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

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* 9:00 Welcome + Objectives of the workshop
* 9:00 Welcome + Objectives of the workshop
* 9:15 '''Existing landscape''' (max. 20 min plus discussion):
* 9:15 '''Existing landscape''' (max. 20 min plus discussion):
** [http://www.genomatix.de/online_help/help/sequence_formats.html existing DNA sequence standards] + their associated tools (database / analysis)
** [http://www.genomatix.de/online_help/help/sequence_formats.html Existing DNA sequence standards] + their associated tools (database / analysis)
** Existing and relevant ontologies + missing ones to support DNA part description
** Existing and relevant ontologies + missing ones to support DNA part description
** Description of the current [http://www.mibbi.org/index.php/Main_Page Minimum Information Required] effort
** Description of the current [http://www.mibbi.org/index.php/Main_Page Minimum Information Required] effort
** Relevant technologies: XML, RDF, Web Services, Cloud Services, ...
** Relevant technologies: UML, XML, RDF, Web Services, Cloud Services, ...


* 9:45 '''Status of BioBrick exchange'''
* 9:45 '''Status of BioBrick exchange'''

Revision as of 19:04, 18 July 2009

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
  • XML/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 + Objectives of the workshop
  • 9:15 Existing landscape (max. 20 min plus discussion):
  • 9:45 Status of BioBrick exchange
    • Update on PoBoL (10 min + 10 min discussion)
    • 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?)
    • 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 ?
  • 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 RDF
  • 16:30 II Implementation working group
    • Tools required to support adoption of the standard
    • Draft Python/Java/Objective-C/Ruby?/C++ API
    • TinkerCell/BrickIt/Clotho/BioBrick Studio integration
  • 18:00 Final discussion
    • Distribute writing of RFC
    • Distribute writing of schema definition (UML, XSD 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.

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