Registry of Standard Biological Models/Basic Component Models/Ribosome binding site (RBS): Difference between revisions

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==ID: Ribosome Binding Site (RBS)==
==ID: Ribosome Binding Site (RBS)==


{| border="1"
|
*'''Description''': RBS promoting translation rate
*'''Description''': RBS promoting translation rate
*'''Hypothesis''':  
*'''Hypothesis''':  
**Continuous and constant translation rate  
**Continuous and constant translation rate  
**Unlimited resource for translation
**Unlimited resource for translation (ribosome, tRNA ...)
*'''Inputs''':
*'''Inputs''':
**none
**[mRNA]
*'''Outputs''':
*'''Outputs''':
**translation-rate
**protein-synthesis-rate
*'''Internal parameters''':
*'''Characteristic parameters''':
**translation-rate
**translation-rate-per-mRNA
| align= "center" | [[Image:VBB_RBS.png|thumb|left|400px|RBS Brick Architecture]]
|}


==CellML structure (CellML 1.1 spec)==
==CellML structure (CellML 1.1 spec)==
*'''Component''': RBS
*'''Component''': RBS
*'''Units''':  
*'''Units''':  
**TBD
**Imported from Environment component
*'''Variables''':
*'''Variables''':
**translationRate (public interface = out / init value = XXX)
**mRNA (public interface= in )
**translationRatePermRNA (public interface = none / init value = XXX)
**protein-synthesis-rate (public interface = out / init value = XXX)


*'''MathML'''
*'''MathML'''
**none
**<amsmath> proteinSynthesisRate =  translationRatePermRNA*[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.cml"
      cmeta:id="RBS"
      name="RBS">
 
<!-- LIST OF COMPONENTS -->
 
<component name="RBS">
 
<variable name="proteinSynthesisRate"        initial_value=""  public_interface="out"  units="moles_per_second"/>
<variable name="nb_mRNA"                    initial_value=""  public_interface="in"  units="mole"/>
<variable name="proteinSynthesisRatePermRNA" initial_value="1"  public_interface="none" units="per_second"/>
<math xmlns="http://www.w3.org/1998/Math/MathML" id="protein synthesis rate">
 
  <apply id="proteinSynthesisRate">
  <eq/>
  <ci>proteinSynthesisRate</ci>
  <apply>
  <times/>
  <ci>proteinSynthesisRatePermRNA</ci>
  <ci>nb_mRNA</ci>
  </apply>
  </apply>
</math>
 
</component>
 
 
<!-- END LIST OF COMPONENTS -->
 
 
 
<!-- LIST OF IMPORTS -->
 
<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>
 
<!-- END LIST OF IMPORTS -->
 
 
<!-- LIST OF CONNECTIONS -->
 
 
<!-- END LIST OF CONNECTIONS -->
 
</model>
</syntax>




==Comments==
==Comments==
*this component is simply a container providing the translation rate of a specific RBS.
*this component provides the synthesis rate of downstream proteins based on [mRNA] and RBS translation rate.
*don't know if it is possible to characterize such a parameter ?
*don't know if it is possible to characterize experimentally the translationRatePermRNA?

Latest revision as of 03:52, 18 January 2008

ID: Ribosome Binding Site (RBS)

  • Description: RBS promoting translation rate
  • Hypothesis:
    • Continuous and constant translation rate
    • Unlimited resource for translation (ribosome, tRNA ...)
  • Inputs:
    • [mRNA]
  • Outputs:
    • protein-synthesis-rate
  • Characteristic parameters:
    • translation-rate-per-mRNA
RBS Brick Architecture

CellML structure (CellML 1.1 spec)

  • Component: RBS
  • Units:
    • Imported from Environment component
  • Variables:
    • mRNA (public interface= in )
    • translationRatePermRNA (public interface = none / init value = XXX)
    • protein-synthesis-rate (public interface = out / init value = XXX)
  • MathML
    • <amsmath> proteinSynthesisRate = translationRatePermRNA*[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.cml"
      cmeta:id="RBS"
      name="RBS">

<component name="RBS">

<variable name="proteinSynthesisRate" initial_value="" public_interface="out" units="moles_per_second"/> <variable name="nb_mRNA" initial_value="" public_interface="in" units="mole"/> <variable name="proteinSynthesisRatePermRNA" initial_value="1" public_interface="none" units="per_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 }[/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

  • this component provides the synthesis rate of downstream proteins based on [mRNA] and RBS translation rate.
  • don't know if it is possible to characterize experimentally the translationRatePermRNA?
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