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

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===Day 1===
===Day 1===


* 9:00 Welcome + Objectives of the workshop
* 9:00 Welcome + Objectives of the workshop
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** The [http://www.mibbi.org/index.php/Main_Page Minimum Information Required] effort
** The [http://www.mibbi.org/index.php/Main_Page Minimum Information Required] effort
** Relevant technologies: RDF, web frameworks, ...
** Relevant technologies: RDF, web frameworks, ...
* 9:45 Status of BioBrick exchange
* 9:45 Status of BioBrick exchange
** Update on [http://pobol.org PoBoL] (10 min + 10 min discussion)
** Update on [http://pobol.org PoBoL] (10 min + 10 min discussion)
** Update on ? (10 min + 10 min discussion)
** Update on ? (10 min + 10 min discussion)
* 10:30 ''Coffee break''
* 10:30 ''Coffee break''
* 10:45 Brainstorming I (two sessions in parallel?)
* 10:45 Brainstorming I (two sessions in parallel?)
** BioBrick schema for experimentalists (BioBrick, BioBrick relations)
** BioBrick schema for experimentalists (BioBrick, BioBrick relations)
** Data requirements for CAD/modelling tools
** Data requirements for CAD/modelling tools
** --other topic--
* 12:00 Report & Discussion on Brainstorming I
* 12:00 Report & Discussion on Brainstorming I
* 12:30 ''Lunch''
* 12:30 ''Lunch''
* 14:00 Brainstorming II:
* 14:00 Brainstorming II:
** BioBrick schema (BioBrick Devices, Versioning)
** BioBrick schema (BioBrick Devices, Versioning)
** CAD/modelling  
** CAD/modelling  
* Reporting on brainstorming sessions
* Reporting on brainstorming sessions
* ''Coffee break''
* ''Coffee break''
* BioBrick data exchange architecture
* BioBrick data exchange architecture
* ''Dinner''
* ''Dinner''

Revision as of 13:18, 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)
  • 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
  • Reporting on brainstorming sessions
  • Coffee break
  • BioBrick data exchange architecture
  • Dinner

Day 2

  • Work in 2 separate groups:
    • Documentation working group (RFCs):
      • Finish Information Required for a BioBrick
      • 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
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