-rate

RBS/mRNA Brick Architecture

CellML structure (CellML 1.1 spec)

• Component: RBS_mRNA
• Units:
  • Imported from Environment component
• Variables:
  • time (public interface = in )
  • translationRate (public interface = none / init value = XXX)
  • K_deg (mRNADegradationRate) (public interface = none / init value = XXX)
  • mRNA (public interface = none / init value = XXX)
  • synthesisRate (public interface = out )

• MathML
  • <amsmath>\frac{d[mRNA]}{d time} = PoPsIN - K_{deg}*[mRNA]</amsmath>
  • <amsmath> synthesisRate = translationRate*[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/RBS+mRNA.cml" 
      cmeta:id="RBS+mRNA" 
      name="RBS+mRNA">
 

<component name="RBS+mRNA">

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

[math]\displaystyle{ \lt apply id="proteinSynthesisRate"\gt \lt eq/\gt \lt ci\gt proteinSynthesisRate\lt /ci\gt \lt apply\gt \lt times/\gt \lt ci\gt proteinSynthesisRatePermRNA\lt /ci\gt \lt ci\gt nb_mRNA\lt /ci\gt \lt /apply\gt \lt /apply\gt \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

• trying to unified the interface between the quasi steady state approximation on the mRNA level and its fully dynamic simulation
• I try to encapsulate the mRNA dynamic inside the RBS component so it can deliver a 'synthesis-rate' flow to the downstream protein element. This way it would be the same interface a the Promoter_RBS_Coupled element.
• Don't know if it is possible to define a system of ODEs in the MathML description part of the component ???