Registry of Standard Biological Models/Registry organization: Difference between revisions

Revision as of 14:29, 10 November 2006

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.

**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

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.

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).
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.

@@ Line 62: / Line 62: @@
 ===DNA Registry --> Model 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:
+*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 (Constituve Promoter, Activated Promoter, RBS, Coding Region, Composite ...)
+**Part type (Constitutive Promoter, Activated Promoter, RBS, Coding Region, Composite ...)
-**ID of the part used on the DNA Registry
+**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???).
-*It is not possible to create a new basic model(e.g. promoter, RBS, enzyme, ...) on the Model Registry without having its DNA counterpart on the DNA registry.
+*Models can be only added to the model registry if that category of parts exists in the parts registry.
 ===Model Registry --> DNA Registry===