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

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

Confirmed date: 26 of July 2009

Confirmed location: Stanford, Y2E2 Building, Room 300


We will try to finalize a consensus draft for a protocol that facilitates the exchange of data describing and related to standard biological parts. The aim of the workshop is to produce some or all of the following:

  • Working schema for describing standard biological parts
  • UML/XML Schema/RDF description of this schema
  • RFC document describing this schema
  • Common API (draft) to help programmers working with this format
  • Extension of this data schema for CAD/reaction modeling tools
  • Documented and agreeable process by which such a framework might be improved over time

Emphasis of this workshop is on work!

Agenda (work in progress)

  • 9:00 Welcome
  • 9:01 Introductions (3 words describing yourself)
  • 9:10 High-level goals
  • 9:15 Discuss and revise our agenda
  • 9:30 Get started (note 15' overlap with next part, needs fixing)
  • 9:30 Existing Landscape (max. 20 min plus discussion):
    • Vincent: Existing DNA sequence standards + their associated tools (database / analysis)
    • Vincent: Description of the current Minimum Information Required effort
    • Raik: Relevant technologies -- RDF
    • cancelled -- Mario: DAS
    • Cesar: Relevant Technologies: Unified Modeling Language (UML)
    • ??: Existing and relevant ontologies + missing ones to support DNA part description
  • 10:00 Status of BioBrick Exchange (needs more time?)
    • Michal: Update on PoBoL (10 min + 5 min discussion) File:Galdzicki PoBoL Update 26072009.pptx
    • Raik: RFC 30 -- data exchange architecture (5 + 5 min)
    • Douglas or Cesar: Update on BioBrick Open Language (BOL) (5 min + 5 min discussion)
    • Cesar: Synthetic Biology Data Transfer Process (SB/DTP) and Standard Biological Part Web Service (5 min + 5 min discussion)
    • Discussion: Vision and use cases of SB data exchange, for example:
      • Public or Local Registry A <---> Public or Local Registry B
      • Registry <---> Software tools (CAD, Bioinformatics, Annotations ...)
  • 10:30 Coffee Break
  • 10:45 Brainstorming I (two sessions in parallel? I vote for keeping the sessions serial. - Cesar)
    • BioBrick schema for experimentalists (BioBrick, BioBrick relations)
    • Data requirements for CAD/modelling tools (minimal characterization?)
    • --other topic--
      • 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 ?
        • Raik 11:13, 24 July 2009 (EDT): I think it's pretty clear that existing formats are not sufficient. Sequence is only a small aspect of the BB description.
  • 12:00 Report & Discussion on Brainstorming I
  • 12:30 Lunch
  • 14:00 Brainstorming II
    • BioBrick Schema (BioBrick Devices & Abstraction Hierarchy, 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
    • Prepare transfer into UML, XML Schema and/or RDF
  • 16:30 II Implementation Working Group
    • Tools required to support adoption of the standard
    • Draft API
      • Candidate Languages/Platforms: Python/??, Java/J2SE/J2EE, Objective-C/Cocoa, Ruby/Rails, C#/.NET, C++/STL
    • TinkerCell/BrickIt/Clotho/BioBrick Studio integration
    • Discuss the development of an online Synthetic Biology "Software Applications Marketplace"
      • A one-stop web site for all available Synthetic Biology software applications
  • 18:00 Final Discussion
    • Distribute writing of RFC
    • Distribute writing of schema definition (UML, XML Schema and/or RDF)
    • Distribute writing of paper
    • Distribute API implementation
    • Identify issues and open questions
  • 19:00 Conclusion
  • 19:30 Dinner

Discussion Board

Vincent 16:50, 3 July 2009 (EDT) : Before the SynBio community starts to draft a BioBrick data exchange standard from scratch, it might be interesting to spend some time to evaluate in details existing standards describing DNA sequences.

For example, I feel that there is a strong case to be made for the use of the Distributed Annotation System (DAS, version 1.53):

  • it would support the description of BioBrick dna sequences and their features.
  • it would enable the description of BioBrick assemblies (using a superpart / subpart system)
  • it is a mature standard with a strong community behind it (EBI, Sanger, EMBL, ...), and with open source tools to implement a client/server architecture.
  • it develops toward the integration of information related to protein structure, sequence alignment, molecular integration (see version v1.53E, v1.6)

Does anyone have a previous experience with DAS ? or any opinion on the advantages / challenges of using DAS to represent BioBricks ? I am happy to put together a document to describe how DAS could support data exchange for BioBricks.