The BioBricks Foundation:Standards/Technical/Exchange: Difference between revisions
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'''Synthetic Biology Data Exchange''' | '''Synthetic Biology Data Exchange''' | ||
This working group | This working group is developing standards and technologies for the description of standard biological parts and the exchange (or networking) of part-related data. | ||
= | |||
= Contact and Participate = | |||
[http://groups.google.com/group/synbiodex Synthetic Biology Data Exchange Group] | |||
= Meetings = | |||
We keep track of our meetings here: http://www.sbolstandard.org/team/meetings | |||
= Synthetic Biology Open Language (SBOL)= | |||
SBOL Website: http://www.sbolstandard.org/ | |||
SBOL is designed to: | |||
*Allow synthetic biologists and genetic engineers to electronically exchange designs. | |||
*Send and receive genetic designs to and from biofabrication centers. | |||
*Facilitate storage of genetic designs in repositories. | |||
*Embed genetic designs in publications. | |||
Read more about SBOL in the [http://www.sbolstandard.org/introduction introduction] | |||
Find the technical details on the [http://www.sbolstandard.org/specification specification page] | |||
= Development History = | |||
== 2010 May - == | |||
* The SBOL project moved to its own website http://www.sbolstandard.org | |||
== 2009 December - 2010 April == | |||
* Galdzicki, M., Rodriguez, C., Chandran, D., Gennari, J.H., and Sauro, H.M. A Semantic Knowledge Base of Standard Biological Parts. [http://cctbio.ece.umn.edu/wiki/index.php/IWBDA:International_Workshop_on_Bio_Design_Automation International Workshop on Bio-Design and Automation 2010], Anaheim, CA [http://cctbio.ece.umn.edu/wiki/images/3/38/IWBDA_Booklet8.pdf pg 30] | |||
== 2009 August - November == | |||
We have divided the working group into sub-topics, each with their own "Nurturer". | We have divided the working group into sub-topics, each with their own "Nurturer". | ||
* [[The_BioBricks_Foundation:Standards/Technical/Exchange/Application_Scenarios| Application Scenarios]] -- [[User:Deepak_Chandran|Deepak Chandran]] | * [[The_BioBricks_Foundation:Standards/Technical/Exchange/Application_Scenarios| Application Scenarios]] -- [[User:Deepak_Chandran|Deepak Chandran]] | ||
* Synthetic Biology Open Language (SBOL) | * '''Synthetic Biology Open Language''' (SBOL) | ||
** [[Core Data Model]] -- [[User:Raik|Raik Gruenberg]] | ** [[The_BioBricks_Foundation:Standards/Technical/Exchange/Core Data Model| Core Data Model]] -- [[User:Raik|Raik Gruenberg]] | ||
** [[SBOL_Script | SBOL Script]] -- [[User:Douglas_Densmore|Doug Densmore]] | ** [[The_BioBricks_Foundation:Standards/Technical/Exchange/SBOL_Script | SBOL Script]] -- [[User:Douglas_Densmore|Doug Densmore]] | ||
** [[Endy:Notebook/ | ***[http://www.sourceforge.net/projects/eugene Eugene (1st pass at a human readable script)] | ||
***[http://www.sourceforge.net/projects/clothocad Spectacles (visualization environment using SBOL Visual symbols)] | |||
** [[Endy:Notebook/Synthetic_Biology_Open_Language | SBOL Visual]] - [[User:Cesar_A._Rodriguez|Cesar Rodriguez]] and [[User:Suzanne_Bartram | Suzie Bartram]] | |||
** [[SBOL_Semantic | SBOL Semantic]] -- [[User:Michal_Galdzicki | Michal Galdzicki]] | ** [[SBOL_Semantic | SBOL Semantic]] -- [[User:Michal_Galdzicki | Michal Galdzicki]] | ||
* [[Data Exchange API]] (programming interfaces) -- ''Become a Nurturer!'' | * [[The_BioBricks_Foundation:Standards/Technical/Exchange/Data Exchange API | Data exchange API]] (programming interfaces) -- ''Become a Nurturer!'' | ||
''Further Suggestions:'' | ''Further Suggestions:'' | ||
* [[Part Sequence Annotation]] -- Tim? | * [[Part Sequence Annotation]] -- Tim? | ||
= | == 2009 June - July == | ||
* July 27, 2009 Galdzicki, M., Chandran, D., Sauro, H.M, Cook, D., and Gennari, J. [http://cctbio.ece.umn.edu/iwbda/slides/Chandran_Galdzicki_Nielsen_Bridging_Synthetic_Biology_Design_and_Experiments_using_PoBoL.pptx Bridging Synthetic Biology Models and Experiments using PoBoL.] [http://cctbio.ece.umn.edu/iwbda-2009/ International Workshop on Bio-Design and Automation 2009], San Francisco, CA | |||
* July 26, 2009 [[The_BioBricks_Foundation:Standards/Technical/2009 biobrick data exchange workshop | Synthetic Biology Data Exchange Working Group Meeting]] Stanford, CA 2009 | |||
* | == 2008 Feb - 2009 May == | ||
* [[The_BioBricks_Foundation:Standards/Technical/PoBoL | PoBol: Provisional BioBrick™ Language]] | |||
** Final RFC document submited "Provisional BioBrick™ Language (PoBoL)" [http://hdl.handle.net/1721.1/45537 BBF RFC 31] (2009-05-15) | |||
* Draft of an RDF-based framework for the exchange and integration of Synthetic Biology data. [http://hdl.handle.net/1721.1/45143 BBF RFC 30] (2009-04-24) | |||
* April 26, 2008 [http://www.sbolstandard.org/team/meetings/workshop_book_042208.pdf Standards and Specifications in Synthetic Biology Workshop] Seattle, WA 2008 | |||
The document describing the the first round of discussions (February - April) can be found here: | |||
* [[The BioBricks Foundation:Standards/Technical/Exchange/Old Discussion|Old Discussion]] | |||
Latest revision as of 15:56, 19 March 2012
Synthetic Biology Data Exchange
This working group is developing standards and technologies for the description of standard biological parts and the exchange (or networking) of part-related data.
Contact and Participate
Synthetic Biology Data Exchange Group
Meetings
We keep track of our meetings here: http://www.sbolstandard.org/team/meetings
Synthetic Biology Open Language (SBOL)
SBOL Website: http://www.sbolstandard.org/
SBOL is designed to:
- Allow synthetic biologists and genetic engineers to electronically exchange designs.
- Send and receive genetic designs to and from biofabrication centers.
- Facilitate storage of genetic designs in repositories.
- Embed genetic designs in publications.
Read more about SBOL in the introduction
Find the technical details on the specification page
Development History
2010 May -
- The SBOL project moved to its own website http://www.sbolstandard.org
2009 December - 2010 April
- Galdzicki, M., Rodriguez, C., Chandran, D., Gennari, J.H., and Sauro, H.M. A Semantic Knowledge Base of Standard Biological Parts. International Workshop on Bio-Design and Automation 2010, Anaheim, CA pg 30
2009 August - November
We have divided the working group into sub-topics, each with their own "Nurturer".
- Application Scenarios -- Deepak Chandran
- Synthetic Biology Open Language (SBOL)
- Data exchange API (programming interfaces) -- Become a Nurturer!
Further Suggestions:
- Part Sequence Annotation -- Tim?
2009 June - July
- July 27, 2009 Galdzicki, M., Chandran, D., Sauro, H.M, Cook, D., and Gennari, J. Bridging Synthetic Biology Models and Experiments using PoBoL. International Workshop on Bio-Design and Automation 2009, San Francisco, CA
- July 26, 2009 Synthetic Biology Data Exchange Working Group Meeting Stanford, CA 2009
2008 Feb - 2009 May
- PoBol: Provisional BioBrick™ Language
- Final RFC document submited "Provisional BioBrick™ Language (PoBoL)" BBF RFC 31 (2009-05-15)
- Draft of an RDF-based framework for the exchange and integration of Synthetic Biology data. BBF RFC 30 (2009-04-24)
- April 26, 2008 Standards and Specifications in Synthetic Biology Workshop Seattle, WA 2008
The document describing the the first round of discussions (February - April) can be found here:
