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)

• 9:15 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 -- XML, RDF
  • Mario: Relevant technologies: DAS
  • ??: Existing and relevant ontologies + missing ones to support DNA part description
  • Cesar: Relevant Technologies: Unified Modeling Language (UML)

• 9:45 Status of BioBrick Exchange
  • Michal: Update on PoBoL (10 min + 10 min discussion)
  • Douglas and Cesar: Update on BioBrick Open Language (BOL) and Standard Biological Part Web Service (10 min + 10 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.

• Cesar 19:57, 13 July 2009 (EDT) : I've been using the DAS API of the Parts Registry. It's XML-based which I like, but sparse in providing part metadata.