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

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==ID: Activated Promoter==
==Activated Promoter Architecture==


{| border="1"
|
*'''Description''': Promoter activated by an activator molecule
*'''Description''': Promoter activated by an activator molecule
*'''Hypothesis''':  
*'''Hypothesis''':  
**Simple binding of the activator on the promoter (monod-type equation)
**Binding of the activator on the promoter (Hill-function-type equation)
**Continuous transcription rate with an existing maximum rate of transcription
**Continuous transcription rate with an existing maximum rate of transcription
**Transcription rate depends on number of gene copies
**Transcription rate depends on number of gene copies
*'''Inputs''':
*'''Inputs''':
**activator
**nb-gene-copies
**nb-gene-copies
**activator
*'''Outputs''':
*'''Outputs''':
**PoPs
**PoPs_OUT
*'''Internal parameters''':
*'''Internal parameters''':
**max-transcription-rate (per gene copy)
**max-transcription-rate-per-gene
**sensitivity
**dissociation-constant
**Hill-coefficient
| align= "center" | [[Image:VBB_ActivatedPromoter.png|thumb|left|400px|Activated Promoter Brick Architecture]]
|}


==CellML structure (CellML 1.1 spec)==
==CellML structure (CellML 1.1 spec)==
*'''Component''': ConstitutivePromoter
*'''Component''': ActivatedPromoter
*'''Units''':  
*'''Units''':  
**TBD
**Imported from Environment component
*'''Variables''':
*'''Variables''':
**nbGeneCopies (public interface = in / init value = 1.0)
**nbGeneCopies (public interface = in / init value = 1.0)
**maxTranscriptionRate (public interface = none / init value = XXX)
**maxTranscriptionRate (public interface = none / init value = XXX)
**sensitivity (public interface = none / init value = XXX)
**K (dissociation-constant) (public interface = none / init value = XXX)
**n (Hill-coefficient) (public interface = none / init value = XXX)
**activator (public interface = in )
**activator (public interface = in )
**PoPsOUT (public interface = out / init value = 0.)
**PoPsOUT (public interface = out / init value = 0.)
*'''MathML'''
*'''MathML'''
**<amsmath>PoPsOUT = \frac{maxTranscriptionRate*nbGenesCopies*activator}{sensitivity + activator}</amsmath>
**<amsmath>PoPsOUT = \frac{nbGenesCopies*maxTranscriptionRate*[activator]^{n}}{K^{n} + [activator]^{n}}</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/activated_promoter.cml"
      cmeta:id="activated_promoter"
      name="activated_promoter">
 
<!-- LIST OF COMPONENTS -->
 
<component name="activated_promoter">
<variable name="mRNAsynthesisRate"        initial_value=""  public_interface="out"  units="moles_per_second"/>
<variable name="nb_gene"                  initial_value="1"  public_interface="none" units="dimensionless"/>
<variable name="mRNAsynthesisRatePerGene"  initial_value="1"  public_interface="none" units="moles_per_second"/>
<variable name="dissociation_constant"    initial_value="1"  public_interface="none" units="dimensionless"/>
<variable name="hill_coefficient"          initial_value="2"  public_interface="none" units="dimensionless"/>
<variable name="nb_activator"              initial_value=""  public_interface="in"  units="mole"/>
 
<math xmlns="http://www.w3.org/1998/Math/MathML" id="mRNA synthesis rate">
 
  <apply id="mRNAsynthesisRate">
  <eq/>
  <ci>mRNAsynthesisRate</ci>
  <apply>
  <divide/>
  <apply>
  <times/>
  <ci>mRNAsynthesisRatePerGene</ci>
  <ci>nb_gene</ci>
  <apply>
  <power/>
  <ci>nb_activator</ci>
  <ci>hill_coefficient</ci>
  </apply>
  </apply><apply><plus/>
  <apply>
  <power/>
  <ci>dissociation_constant</ci>
  <ci>hill_coefficient</ci>
  </apply>
  <apply>
  <power/>
  <ci>nb_activator</ci>
  <ci>hill_coefficient</ci>
  </apply>
  </apply>
  </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==

Latest revision as of 03:47, 18 January 2008

Activated Promoter Architecture

  • Description: Promoter activated by an activator molecule
  • Hypothesis:
    • Binding of the activator on the promoter (Hill-function-type equation)
    • Continuous transcription rate with an existing maximum rate of transcription
    • Transcription rate depends on number of gene copies
  • Inputs:
    • activator
    • nb-gene-copies
  • Outputs:
    • PoPs_OUT
  • Internal parameters:
    • max-transcription-rate-per-gene
    • dissociation-constant
    • Hill-coefficient
Activated Promoter Brick Architecture

CellML structure (CellML 1.1 spec)

  • Component: ActivatedPromoter
  • Units:
    • Imported from Environment component
  • Variables:
    • nbGeneCopies (public interface = in / init value = 1.0)
    • maxTranscriptionRate (public interface = none / init value = XXX)
    • K (dissociation-constant) (public interface = none / init value = XXX)
    • n (Hill-coefficient) (public interface = none / init value = XXX)
    • activator (public interface = in )
    • PoPsOUT (public interface = out / init value = 0.)
  • MathML
    • <amsmath>PoPsOUT = \frac{nbGenesCopies*maxTranscriptionRate*[activator]^{n}}{K^{n} + [activator]^{n}}</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/activated_promoter.cml" 
      cmeta:id="activated_promoter" 
      name="activated_promoter">

<component name="activated_promoter">

<variable name="mRNAsynthesisRate" initial_value="" public_interface="out" units="moles_per_second"/> <variable name="nb_gene" initial_value="1" public_interface="none" units="dimensionless"/> <variable name="mRNAsynthesisRatePerGene" initial_value="1" public_interface="none" units="moles_per_second"/> <variable name="dissociation_constant" initial_value="1" public_interface="none" units="dimensionless"/> <variable name="hill_coefficient" initial_value="2" public_interface="none" units="dimensionless"/> <variable name="nb_activator" initial_value="" public_interface="in" units="mole"/>


[math]\displaystyle{ \lt apply id="mRNAsynthesisRate"\gt \lt eq/\gt \lt ci\gt mRNAsynthesisRate\lt /ci\gt \lt apply\gt \lt divide/\gt \lt apply\gt \lt times/\gt \lt ci\gt mRNAsynthesisRatePerGene\lt /ci\gt \lt ci\gt nb_gene\lt /ci\gt \lt apply\gt \lt power/\gt \lt ci\gt nb_activator\lt /ci\gt \lt ci\gt hill_coefficient\lt /ci\gt \lt /apply\gt \lt /apply\gt \lt apply\gt \lt plus/\gt \lt apply\gt \lt power/\gt \lt ci\gt dissociation_constant\lt /ci\gt \lt ci\gt hill_coefficient\lt /ci\gt \lt /apply\gt \lt apply\gt \lt power/\gt \lt ci\gt nb_activator\lt /ci\gt \lt ci\gt hill_coefficient\lt /ci\gt \lt /apply\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

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