The BioBricks Foundation:Standards/Technical/2009 biobrick data exchange workshop: Difference between revisions
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* Working schema for describing standard biological parts | * Working schema for describing standard biological parts | ||
* XML/RDF description of this schema | * UML/XML Schema/RDF description of this schema | ||
* RFC document describing this schema | * RFC document describing this schema | ||
* Common API (draft) to help programmers working with this format | * Common API (draft) to help programmers working with this format | ||
* Extension of this data schema for CAD / reaction modeling tools | * Extension of this data schema for CAD/reaction modeling tools | ||
* Documented and agreeable process by which such a framework might be improved over time | * Documented and agreeable process by which such a framework might be improved over time | ||
Revision as of 19:19, 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
- 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 + Objectives of the Workshop
- 9:15 Existing Landscape (max. 20 min plus discussion):
- Existing DNA sequence standards + their associated tools (database / analysis)
- Existing and relevant ontologies + missing ones to support DNA part description
- Description of the current Minimum Information Required effort
- Relevant technologies: UML, XML, RDF, Web Services, Cloud Services, ...
- 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.
- 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.