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

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** CAD/modelling  
** CAD/modelling  
* 15:00 Report & Discussion on Brainstorming II
* 15:00 Report & Discussion on Brainstorming II
* 15:30 Discussion: Data exchange architecture


* ''Coffee break''
* 16:15 ''Coffee break''


* BioBrick data exchange architecture
* 16:30 I '''Documentation working group'''
* ''Dinner''
** finalize schema for BioBricks, devices & classification
** 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


===Day 2===
* 18:00 '''Final discussion'''
** distribute writing of RFC
** distribute writing of RDF
** distribute writing of paper
** distribute API implementation


* Work in 2 separate groups:
* 19:00 '''Conclusion'''
** Documentation working group (RFCs):
 
*** Finish Information Required for a BioBrick
* 19:30 ''Dinner''
*** Finish Information Required for a Device
*** Draft RDF decription
** Implementation  working group:
*** Tools required to support the adoption of the standard
*** Draft Python/Java/C++ API
*** TinkerCell/BrickIt/Clotho integration
* Reporting on working sessions (everyone)
* Draft and distribute writing of RFCs
* Draft and distribute writing of paper
* Conclusion + what's next

Revision as of 13:43, 30 June 2009

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

Tentative date: 26 and or 25th 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)

Day 1

  • 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
  • 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--
  • 12:00 Report & Discussion on Brainstorming I
  • 12:30 Lunch
  • 14:00 Brainstorming II
    • BioBrick schema (BioBrick Devices, Versioning)
    • CAD/modelling
  • 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
    • 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
    • distribute writing of paper
    • distribute API implementation
  • 19:00 Conclusion
  • 19:30 Dinner
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