Registry of Standard Biological Models/Registry organization

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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

Terminator

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.


To do list

Building a library of generic models:

  • List all type of BioBricks available on the DNA Registry. (work in progress)
  • Define for each type its interface (inputs/outputs) + associated units. (work in progress)
  • Create for each type a generic CellML description + provide detailed derivation/assumptions. (to be done)
  • Define metadata needed for each type. (to be done)

Communication with the DNA Registry:

  • Define info needed from DNA registry (work in progress)

Using MediaWiki script to support a Registry:

  • Check how CellML info can be stored and accessed on a wiki page (to create new models and to assemble models). (to be done)
  • Investigate the construction of a 'Special Page' to access models from Registry. (to be done)
  • Investigate the construction of a 'Special Page' to build new models from existing models-import mechanism in CellML) . (to be done)
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