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 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)