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

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==ID: Protein molecule==
==Protein model architecture==


*'''Description''': Protein molecule
{| border="1"
|
*'''Description''': Protein molecule module
*'''Hypothesis''':  
*'''Hypothesis''':  
**Protein molecules are produced following the binding of a mRNA by a ribosome.
**Protein molecules are produced following the binding of a mRNA by a ribosome.
**Protein production is continuous.
**Protein degradation follows an exponential decay law
**unlimited resources for translation.
**unlimited resources for translation (ribosomes, tRNA ...).
*'''Inputs''':
*'''Inputs''':
**protein-synthesis-rate
**time
**RiPS_IN (RIbosomes Per Second INput)
*'''Outputs''':
*'''Outputs''':
**[Protein]
**[Protein] concentration
*'''Internal parameters''':
*'''Characteristic parameters''':
**protein-degradation-rate
**proteinDegradationRate (depends on degradation pathway or growth dilution due to division rate)
| align= "center" | [[Image:VBB_Protein.png|thumb|left|400px|Protein Brick Architecture (to be updated)]]
|}


==CellML structure (CellML 1.1 spec)==
==CellML structure (CellML 1.1 spec)==
*'''Component''': protein-molecule
*'''Component''': protein-molecule
*'''Units''':  
*'''Units''':  
**TBD
**Imported from Environment component
*'''Variables''':
*'''Variables''':
**time (public interface = in)
**time (public interface = in)
**proteinSynthesisRate (public interface = in )
**RiPS_IN (public interface = in )
**proteinDegradationRate (public interface = none / init value = XXX)
**proteinDegradationRate (public interface = none / init value = (depends on the protein))
**protein (public interface = out)
**protein (public interface = out / init value = 0.0 - maybe init value should also be an input parameter-)
*'''MathML'''
*'''MathML'''
**<amsmath>\frac{d[protein]}{dtime} = proteinSynthesisRate - [protein]*proteinDegradationRate </amsmath>
**<math>\frac{d[protein]}{dtime} = RiPS_{IN} - proteinDegradationRate*[protein] </math>


==Examples==
==Examples==
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|other part || other file
|other part || other file
|}
|}
==CellML File==
[http://openwetware.org/index.php?title=Registry_of_Standard_Biological_Models/Basic_Component_Models/Protein/CellML_Code&action=raw 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">
 
<!-- LIST OF COMPONENTS -->
<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 xmlns="http://www.w3.org/1998/Math/MathML">
  <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>
</math>
</component>
<!-- END LIST OF COMPONENTS -->
<!-- LIST OF IMPORTS -->
<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>
<!-- END LIST OF IMPORTS -->
</model>
</syntax>


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

Latest revision as of 04:14, 19 January 2008

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]

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"/>

[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]

</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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