Registry of Standard Biological Models/Registry organization

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(DNA Registry --> Model Registry)
(Implementation)
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== Implementation ==
== Implementation ==
*The registry of BioBrick models will be implemented as a new Registry (run on a different server than the DNA registry).
*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:
+
**A proof of concept version could be demonstrated on OWW.
 +
*At first, full integration within the MediaWiki framework will be explored (i.e. no need for an additional database as used on the parts registry):
**models will be curated as standard wiki pages.
**models will be curated as standard wiki pages.
**possible need to implement Special Pages or Extensions.
**possible need to implement Special Pages or Extensions.
*interactions with the DNA Registry might require changes on the DNA Registry side.
*interactions with the DNA Registry might require changes on the DNA Registry side.

Revision as of 17:30, 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

  • Any supported part (see list above) on the parts registry should have a link to the corresponding page on the model registry. The link will point to a generic 'Special Page' on the Model Registry with a set of information relating to the part described, such as:
    • Part type (Constitutive Promoter, Activated Promoter, RBS, Coding Region, Composite ...)
    • part ID number
    • if it is a composite part, the Registry should provide through the link the sequence of the atomic parts (or maybe the subparts???).
  • Models can be only added to the model registry if that category of parts exists in the parts 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).
    • A proof of concept version could be demonstrated on OWW.
  • At first, full integration within the MediaWiki framework will be explored (i.e. no need for an additional database as used on the parts registry):
    • 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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