posted Mar 21, 2013, 10:26 AM by Ernst Oberortner
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updated Mar 21, 2013, 10:31 AM
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The SBOL community will held their 9th workshop from Apr 24th - 26th, 2012 at Newcastle University, Newcastle, UK. Further information is provided here.
If you are planning attending the Workshop, then please register here |
posted Feb 22, 2013, 9:26 AM by Ernst Oberortner
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updated Mar 21, 2013, 11:52 AM
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There is a possibility that one or more journals in the future will consider accepting SBOL files as part of manuscript submissions. In order to highlight authors who do submit SBOL information, it has been suggested that such papers be given some form of recognition through the use of SBOL compliance badges. It has been proposed to design two badges initially, these include:
1. “SBOL Standard” compliant which would mean that the design is available in SBOL format in a public repository.
2. "SBOL Visual" compliant which would mean that designs in the paper are depicted using SBOL Visual.
We would like to issue a competition to anyone who might wish to come up with the design for two badges that would correspond to the above categories. A $50 Amazon online gift card will be awarded to the winner, plus a free copy of the book "Enzyme Kinetics for Systems Biologists", 2nd Edition. Runner ups will be awarded honorable mentions.
Submission of the compliance badges should preferably be in a vector format such as eps, AI, PDF or SVG. Competitors can submit badges in png format if this is unavoidable. An example of a set of icons but from a different domain, can be seen here
The deadline for submitting the icons will be the 2nd April, 2013. The winner will be decided by an SBOL community vote by the end of April 2013. Anyone is welcome to submit icons for the prize!
Submission:
Please send your stickers to the SBOL Editors. |
posted Oct 4, 2012, 6:02 AM by Mandy Wilson
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updated Nov 16, 2012, 10:39 AM by Ernst Oberortner
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posted Jun 7, 2012, 6:30 AM by Ernst Oberortner
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updated Jun 13, 2012, 11:59 AM
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Location: Marriott Courtyard Hotel, San Francisco, CADate: June 5th, 2012
The major outcomes are: - Discussion on the relationship between SBOL and SBML for the SBOL Modeling extension- Tendency to a "centralized" development team for libSBOL- The brainstorming sessions emphasized the need for maintaining and then stimulating more industry involvement
Attendees: JC Anderson (University of California, Berkeley) Allan Kuchinsky (Agilent Technologies) Darren Platt (Amyris Biotechnologies) Swapnil Bhatia (Boston University) Joanna Chen (Joint BioEnergy Institute) Douglas Densmore (Boston University) Cassie Huang (Boston University) Ernst Oberortner (Boston University) Cesar Rodriguez (Genome Compiler) Raik Grünberg (University of Montreal) Anil Wipat (Newcastle University) Matthew Pocock (Newcastle University) Nicholas Roehner (University of Utah) Michal Galdzicki (University of Washington) Jennifer Hallinan (Newcastle University) Nathan J. Hillson (Joint BioEnergy Institute) Florencio Mazzoldi (Autodesk) Sunny Park (Newcastle University) Almer van der Sloot (University of Montreal)
Remote Attendees:
Mandy Wilson (Virginia Bioinformatics Institute) Aaron Adler (BBN) Jacob Beal (BBN) Jeffrey Johnson (University of Washington) Chris Myers (University of Utah) Umesh P. (University of Kerala) Hector Plahar (Joint BioEnergy Institute)
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posted Jan 14, 2012, 8:12 PM by Michal Galdzicki
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updated Feb 22, 2012, 12:30 PM by Ernst Oberortner
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January 5-6, 2012
University of Washington
Seattle, WA
Outcomes of the 6th SBOL Workshop, Seattle 2012
- Demonstrated successful exchange of SBOL v1.0.0 data using libSBOLxml
- Received feedback on use of SBOL visual
- Needed is a statement of values of SBOL community
- Recommended a single serialization
- Nominated 2 additional SBOL editors, for 5 editors total
- Elected Herbert Sauro as chair of SBOL
- Recommended to establish extension working groups
- Established centralized test case management
Deadlines agreed to:
- Specification revisions due Friday 1/27/2012
- Java library and XSD due in 1 month
- Call for SBOL v1.1.0 ratification vote - Mon 1/30/2012 following release of final pdf on 1/27/12
Thirty-three SBOL developers met at the University of Washington, Seattle to discuss the development of SBOL extensions. The workshop was attended by U.S. and U.K. academic researchers as well as industry representatives.
| Allan Kuchinsky (Agilent Technologies) |
Cesar Rodriguez (Genome Compiler) |
Chris Myers (University of Utah) |
| Darren Platt (Amyris Biotechnologies) |
Jackie Quinn (Harvard University) |
Nicholas Roehner (University of Utah) |
| Carlos Olguin (Autodesk) |
Guy-Bart Stan (Imperial College London) |
Daniel Cook (University of Washington) |
| Jake Beal (BBN Technologies) |
Richard Kitney (Imperial College London) |
Deepak Chandran (University of Washington) |
| Marc Juul Christoffersen (BIOFAB) |
Raik Grünberg (University of Montreal) |
Jeff Johnson (University of Washington) |
| Cassie Huang (Boston University) |
Yizhi (Patrick) Cai (Johns Hopkins) |
John Gennari (University of Washington) |
| Doug Densmore (Boston University) |
Sridhar Ranganathan (Life Technologies) |
Kyung Kim (University of Washington) |
| Ernst Oberortner (Boston University) |
Anil Wipat (Newcastle University) |
Wilbert Copeland (University of Washington) |
| Swapnil Bhatia (Boston University) |
Goksel Misirli (Newcastle University) |
Michal Galdzicki (University of Washington) |
| Evren Sirin (Clark & Parsia) |
Matthew Pocock (Newcastle University) |
Herbert Sauro (University of Washington) |
| Alan Villalobos (DNA2.0) |
Drew Endy (Stanford University & BIOFAB) |
Mandy Wilson (Virginia Bioinformatics Institute) |
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posted Oct 5, 2011, 2:53 PM by Michal Galdzicki
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updated Oct 5, 2011, 2:55 PM
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The draft specification of SBOL 1.0.0 is available for public comment. We define: 1. the vocabulary, a set of preferred terms and 2. the core data model, a common computational representation, to enable the electronic exchange of information describing DNA components used in synthetic biology.
DOI 1721.1/66172
http://dspace.mit.edu/handle/1721.1/66172
Add your comments to the RFC here. Once the draft is finalized in December 2011 we will begin to start considering extensions to SBOL which is where it gets much more exciting. |
posted Jul 20, 2011, 6:29 AM by Herbert Sauro
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updated Jul 20, 2011, 6:53 AM by Michal Galdzicki
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The UK BBSRC recently held a workshop in Newcastle on standards in synthetic biology. Organized by Neil Wipat and Jen Hallinan, details of the workshop were recorded by Allyson Lister and can be found at her blog. |
posted Jun 23, 2011, 5:13 PM by Herbert Sauro
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updated Jul 7, 2011, 4:00 PM by Michal Galdzicki
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8 June, 2011 (San Diego)
We are pleased to announce the appointment of the following individuals as SBOL editors
Michal Galdzicki (UW)
Cesar Rodriguez (BIOFAB)
Mandy Wilson (VBI) |
posted Sep 3, 2010, 6:04 PM by Michal Galdzicki
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updated Oct 17, 2011, 12:42 PM by Michal Galdzicki
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24 February, 2011 (Seattle)
Our initial version of the SBPkb is now online. The knowledgebase of standard biological parts from the Registry of Standard Biological Parts at MIT. See example queries. |
posted Jun 8, 2010, 9:58 AM by Michal Galdzicki
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updated Jun 8, 2010, 10:02 AM by Michal Galdzicki
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Welcome to SBOLstandard.org! We are working towards the definition of open information exchange standards for the synthetic biology community. Our goal is to create the tools necessary to allow data to flow between software applications for synthetic biologists. I look forward to seeing many of you at this years IWBDA in Anaheim, CA mike |
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