Registry of Standard Biological Models/Basic Component Models/Protein

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Protein model architecture

  • Description: Protein molecule module
  • Hypothesis:
    • Protein molecules are produced following the binding of a mRNA by a ribosome.
    • Protein degradation follows an exponential decay law
    • unlimited resources for translation (ribosomes, tRNA ...).
  • Inputs:
    • time
    • RiPS_IN (RIbosomes Per Second INput)
  • Outputs:
    • [Protein] concentration
  • Characteristic parameters:
    • proteinDegradationRate (depends on degradation pathway or growth dilution due to division rate)
Protein Brick Architecture (to be updated)

CellML structure (CellML 1.1 spec)

  • Component: protein-molecule
  • Units:
    • Imported from Environment component
  • Variables:
    • time (public interface = in)
    • RiPS_IN (public interface = in )
    • proteinDegradationRate (public interface = none / init value = (depends on the protein))
    • protein (public interface = out / init value = 0.0 - maybe init value should also be an input parameter-)
  • MathML
    • [math]\displaystyle{ \frac{d[protein]}{dtime} = RiPS_{IN} - proteinDegradationRate*[protein] }[/math]


BioBricks from Registry CellML file
<bbpart>BBa_E0040</bbpart> ==> GFP protein Media:BBa_E0040_Model.xml
other part other file

CellML File

CellMl Code

<syntax type = 'xml'>

<?xml version="1.0"?>

<model xmlns=""


<component name="Protein">

     <variable name="proteinDegradationRate"     initial_value="0.01"   public_interface="none" units="per_second"/>
     <variable name="proteinConcentration"       initial_value="0"     public_interface="out"  units="mole"/>
     <variable name="RiPS_IN"                    initial_value="none"  public_interface="in"   units="moles_per_second"/>
     <variable name="time"                       initial_value="none"  public_interface="in"   units="second"/>

[math]\displaystyle{ \lt apply id="rate of change of protein"\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 proteinConcentration\lt /ci\gt \lt /apply\gt \lt apply\gt \lt minus/\gt \lt ci\gt RiPS_IN\lt /ci\gt \lt apply\gt \lt times/\gt \lt ci\gt proteinDegradationRate\lt /ci\gt \lt ci\gt proteinConcentration\lt /ci\gt \lt /apply\gt \lt /apply\gt \lt /apply\gt }[/math]


<import xmlns:xlink=""

     <units name="per_second"       units_ref="per_second"/>
     <units name="moles_per_second" units_ref="moles_per_second"/>


</model> </syntax>


  • This component represents a Protein. It is characterized by the degradation rate of the protein.
  • It requires a 'RiPS-IN' input signal, it is provided by a RBS component, or a Promoter+RBS component