Registry of Standard Biological Models/Registry organization

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  • 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.


Supported parts

Generic Virtual BioBricks Architecture
Virtual BioBrick Environment



Virutal BioBrick Regulator




Virutal BioBrick Regulator











Coding 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).


  • 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)