Registry of Standard Biological Models/Basic Component Models/Ribosome binding site (RBS): Difference between revisions
(One intermediate revision by the same user not shown) | |||
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*'''Component''': RBS | *'''Component''': RBS | ||
*'''Units''': | *'''Units''': | ||
** | **Imported from Environment component | ||
*'''Variables''': | *'''Variables''': | ||
**mRNA (public interface= in ) | **mRNA (public interface= in ) | ||
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*'''MathML''' | *'''MathML''' | ||
**<amsmath> proteinSynthesisRate = mRNA | **<amsmath> proteinSynthesisRate = translationRatePermRNA*[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.cml" | |||
cmeta:id="RBS" | |||
name="RBS"> | |||
<!-- LIST OF COMPONENTS --> | |||
<component name="RBS"> | |||
<variable name="proteinSynthesisRate" initial_value="" public_interface="out" units="moles_per_second"/> | |||
<variable name="nb_mRNA" initial_value="" public_interface="in" units="mole"/> | |||
<variable name="proteinSynthesisRatePermRNA" initial_value="1" public_interface="none" units="per_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> | |||
</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> | |||
Latest revision as of 03:52, 18 January 2008
ID: Ribosome Binding Site (RBS)
|
CellML structure (CellML 1.1 spec)
- Component: RBS
- Units:
- Imported from Environment component
- Variables:
- mRNA (public interface= in )
- translationRatePermRNA (public interface = none / init value = XXX)
- protein-synthesis-rate (public interface = out / init value = XXX)
- MathML
- <amsmath> proteinSynthesisRate = translationRatePermRNA*[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.cml" cmeta:id="RBS" name="RBS">
<component name="RBS">
<variable name="proteinSynthesisRate" initial_value="" public_interface="out" units="moles_per_second"/> <variable name="nb_mRNA" initial_value="" public_interface="in" units="mole"/> <variable name="proteinSynthesisRatePermRNA" initial_value="1" public_interface="none" units="per_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 }[/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
- this component provides the synthesis rate of downstream proteins based on [mRNA] and RBS translation rate.
- don't know if it is possible to characterize experimentally the translationRatePermRNA?