Registry of Standard Biological Models/Basic Component Models/mRNA
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mRNA molecule architecture
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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.