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.

Confirmed date: 26 of July 2009

Confirmed location: Stanford, Y2E2 Building, Room
300

Objective

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) 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
    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 v1.53Ev1.6)

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.

Updated on Dec 6, 2012 by Michal Galdzicki (Version
7)


Attachments (1)

Galdzicki_PoBoL_Update_26072009.pptx
– on Dec 6,
2012
by Michal Galdzicki
(Version 4)