Registry of Standard Biological Models/Registry organization - Revision history

Barry Canton: Registry of Standard Biological Models/General Architecture Discussion moved to Registry of Standard Biological Models/Registry organization

2007-09-26T14:46:12Z

Registry of Standard Biological Models/General Architecture Discussion moved to Registry of Standard Biological Models/Registry organization

←Older revision

Revision as of 14:46, 26 September 2007

Vincent Rouilly at 20:13, 11 November 2006

2006-11-11T20:13:30Z

←Older revision		Revision as of 20:13, 11 November 2006
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	!		!
	[[Registry of Standard Biological Models/Basic_Component_Models/Protein\|Protein]]		[[Registry of Standard Biological Models/Basic_Component_Models/Protein\|Protein]]
		+	\|-
		+	\|[[Image:VBB_Terminator_Icon.png\|center\|30px\|Terminator]]
		+	!
		+	[[Registry of Standard Biological Models/Basic_Component_Models/Terminator\|Terminator]]
	\|}		\|}

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	**possible need to implement Special Pages or Extensions.		**possible need to implement Special Pages or Extensions.
	*interactions with the DNA Registry might require changes on the DNA Registry side.		*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. <font color=green> (work in progress)</font>
		+	*Define for each type its interface (inputs/outputs) + associated units. <font color=green> (work in progress)</font>
		+	*Create for each type a generic CellML description + provide detailed derivation/assumptions.<font color=red> (to be done)</font>
		+	*Define metadata needed for each type.<font color=red> (to be done)</font>
		+
		+	'''Communication with the DNA Registry:'''
		+	*Define info needed from DNA registry <font color=green> (work in progress)</font>
		+
		+	'''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). <font color=red> (to be done)</font>
		+	*Investigate the construction of a 'Special Page' to access models from Registry.<font color=red> (to be done)</font>
		+	*Investigate the construction of a 'Special Page' to build new models from existing models-import mechanism in CellML) .<font color=red> (to be done)</font>

Barry Canton: /* Implementation */

2006-11-10T21:30:48Z

Implementation

←Older revision		Revision as of 21:30, 10 November 2006
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	== Implementation ==		== Implementation ==
	*The registry of BioBrick models will be implemented as a new Registry (run on a different server than the DNA registry).		*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:	+	**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.		**models will be curated as standard wiki pages.
	**possible need to implement Special Pages or Extensions.		**possible need to implement Special Pages or Extensions.
	*interactions with the DNA Registry might require changes on the DNA Registry side.		*interactions with the DNA Registry might require changes on the DNA Registry side.

Barry Canton: /* DNA Registry --> Model Registry */

2006-11-10T21:29:42Z

DNA Registry --> Model Registry

←Older revision		Revision as of 21:29, 10 November 2006
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	===DNA Registry --> Model Registry===		===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???).		**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===		===Model Registry --> DNA Registry===

Vincent Rouilly: /* Interactions with DNA Registry */

2006-11-10T16:45:52Z

Interactions with DNA Registry

←Older revision		Revision as of 16:45, 10 November 2006
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-	== Interactions with DNA Registry ==	+	== Interactions with the 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:	+	===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:
	**Part type (Constituve Promoter, Activated Promoter, RBS, Coding Region, Composite ...)		**Part type (Constituve Promoter, Activated Promoter, RBS, Coding Region, Composite ...)
	**ID of the part used on the DNA Registry		**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???).		**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.
		+
		+
		+	===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 ==		== Implementation ==

Vincent Rouilly: /* Interactions with DNA Registry */

2006-11-10T16:18:17Z

Interactions with DNA Registry

←Older revision		Revision as of 16:18, 10 November 2006
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	== Interactions with DNA Registry ==		== 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 ==		== Implementation ==

Vincent Rouilly at 16:03, 10 November 2006

2006-11-10T16:03:21Z

New page

__NOTOC__
==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 ===
{| style="width:90%; height:100px" border="1" align="center"
|+ '''Generic Virtual BioBricks Architecture'''
|-
|[[Image:VBB_Environment_Icon.png|center|30px|Virtual BioBrick Environment]]
!
[[Registry of Standard Biological Models/Basic_Component_Models/BioBrick Environment|Environment]]
!
[[Registry of Standard Biological Models/Basic_Component_Models/BioBrick Plasmid|Plasmid]]
|-
|[[Image:VBB_Regulator_Icon.png|center|30px|Virutal BioBrick Regulator]]
!
[[Registry of Standard Biological Models/Basic_Component_Models/Constitutive_Promoter|Constitutive_Promoter]]
!
[[Registry of Standard Biological Models/Basic_Component_Models/Activated_Promoter|Activated_Promoter]]
!
[[Registry of Standard Biological Models/Basic_Component_Models/Repressed Promoter|Repressed_Promoter]]
|-
| |[[Image:VBB_Regulator_Icon.png| center |30px|Virutal BioBrick Regulator]][[Image:VBB_RBS_Icon.png| center |30px|PromoterRBS]]
!
[[Registry of Standard Biological Models/Basic_Component_Models/Promoter_RBS_Coupled|Promoter_RBS_Coupled]]
!
[[Registry of Standard Biological Models/Basic_Component_Models/Activated_Promoter_RBS_Coupled|Activated_Promoter_RBS_Coupled]]
!
[[Registry of Standard Biological Models/Basic_Component_Models/Repressed_Promoter_RBS_Coupled|Repressed_Promoter_RBS_Coupled]]
|-
|[[Image:VBB_RBS_Icon.png|center|30px|RBS]]
!
[[Registry of Standard Biological Models/Basic_Component_Models/Ribosome_binding_site_(RBS)|RBS]]
|-
|[[Image:VBB_Riboswitch_Icon.png|center|30px|RBS]]
!
[[Registry of Standard Biological Models/Basic_Component_Models/Riboswitch|Riboswitch]]
|-
|[[Image:VBB_mRNA_Icon.png|center|30px|mRNA]]
!
[[Registry of Standard Biological Models/Basic_Component_Models/mRNA|mRNA]]
|-
|[[Image:VBB_RBS_Icon.png|30px|RBS]][[Image:VBB_mRNA_Icon.png|30px|mRNA]]
!
[[Registry of Standard Biological Models/Basic_Component_Models/RBS_mRNA|RBS_mRNA]]
|-
|[[Image:VBB_CodingProtein_Icon.png|center|30px|Coding Protein]]
!
[[Registry of Standard Biological Models/Basic_Component_Models/Protein|Protein]]
|}

=== Supported user actions ===

== Interactions with DNA Registry ==

== 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.