Registry of Standard Biological Models/Basic Component Models/mRNA: Difference between revisions

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==ID: mRNA molecule==
==mRNA molecule architecture==


{| border="1"
|
*'''Description''': mRNA molecule
*'''Description''': mRNA molecule
*'''Hypothesis''':  
*'''Hypothesis''':  
**mRNA molecules are produced following the binding of a promoter by a polymerase
**mRNA molecules are produced following the binding of a promoter by a polymerase
**mRNA production is continuous
**mRNA production is continuous (no stochastic effect)
**unlimited resources for transcription
**unlimited resources for transcription (excess of polymerases ...)
*'''Inputs''':
*'''Inputs''':
**PoPs-IN
**PoPs-IN
**time
*'''Outputs''':
*'''Outputs''':
**[mRNA]
**[mRNA]
*'''Internal parameters''':
*'''Characteristic parameters''':
**mRNA-degradation-rate
**mRNA-degradation-rate
| align= "center" | [[Image:VBB_mRNA.png|thumb|left|400px|mRNA Brick Architecture]]
|}


==CellML structure (CellML 1.1 spec)==
==CellML structure (CellML 1.1 spec)==
*'''Component''': mRNA-molecule
*'''Component''': mRNA-molecule
*'''Units''':  
*'''Units''':  
**TBD
**Imported from Environment component
*'''Variables''':
*'''Variables''':
**time (public interface = in)
**time (public interface = in)
**PoPsIN (public interface = in )
**PoPsIN (public interface = in )
**mRNADegradationRate (public interface = none / init value = XXX)
**K_{deg} (mRNADegradationRate) (public interface = none / init value = XXX)
**mRNA (public interface = out / init value = 0.)
**mRNA (public interface = out / init value = 0.)
*'''MathML'''
*'''MathML'''
**<amsmath>\frac{dmRNA}{dtime} = PoPsIN - mRNA*mRNADegradationRate </amsmath>
**<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">
 
<!-- LIST OF COMPONENTS -->
 
<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 xmlns="http://www.w3.org/1998/Math/MathML">
 
  <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>
 
 
<!-- END LIST OF COMPONENTS -->
 
 
<!-- LIST OF CONNECTIONS -->
 
 
<!-- END LIST OF CONNECTIONS -->
 
 
<!-- 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 -->
 
</model>
</syntax>




==Comments==
==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.
*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.

Latest revision as of 03:55, 18 January 2008

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{ \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

  • 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.
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