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) [[Image: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.


 * 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.