Registry of Standard Biological Models/Basic Component Models/RBS mRNA

ID: Ribosome Binding Site (RBS)

Description: RBS_mRNA Hypothesis: Continuous and constant transcription and translation rate Unlimited resource for transcription and translation Inputs: time PoPs IN Outputs: [mRNA] synthesis-rate Characteristic parameters: mRNA degradation rate translation-rate

RBS/mRNA Brick 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>

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 ???