Registry of Standard Biological Models/Basic Component Models/RBS mRNA: Difference between revisions
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==ID: Ribosome Binding Site (RBS)== | ==ID: Ribosome Binding Site (RBS)== | ||
*'''Description''': | *'''Description''': RBS_mRNA | ||
*'''Hypothesis''': | *'''Hypothesis''': | ||
**Continuous and constant translation rate | **Continuous and constant transcription and translation rate | ||
**Unlimited resource for translation | **Unlimited resource for transcription and translation | ||
*'''Inputs''': | *'''Inputs''': | ||
**PoPs IN | **PoPs IN | ||
| Line 33: | Line 33: | ||
==Comments== | ==Comments== | ||
*trying to unified the interface between the quasi steady state approximation on the mRNA level and its fully dynamic simulation | *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 ??? | *Don't know if it is possible to define a system of ODEs in the MathML description part of the component ??? | ||
Revision as of 12:32, 7 September 2006
ID: Ribosome Binding Site (RBS)
- Description: RBS_mRNA
- Hypothesis:
- Continuous and constant transcription and translation rate
- Unlimited resource for transcription and translation
- Inputs:
- PoPs IN
- Outputs:
- synthesis-rate
- Internal parameters:
- translation-rate
- mRNA
- mRNA degradation rate
CellML structure (CellML 1.1 spec)
- Component: RBS_mRNA
- Units:
- TBD
- Variables:
- time (public interface = in )
- translationRate (public interface = none / init value = XXX)
- 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 - [mRNA]*mRNADegradationRate </amsmath>
- <amsmath> synthesisRate = [mRNA]*translationRate </amsmath>
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 ???
