The BioBricks Foundation:Standards/Technical/2009 biobrick data exchange workshop: Difference between revisions

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The workshop is planned as a satellite to the First International Workshop on Bio-Design Automation [http://cctbio.ece.umn.edu/iwbda/index.html IWBDA].
The workshop is planned as a satellite to the First International Workshop on Bio-Design Automation [http://cctbio.ece.umn.edu/iwbda/index.html IWBDA].


Tentative date: 26 of July 2009
'''Tentative date''': 26 of July 2009
 
Tentative location: Stanford


'''Tentative location''': Stanford


==Objective==
==Objective==
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Emphasis of this workshop is on ''work''!
Emphasis of this workshop is on ''work''!


==tentative Agenda (not confirmed)==
==Tentative Agenda (not confirmed)==
 
 


* 9:00 Welcome + Objectives of the workshop
* 9:00 Welcome + Objectives of the workshop
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** [http://www.genomatix.de/online_help/help/sequence_formats.html existing DNA sequence standards] + their associated tools (database / analysis)
** [http://www.genomatix.de/online_help/help/sequence_formats.html existing DNA sequence standards] + their associated tools (database / analysis)
** Existing and relevant ontologies + missing ones to support DNA part description
** Existing and relevant ontologies + missing ones to support DNA part description
** The [http://www.mibbi.org/index.php/Main_Page Minimum Information Required] effort
** Description of the current [http://www.mibbi.org/index.php/Main_Page Minimum Information Required] effort
** Relevant technologies: RDF, web frameworks, ...
** Relevant technologies: RDF, web frameworks, ...


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** Update on ? (10 min + 10 min discussion)
** Update on ? (10 min + 10 min discussion)
** Discussion: Vision and use cases of SB data exchange
** Discussion: Vision and use cases of SB data exchange
*** Public Registry A <---> Public Registry B
*** Public Registry <---> Local Registry
*** Local Registry <---> Local Registry
*** Registry <---> Software tools (CAD, Bioinformatics, Annotations ...)


* ''10:30 Coffee break''
* ''10:30 Coffee break''
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** Data requirements for CAD/modelling tools
** Data requirements for CAD/modelling tools
** --other topic--
** --other topic--
*** '''[[User:Vincent Rouilly|Vincent]] 03:22, 1 July 2009 (EDT)''': Suggestion: Data exchange scenarii:
*** '''[[User:Vincent Rouilly|Vincent]] 05:13, 1 July 2009 (EDT)''': Suggestion: Interface between a BioBrick description and its characterisation data ?
**** Public Registry <---> Public Registry
*** '''[[User:Vincent Rouilly|Vincent]] 05:13, 1 July 2009 (EDT)''': Suggestion: Is there a need for a dedicated BB ontologie to describe certain properties of a BioBrick (BB Standard, Scar, Subparts, ...), or existing ontologies are covering everything we could need ?
**** Public Registry <---> Local Registry
**** Local Registry <---> Local Registry
**** Registry <---> Software tools (CAD, Bioinformatics, Annotations ...)  
 
* 12:00 Report & Discussion on Brainstorming I
* 12:00 Report & Discussion on Brainstorming I


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* 14:00 '''Brainstorming II'''
* 14:00 '''Brainstorming II'''
** BioBrick schema (BioBrick Devices, Versioning)
** BioBrick schema (BioBrick Devices, Versioning)
*** '''[[User:Vincent Rouilly|Vincent]] 05:13, 1 July 2009 (EDT)''': BioBrick Devices: is it about abstraction hierarchy representation ?
** CAD/modelling  
** CAD/modelling  
*** '''[[User:Vincent Rouilly|Vincent]] 03:22, 1 July 2009 (EDT)''': Is it an extension of the first 'CAD' brainstorming session ? Or something different ?
*** '''[[User:Vincent Rouilly|Vincent]] 03:22, 1 July 2009 (EDT)''': Is it an extension of the first 'CAD' brainstorming session ? Or something different ?
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* 16:30 I '''Documentation working group'''
* 16:30 I '''Documentation working group'''
** finalize schema for BioBricks, devices & classification
** finalize schema for BioBricks, devices & classification
*** '''[[User:Vincent Rouilly|Vincent]] 05:13, 1 July 2009 (EDT)''': Are we talking about a 'check-list' document AND its RDF description ? or only a RDF description ?
** draft RFC for BioBrick data exchange standard
** draft RFC for BioBrick data exchange standard
* 16:30 II '''Implementation working group'''
* 16:30 II '''Implementation working group'''

Revision as of 02:13, 1 July 2009

The workshop is planned as a satellite to the First International Workshop on Bio-Design Automation IWBDA.

Tentative date: 26 of July 2009

Tentative location: Stanford

Objective

We will try to finalize a consensus draft for a protocol that facilitates the exchange and publication of BioBrick-related data. The aim would be to end up with:

  • a data schema for the description of BioBricks, Devices and relations
  • a RDF/XML description of this schema
  • an RFC document describing this schema
  • a common API (draft) to help programmers working with this format
  • an extension of this data schema for CAD / reaction modeling tools

Emphasis of this workshop is on work!

Tentative Agenda (not confirmed)

  • 9:00 Welcome + Objectives of the workshop
  • 9:15 Existing landscape (max. 20 min plus discussion):
  • 9:45 Status of BioBrick exchange
    • Update on PoBoL (10 min + 10 min discussion)
    • Update on ? (10 min + 10 min discussion)
    • Discussion: Vision and use cases of SB data exchange
      • Public Registry A <---> Public Registry B
      • Public Registry <---> Local Registry
      • Local Registry <---> Local Registry
      • Registry <---> Software tools (CAD, Bioinformatics, Annotations ...)
  • 10:30 Coffee break
  • 10:45 Brainstorming I (two sessions in parallel?)
    • BioBrick schema for experimentalists (BioBrick, BioBrick relations)
    • Data requirements for CAD/modelling tools
    • --other topic--
      • Vincent 05:13, 1 July 2009 (EDT): Suggestion: Interface between a BioBrick description and its characterisation data ?
      • Vincent 05:13, 1 July 2009 (EDT): Suggestion: Is there a need for a dedicated BB ontologie to describe certain properties of a BioBrick (BB Standard, Scar, Subparts, ...), or existing ontologies are covering everything we could need ?
  • 12:00 Report & Discussion on Brainstorming I
  • 12:30 Lunch
  • 14:00 Brainstorming II
    • BioBrick schema (BioBrick Devices, Versioning)
      • Vincent 05:13, 1 July 2009 (EDT): BioBrick Devices: is it about abstraction hierarchy representation ?
    • CAD/modelling
      • Vincent 03:22, 1 July 2009 (EDT): Is it an extension of the first 'CAD' brainstorming session ? Or something different ?
  • 15:00 Report & Discussion on Brainstorming II
  • 15:30 Discussion: Data exchange architecture
  • 16:15 Coffee break
  • 16:30 I Documentation working group
    • finalize schema for BioBricks, devices & classification
      • Vincent 05:13, 1 July 2009 (EDT): Are we talking about a 'check-list' document AND its RDF description ? or only a RDF description ?
    • draft RFC for BioBrick data exchange standard
  • 16:30 II Implementation working group
    • Tools required to support adoption of the standard
    • Draft Python/Java/C++ API
    • TinkerCell/BrickIt/Clotho integration
  • 18:00 Final discussion
    • distribute writing of RFC
    • distribute writing of RDF and/or other schema definition
    • distribute writing of paper
    • distribute API implementation
  • 19:00 Conclusion
  • 19:30 Dinner
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