Registry of Standard Biological Models/Basic Component Models

Here is a list of basic components available in the DNA Registry, each link intends to illustrate different modeling approaches and CellML descriptions:

• Building blocks:
  • Constitutive Promoter
  • Activated Promoter
  • Repressed Promoter
  • Ribosome binding site (RBS)
  • Promoter_RBS_Coupled
  • Activated_Promoter_RBS_Coupled
  • Repressed_Promoter_RBS_Coupled
  • mRNA
  • Protein

• attempt to fuse RBS and mRNA concepts together. it could show a more universal interface, equivalent to the promoter_RBS_coupled
  • RBS_mRNA

• Gene expression modeling (using the IMPORT of the previously defined building blocks):
  • mRNA and protein full dynamic modeling
    • Constitutive_mRNA_Protein_Expression_Dynamic -> ConstitutivePromoter + mRNA + RBS + Protein
    • Activated_mRNA_Protein_Expression_Dynamic -> ActivatedPromoter + mRNA + RBS + Protein
    • Repressed_mRNA_Protein_Expression_Dynamic -> RepressedPromoter + mRNA + RBS + Protein
  • Protein dynamic modeling using quasi steady state approx on mRNA
    • Constitutive_mRNA_Protein_Expression_Dynamic -> ConstitutivePromoter_RBS_Coupled + Protein
    • Activated_mRNA_Protein_Expression_Dynamic -> ActivatedPromoter_RBS_Coupled + Protein
    • Repressed_mRNA_Protein_Expression_Dynamic -> RepressedPromoter_RBS_Coupled + Protein

• Inverter

• Oscillator