Registry of Standard Biological Models/Basic Component Models/RBS mRNA: Difference between revisions
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**<amsmath> synthesisRate = translationRate*[mRNA] </amsmath> | **<amsmath> synthesisRate = translationRate*[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+mRNA.cml" | |||
cmeta:id="RBS+mRNA" | |||
name="RBS+mRNA"> | |||
<!-- LIST OF COMPONENTS --> | |||
<component name="RBS+mRNA"> | |||
<variable name="mRNAsynthesisRate" initial_value="" public_interface="in" units="moles_per_second"/> | |||
<variable name="nb_mRNA" initial_value="0" public_interface="none" units="mole"/> | |||
<variable name="mRNAdegradationRate" initial_value="1" public_interface="none" units="per_second"/> | |||
<variable name="proteinSynthesisRatePermRNA" initial_value="1" public_interface="none" units="per_second"/> | |||
<variable name="proteinSynthesisRate" initial_value="" public_interface="out" units="moles_per_second"/> | |||
<variable name="time" initial_value="" public_interface="in" units="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> | |||
<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 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 03:53, 18 January 2008
Ribosome Binding Site + mRNA architecture
|
CellML structure (CellML 1.1 spec)
- Component: RBS_mRNA
- Units:
- Imported from Environment component
- Variables:
- time (public interface = in )
- translationRate (public interface = none / init value = XXX)
- K_deg (mRNADegradationRate) (public interface = none / init value = XXX)
- mRNA (public interface = none / init value = XXX)
- synthesisRate (public interface = out )
- MathML
- <amsmath>\frac{d[mRNA]}{d time} = PoPsIN - K_{deg}*[mRNA]</amsmath>
- <amsmath> synthesisRate = translationRate*[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+mRNA.cml" cmeta:id="RBS+mRNA" name="RBS+mRNA">
<component name="RBS+mRNA">
<variable name="mRNAsynthesisRate" initial_value="" public_interface="in" units="moles_per_second"/> <variable name="nb_mRNA" initial_value="0" public_interface="none" units="mole"/> <variable name="mRNAdegradationRate" initial_value="1" public_interface="none" units="per_second"/> <variable name="proteinSynthesisRatePermRNA" initial_value="1" public_interface="none" units="per_second"/> <variable name="proteinSynthesisRate" initial_value="" public_interface="out" units="moles_per_second"/> <variable name="time" initial_value="" public_interface="in" units="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
\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
- trying to unified the interface between the quasi steady state approximation on the mRNA level and its fully dynamic simulation
- I try to encapsulate the mRNA dynamic inside the RBS component so it can deliver a 'synthesis-rate' flow to the downstream protein element. This way it would be the same interface a the Promoter_RBS_Coupled element.
- Don't know if it is possible to define a system of ODEs in the MathML description part of the component ???