Registry of Standard Biological Models/Basic Component Models/Constitutive Protein Expression Dynamic
ID: Constitutive mRNA/Protein expression
- Description: Constitutive Protein expression
- Hypothesis:
- central dogma: gene -> mRNA -> protein
- quasi steady state on mRNA expression
- all hypothesis applicable to sub-parts
- Inputs:
- nb-gene-copies
- Outputs:
- [Protein]
- Internal parameters:
- ???
CellML structure (CellML 1.1 spec)
- Component: ConstitutiveProteinExpression
- Units:
- TBD
- Imports:
- Components:
- ConstituvePromoter_RBS_Coupled
- Protein
- Components:
- Variables:
- time (public interface = in)
- nbGeneCopies (public interface = in)
- protein (public interface = out / init value = 0.)
- MathML
- none
Examples
BioBricks from Registry | CellML file |
---|---|
<bbpart>BBa_I7101</bbpart> ==> GFP protein expression from TetR | Media:BBa_I7101_Model.xml |
other part | other file |
CellML Code
<syntax type = 'xml'> <?xml version="1.0"?>
<model xmlns="http://www.cellml.org/cellml/1.1#"
xmlns:cmeta="http://www.cellml.org/metadata/1.0#" xml:base="file:///C:/CellML_models/protein-generator.cml" cmeta:id="protein-generator" name="protein-generator">
<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/...&action=raw"> <component component_ref="Protein" name="Protein"/>
</import>
<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/...&action=raw">
<component component_ref="promoter-RBS_constitutive" name="promoter-RBS_constitutive"/>
</import>
<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/...&action=raw">
<component component_ref="Plasmid" name="Plasmid"/>
</import>
<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/...&action=raw">
<units name="moles_per_second" units_ref="moles_per_second"/> <units name="per_second" units_ref="per_second"/>
</import>
<group>
<relationship_ref name="protein-generator" relationship="encapsulation"/>
<component_ref component="protein-generator"> <component_ref component="promoter-RBS_constitutive"/> <component_ref component="Protein"/> <component_ref component="Plasmid"/> </component_ref>
</group>
<component name="protein-generator">
<variable name="time" public_interface="in" private_interface="out" units="second"/> <variable name="proteinConcentration" public_interface="out" private_interface="in" units="second"/>
</component>
<connection>
<map_components component_1="Plasmid" component_2="promoter-RBS_constitutive"/>
<map_variables variable_1="nbGeneCopiesOut" variable_2="nbGeneCopiesIn"/>
</connection>
<connection> <map_components component_1="promoter-RBS_constitutive" component_2="Protein"/> <map_variables variable_1="RiPSOut" variable_2="RiPSIn"/> </connection>
<connection>
<map_components component_1="Protein" component_2="protein-generator"/> <map_variables variable_1="time" variable_2="time"/>
</connection>
<connection>
<map_components component_1="Protein" component_2="protein-generator"/> <map_variables variable_1="proteinConcentration" variable_2="proteinConcentration"/>
</connection>
</model> </syntax>
Comments
- No too sure how to connect the components together following the import
- Do I have to declare all the variables I need to use from the imported components ?
- How do I 'trigger' the dynamic behaviour of the sub-components ?