NIST Synthetic Biology Standards Workshop: March 31

The NIST Synthetic Biology Standards Consortium (SBSC) workshop is coming up on March 31, 2015.  Several members of the SBOL Developers group will be showing a strong presence on the Digital Biological Information panel.  For more information on SBSC visit: http://jimb.stanford.edu/sbsc

SBOL 12 Workshop Report

The 12th SBOL workshop took place as part of HARMONY 2015 on April 20-24, 2015, at  at the Leucorea Wittenberg, part of the Martin Luther University Halle-Wittenberg, Germany.

Here are the outcomes of the meeting:

  1. SBOL 2.0 Specification
    1. Significant work was performed on the specification, no decision TODOs remain.  Goal is to finish writing by SEED.
    2. Ontologies selected, when possible, for those needing them. Identifiers.org  to provide the ontology terms.
    3. No significant changes to data model though some required fields changed to optional, especially those with no clear ontology.  Other minor changes include: Interactions no longer require a participation, displayId was moved to Identified, roles removed from Model. Roles in other entities were made optional.
    4. Discussed the linking of ModuleDefinition entities to corresponding ComponentDefinitions
  2. libSBOLj 2.0 Release
    1. Agreed that beta release will support only compliant URIs.
      1. TopLevel: <prefix>/<type>/<displayId>/<version>
      2. 1st level child: <prefix>/<type>/<parentId>/<displayId>/<version>
      3. NOTE: also decided <version> is optional.
    2. Agreed that validation errors would be reported through exceptions.
    3. Agreed that beta release would have complete docs with simple examples.
    4. Tested libSBOLj in several applications:
      1. Nicholas Roehner – SBOL to SBML converter.
      2. Tramy Nguyen – SBML to SBOL converter.
      3. Newcastle Group – VirtualParts Repository, SBOL Stack, and SynBad
      4. Bryan Der – Cello
      5. Neil Swanston – (Metabolic) SBML to SBOL converter. Integration with genome-scale models.
    5. Beta release planned before SEED.
  3. Publication Plan
    1. Abstract on 2.0 submitted to IWBDA.  Hope to submit to special ACS Synthetic Biology special issue.
    2. SBOLv paper is currently under review.
    3. libSBOLj paper under review at IEEE Life Science Letters
    4. libSBOLc paper under development.
  4. Outreach Plan
    1. Decided to make a new sbol-announce mailing list, make sbol-dev and sbol-visual public lists, and add old SBOL editors to sbol-editors list.
    2. Discussed several improvements to website such as making logos more prominent, better emphasis of international community and industrial supporters. We also need to keep the SBOL tools up to date.
    3. Talked about international advisory board for SBOL
    4. A SEED talk is scheduled to talk about SBOL, the community, and supporting tools
  5. SBOLv and SBGN
    1. Had dedicated session to interaction with SBGN.
    2. Got a better understanding of the SBGN capabilities.
    3. Conveyed our requirements to SBGN.
    4. Matthew Pocock will continue to follow up with them.

 

SBOL at SEED 2015

The latest developments in SBOL were presented to the synthetic biology community at the 2015 Synthetic Biology: Engineering, Evolution & Design (SEED) conference. There was a lot of interest, and as a result we have new members subscribed to the SBOL-dev emailing list.

On behalf of the SBOL community, Jake Beal gave a talk titled “Synthetic Biology Open Language (SBOL): Community-Driven Standard for Communication of Synthetic Biology Designs”. He announced the community adopted, alpha version of the SBOL 2.0 draft specification.

A poster for SBOL Visual was also presented at the conference.

 

COMBINE 2015: The next SBOL Workshop will take place October 12-16, 2015 concurrent with COMBINE 2015 at the University of Utah in Salt Lake City, USA

Registration is now open for COMBINE 2015 which will be held at the University of Utah in Salt Lake City from October 12 to 16:
http://co.mbine.org/events/COMBINE_2015
In addition to the presentations on various COMBINE standards such as SBOL, there will be breakout sessions every afternoon to discuss future directions for SBOL.  Therefore, we would like to have a good representation from our community present.
Please complete the registration as soon as possible and certainly before October 1st, so we have an accurate head count for the catering.  While there is a registration fee of US$250 to cover breaks, lunches, and a banquet, we have received funds from NSF to cover the registration fees for students, postdoctoral researchers, other junior researchers, as well as, participants from underrepresented groups working on systems and synthetic biology standards.  We have also received funds from NSF to provide partial travel support and lodging (based on double occupancy) for US-based students, postdoctoral scholars, and participants from underrepresented groups.  If you are eligible for either of these awards, please fill out the application for these funds before registering.  Funds will be distributed as applications are received until exhausted, so please submit your application as soon as possible.  
 
For those that do not fit in the categories listed above and need help with expenses, we may have some limited funds to support some SBOL participant expenses.  You may fill out the same application, but please note in the Statement of Participation that you want to be considered for these funds instead.
 
I would also like to point out that lodging is available at US$109 per night at the University of Utah Guest House.  Our room block is limited in size, and it expires on September 14th, so please book your rooms as soon as possible.
 
Finally, abstract submission is also now open.  To be considered for a presentation slot, you must submit your abstract before September 1st.
 
Thank you and we look forward to welcoming you to Salt Lake City in October.
 
Chris Myers

Please join us for the SBOL Community Outreach Meeting at IWBDA!

Coming up on August 19th, at the International Workshop on Bio-Design Automation, at the University of Washington campus, Kane Hall 210, in Seattle, WA! If you are a synthetic biologist and not very familiar with the efforts of the SBOL Developers group, this is a great opportunity to learn more about it. The outreach session will include a demo of software tools enabled by SBOL and guided breakout discussions in which we imagine the future of synthetic biology.
If you are already a member of the SBOL Developers group, whether new or veteran, this is a great opportunity to catch up on the latest news and discuss the future of the community.

The schedule is below:
13:30 – 14:00 Introduction to SBOL
14:00 – 15:00 Live demos of SBOL-based tools
15:00 – 15:30 Coffee Break
15:30 – 17:00 Input from the Bench
17:00 – 17:30 Roadmap and integration with other communities and standards

Please join us!

Sincerely,
The SBOL Chair & Editors

SBOL 14 Registration Open

Registration is now open for the 14th SBOL Workshop, which will run March 14-16, 2016 in Boston.  Visit the workshop page for details and registration.