Registry of Standard Biological Models/Basic Component Models: Difference between revisions

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Here is a list of basic components available in the DNA Registry, each link intends to illustrate different modeling approaches and CellML descriptions:
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:
{| style="width:90%; height:100px" border="1" align="center"
**[[Registry of Standard Biological Models/Basic_Component_Models/BioBrick Environment|BioBrick Environment]]
|+ '''Generic Virtual BioBricks Architecture'''
** [[Registry of Standard Biological Models/Basic_Component_Models/Constitutive Promoter|Constitutive Promoter]]
|-
** [[Registry of Standard Biological Models/Basic_Component_Models/Activated Promoter|Activated Promoter]]
|[[Image:VBB_Environment_Icon.png|center|30px|Virtual BioBrick Environment]]
** [[Registry of Standard Biological Models/Basic_Component_Models/Repressed Promoter|Repressed Promoter]]
!
** [[Registry of Standard Biological Models/Basic_Component_Models/Ribosome binding site (RBS)|Ribosome binding site (RBS)]]
[[Registry of Standard Biological Models/Basic_Component_Models/BioBrick Environment|Environment]]
** [[Registry of Standard Biological Models/Basic_Component_Models/Promoter_RBS_Coupled |Promoter_RBS_Coupled ]]
!
** [[Registry of Standard Biological Models/Basic_Component_Models/Activated_Promoter_RBS_Coupled |Activated_Promoter_RBS_Coupled ]]
[[Registry of Standard Biological Models/Basic_Component_Models/BioBrick Plasmid|Plasmid]]
** [[Registry of Standard Biological Models/Basic_Component_Models/Repressed_Promoter_RBS_Coupled |Repressed_Promoter_RBS_Coupled ]]
|-
** [[Registry of Standard Biological Models/Basic_Component_Models/mRNA|mRNA]]
|[[Image:VBB_Regulator_Icon.png|center|30px|Virutal BioBrick Regulator]]
** [[Registry of Standard Biological Models/Basic_Component_Models/Protein|Protein]]
!
[[Registry of Standard Biological Models/Basic_Component_Models/Constitutive_Promoter|Constitutive_Promoter]]
!
[[Registry of Standard Biological Models/Basic_Component_Models/Activated_Promoter|Activated_Promoter]]
!
[[Registry of Standard Biological Models/Basic_Component_Models/Repressed Promoter|Repressed_Promoter]]
|-
| |[[Image:VBB_Regulator_Icon.png| center |30px|Virutal BioBrick Regulator]][[Image:VBB_RBS_Icon.png| center |30px|PromoterRBS]]  
!
[[Registry of Standard Biological Models/Basic_Component_Models/Promoter_RBS_Coupled|Promoter_RBS_Coupled]]
!
[[Registry of Standard Biological Models/Basic_Component_Models/Activated_Promoter_RBS_Coupled|Activated_Promoter_RBS_Coupled]]
!
[[Registry of Standard Biological Models/Basic_Component_Models/Repressed_Promoter_RBS_Coupled|Repressed_Promoter_RBS_Coupled]]
|-
|[[Image:VBB_RBS_Icon.png|center|30px|RBS]]
!
[[Registry of Standard Biological Models/Basic_Component_Models/Ribosome_binding_site_(RBS)|RBS]]
|-
|[[Image:VBB_mRNA_Icon.png|center|30px|mRNA]]
!
[[Registry of Standard Biological Models/Basic_Component_Models/mRNA|mRNA]]
|-
|[[Image:VBB_RBS_Icon.png|30px|RBS]][[Image:VBB_mRNA_Icon.png|30px|mRNA]]
!
[[Registry of Standard Biological Models/Basic_Component_Models/RBS_mRNA|RBS_mRNA]]
|-
|[[Image:VBB_CodingProtein_Icon.png|center|30px|Coding Protein]]
!
[[Registry of Standard Biological Models/Basic_Component_Models/Protein|Protein]]
|}


*attempt to fuse RBS and mRNA concepts together. it could show a more universal interface, equivalent to the promoter_RBS_coupled
[[Registry of Standard Biological Models/Model_Catalog| '''Catalog of available models''']]
** [[Registry of Standard Biological Models/Basic_Component_Models/RBS_mRNA|RBS_mRNA]]




*Gene expression modeling (using the IMPORT of the previously defined building blocks):
{| style="width:90%; height:100px" border="1" align="center"
**mRNA and protein full dynamic modeling
|+ '''Generic Virtual BioBricks Assemblies'''
***[[Registry of Standard Biological Models/Basic_Component_Models/Constitutive_mRNA_Protein_Expression_Dynamic|Constitutive_mRNA_Protein_Expression_Dynamic]] -> ConstitutivePromoter + mRNA + RBS + Protein
|-
***[[Registry of Standard Biological Models/Basic_Component_Models/Activated_mRNA_Protein_Expression_Dynamic|Activated_mRNA_Protein_Expression_Dynamic]] -> ActivatedPromoter + mRNA + RBS + Protein
|[[Image:VBB_ProteinGenerator_Icon.png|center|30px|Virutal BioBrick Protein Generator]]
***[[Registry of Standard Biological Models/Basic_Component_Models/Repressed_mRNA_Protein_Expression_Dynamic|Repressed_mRNA_Protein_Expression_Dynamic]] -> RepressedPromoter + mRNA + RBS + Protein
!
**Protein dynamic modeling using quasi steady state approx on mRNA
[[Registry of Standard Biological Models/Basic_Component_Models/Constitutive_mRNA_Protein_Expression_Dynamic|Constitutive_Protein_Generator]]
***[[Registry of Standard Biological Models/Basic_Component_Models/Constitutive_Protein_Expression_Dynamic|Constitutive_Protein_Expression_Dynamic]] -> ConstitutivePromoter_RBS_Coupled + Protein
!
***[[Registry of Standard Biological Models/Basic_Component_Models/Activated_Protein_Expression_Dynamic|Activated_Protein_Expression_Dynamic]] -> ActivatedPromoter_RBS_Coupled + Protein
[[Registry of Standard Biological Models/Basic_Component_Models/Activated_mRNA_Protein_Expression_Dynamic|Activated_Protein_generator]]
***[[Registry of Standard Biological Models/Basic_Component_Models/Repressed_Protein_Expression_Dynamic|Repressed_Protein_Expression_Dynamic]] -> RepressedPromoter_RBS_Coupled + Protein
!
[[Registry of Standard Biological Models/Basic_Component_Models/Repressed_mRNA_Protein_Expression_Dynamic|Repressed_Protein_Generator]]
|-
|[[Image:VBB_ProteinGenerator_Icon.png|30px|Virutal BioBrick Protein Generator, Quasi steady state approx on mRNA]]'''(QSS)'''
!
[[Registry of Standard Biological Models/Basic_Component_Models/Constitutive_Protein_Expression_Dynamic|Constitutive_Protein_Generator]]
!
[[Registry of Standard Biological Models/Basic_Component_Models/Activated_Protein_Expression_Dynamic|Activated_Protein_Generator]]
!
[[Registry of Standard Biological Models/Basic_Component_Models/Repressed_Protein_Expression_Dynamic|Repressed_Protein_Generator]]
|-
| |[[Image:VBB_Inverter_Icon.png|center|30px|Virutal BioBrick Inverter]]
!
[[Registry of Standard Biological Models/Basic_Component_Models/Inverter|Inverter (QSS)]]
|-
|[[Image:VBB_Oscillator_Icon.png|center|30px|Virtual BioBrick Oscillator]]
!
[[Registry of Standard Biological Models/Basic_Component_Models/Oscillator|Oscillator (QSS)]]
|}


*[[Registry of Standard Biological Models/Basic_Component_Models/Inverter|Inverter]]
[[Registry of Standard Biological Models/Model_Catalog| '''Catalog of available models''']]
 
*[[Registry of Standard Biological Models/Basic_Component_Models/Oscillator|Oscillator]]

Latest revision as of 05:21, 15 September 2006

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

Generic Virtual BioBricks Architecture
Virtual BioBrick Environment
Virtual BioBrick Environment

Environment

Plasmid

Virutal BioBrick Regulator
Virutal BioBrick Regulator

Constitutive_Promoter

Activated_Promoter

Repressed_Promoter

Virutal BioBrick Regulator
Virutal BioBrick Regulator
PromoterRBS
PromoterRBS

Promoter_RBS_Coupled

Activated_Promoter_RBS_Coupled

Repressed_Promoter_RBS_Coupled

RBS
RBS

RBS

mRNA
mRNA

mRNA

RBSmRNA

RBS_mRNA

Coding Protein
Coding Protein

Protein

Catalog of available models


Generic Virtual BioBricks Assemblies
Virutal BioBrick Protein Generator
Virutal BioBrick Protein Generator

Constitutive_Protein_Generator

Activated_Protein_generator

Repressed_Protein_Generator

Virutal BioBrick Protein Generator, Quasi steady state approx on mRNA(QSS)

Constitutive_Protein_Generator

Activated_Protein_Generator

Repressed_Protein_Generator

Virutal BioBrick Inverter
Virutal BioBrick Inverter

Inverter (QSS)

Virtual BioBrick Oscillator
Virtual BioBrick Oscillator

Oscillator (QSS)

Catalog of available models

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