Registry of Standard Biological Models/Registry organization

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
RBS RBS	Riboswitch
mRNA	mRNA
	RBS_mRNA
Coding Protein	Protein
Terminator Terminator	Terminator

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)