Registry of Standard Biological Models/Basic Component Models/Protein

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< Registry of Standard Biological Models | Basic Component Models
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Contents

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)
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
    • \frac{d[protein]}{dtime} = RiPS_{IN} - proteinDegradationRate*[protein]

Examples

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="http://www.cellml.org/cellml/1.0#"

      xmlns:cmeta="http://www.cellml.org/metadata/1.0#"
      xml:base="file:///C:/CellML_models/protein.cml"
      cmeta:id="protein"
      name="protein">
 

<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"/>

Failed to parse (lexing error): <apply id="rate of change of protein"> <eq/> <apply> <diff/> <bvar> <ci>time</ci> </bvar> <ci>proteinConcentration</ci> </apply> <apply> <minus/> <ci>RiPS_IN</ci> <apply> <times/> <ci>proteinDegradationRate</ci> <ci>proteinConcentration</ci> </apply> </apply> </apply>


</component>



<import xmlns:xlink="http://www.w3.org/1999/xlink"

             xlink:href="http://openwetware.org/index.php?title=Registry_of_Standard_Biological_Models/Basic_Component_Models/Units&action=raw">
     <units name="per_second"       units_ref="per_second"/>
     <units name="moles_per_second" units_ref="moles_per_second"/>

</import>



</model> </syntax>

Comments

  • 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
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