Registry of Standard Biological Models/Registry organization

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== Interactions with DNA Registry ==
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== Interactions with the DNA Registry ==
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*A link to the Registry of Models should be provided from any DNA Registry part:The link will point to a 'Special Page' on the Model Registry with a set of information relating to the part described, such as:
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===DNA Registry --> Model Registry===
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*A link to the Registry of Models should be provided from any DNA Registry part.The link will point to a 'Special Page' on the Model Registry with a set of information relating to the part described, such as:
**Part type (Constituve Promoter, Activated Promoter, RBS, Coding Region, Composite ...)
**Part type (Constituve Promoter, Activated Promoter, RBS, Coding Region, Composite ...)
**ID of the part used on the DNA Registry
**ID of the part used on the DNA Registry
**if it is a composite part, the Registry should provide through the link the sequence of the atomic parts (or maybe the subparts???).
**if it is a composite part, the Registry should provide through the link the sequence of the atomic parts (or maybe the subparts???).
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*It is not possible to create a new basic model(e.g. promoter, RBS, enzyme, ...) on the Model Registry without having its DNA counterpart on the DNA registry.
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===Model Registry --> DNA Registry===
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*Could query DNA Registry with a given model to get all the existing DNA parts described by such a model.
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*A new assembly of models (from existing part models) could be used to register a new assembly (composite part) on the DNA Registry.
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*Part models should be used to constrain characterization of parts (maybe an other Registry dedicated to characterization).
== Implementation ==
== Implementation ==

Revision as of 12:45, 10 November 2006

Scope

  • Define features of the future Registry of BioBrick Models:
    • Supported parts and associated models.
    • Supported user actions (edit, browse, search ...)
  • Specify interactions with the existing physical DNA Registry.
  • Detail choices in term of implementation.

Features

Supported parts

Generic Virtual BioBricks Architecture
Virtual BioBrick Environment

Environment

Plasmid

Virutal BioBrick Regulator

Constitutive_Promoter

Activated_Promoter

Repressed_Promoter

Virutal BioBrick Regulator
PromoterRBS

Promoter_RBS_Coupled

Activated_Promoter_RBS_Coupled

Repressed_Promoter_RBS_Coupled

RBS

RBS

Riboswitch

mRNA

mRNA

RBSmRNA

RBS_mRNA

Coding Protein

Protein

Supported user actions

Interactions with the DNA Registry

DNA Registry --> Model Registry

  • A link to the Registry of Models should be provided from any DNA Registry part.The link will point to a 'Special Page' on the Model Registry with a set of information relating to the part described, such as:
    • Part type (Constituve Promoter, Activated Promoter, RBS, Coding Region, Composite ...)
    • ID of the part used on the DNA Registry
    • if it is a composite part, the Registry should provide through the link the sequence of the atomic parts (or maybe the subparts???).
  • It is not possible to create a new basic model(e.g. promoter, RBS, enzyme, ...) on the Model Registry without having its DNA counterpart on the DNA registry.


Model Registry --> DNA Registry

  • Could query DNA Registry with a given model to get all the existing DNA parts described by such a model.
  • A new assembly of models (from existing part models) could be used to register a new assembly (composite part) on the DNA Registry.
  • Part models should be used to constrain characterization of parts (maybe an other Registry dedicated to characterization).

Implementation

  • The registry of BioBrick models will be implemented as a new Registry (run on a different server than the DNA registry).
  • At first, a full integration within the mediaWiki framework will be explored:
    • models will be curated as standard wiki pages.
    • possible need to implement Special Pages or Extensions.
  • interactions with the DNA Registry might require changes on the DNA Registry side.
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