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

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):
  • existing DNA sequence standards + their associated tools (database / analysis)
  • Existing and relevant ontologies + missing ones to support DNA part description
  • The Minimum Information Required effort
  • Relevant technologies: RDF, web frameworks, ...

• 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--
    • Vincent 03:22, 1 July 2009 (EDT): Suggestion: Data exchange scenarii:
      • Public Registry <---> Public Registry
      • Public Registry <---> Local Registry
      • Local Registry <---> Local Registry
      • Registry <---> Software tools (CAD, Bioinformatics, Annotations ...)

• 12:00 Report & Discussion on Brainstorming I

• 12:30 Lunch

• 14:00 Brainstorming II
  • BioBrick schema (BioBrick Devices, Versioning)
  • 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
  • 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