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

Interactions with DNA Registry

• A link to the Registry of Models should be provided from any DNA Registry part:The link will point to a 'Special Page' on the Model Registry with a set of information relating to the part described, such as:
  • Part type (Constituve Promoter, Activated Promoter, RBS, Coding Region, Composite ...)
  • ID of the part used on the DNA Registry
  • if it is a composite part, the Registry should provide through the link the sequence of the atomic parts (or maybe the subparts???).

Implementation

• 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:
  • 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.