Introduction to SBOL

SBOL is…

An open standard for the representation of in silico biological designs.
SBOL provides a data format composed of genetic vocabulary terms called SBOL Data.
SBOL also provides schematic glyphs to graphically depict genetic designs called SBOL Visual.
SBOL is intended for users and software developers involved in the biology community and scientist working within a wet lab.


Applications

If you want to design genetic constructs and biological systems, you might want to look at the software tools that support SBOL.

SBOL-supporting tools ensures lossless data conversion when moving between tools. SBOL also allows you to describe more complex design information than traditional sequence representation of a genetic circuit.

Wet Lab

If you work in a wet lab, consider storing your genetic part and construct designs in the growing number of repositories that support SBOL to allow other researchers easy access and reuse of your designs in their projects.

Try having a look at the iGEM Registry of Standard Biological Parts, the Joint BioEnergy Institute’s Inventory of Composable Elements (ICE), SynBioHub, Benchling, and the Standard Virtual Parts Repository.





Software Development

If you are a software developer, you should consider adding SBOL support to your software using one of the SBOL libraries. Adding SBOL support to your software allows your tools to interoperate with the growing ecosystem of software tools that support SBOL.

Feature Request

You can propose your feature request to the SBOL data model or to SBOL visual glyphs by submitting an SEP to our Github repositories. Live discussions amongst the SBOL community is going on now! You can view and comment on the discussions by clicking on the open GitHub issues.

Weekly Update

Weekly Update

Apr. 18th, 2018

HARMONY:

Oxford, UK on Jun. 18th – 22nd

[INFORMATION] [REGISTRATION]

HARMONY is an annual hackathon meeting where computational biologists from the COMBINE community come together to discuss their current status on the development of data standards for the biology community.

An attendance survey will be sent out within the next couple of days. We ask that those who plan on attending the SBOL breakout sessions to complete the survey so the editors could get a good idea on who to expect at the meeting, both locally and virtually.

SBOL Workshop @ SEED 2018:

Scottsdale, AZ on Jun. 3rd – 7th

[SBOL WORKSHOP REGISTRATION] [SEED REGISTRATION]

SBOL will be holding a workshop at SEED on June 7th.
At this workshop, we will be having a variety of CAD tools presenting their take on how SBOL is used in their tool. So far, these are the tools that will be demoed at the workshop.

Repositories: SynBioHub and JBEI ICE
Design Tools: Cello, iBioSim, SBOLDesigner, and RBS Calculator
Test Tools: BOOST and TASBE

The SBOL workshop will be open to all SEED attendees.
Registration is required to attend the SBOL workshop.
Registration form is now open and will be FREE for all SEED attendees.
A registristration fee will be applied to non SEED attendees who wish to attend the SBOL workshop.
More information about what to expect at the SBOL workshop can be found here.

Google Summer of Code 2018:

Student applications are now closed!
The SBOL editors would like to wish potential students the best of luck on their final phase of the application process.
We look forward to hearing the names of the accepted students and projects that will be involved in this year’s program.

Listed below are the four SBOL projects that have been proposed for this year’s program.

Click here to have a look at the available SBOL projects.
More information about this program can be found here.
News that are posted about this program can be found here.
A full timeline of this year’s program can be found here.

SBOL Data:

If you are a software developer and would like to support the latest data model in your tool, click on the links shown below to get the latest release and instructions on how to install. If you are encountering bugs while using the new release, let us know and report your issues to our GitHub issue tracker.

C/C++ (libSBOL) : [Installation] [Release] [Bug Report]
Java (libSBOLj) : [Installation] [Release] [Bug Report]
JavaScript (sboljs) : [Installation ] [Release] [Bug Report]
Python (pySBOL) : [Installation] [Release] [Bug Report]

If you are curious to see what is in the SBOL data model 2.2, view the specification here.
For further questions regarding the implementation of these features, contact the Developers.

SBOL Visual:

Does your software tool support SBOL Visual 2.0.0 glyphs?
If so, let us know by e-mailing the SBOL Editors.
We would like to update our SBOL Applications webpage to inform our community on the latest tools that support SBOL Visual 2.0.0 glyphs.

If you support SBOL Visual glyphs in your software tool but have not updated to 2.0 glyphs, please consider doing so.
Unlike SBOL Visual 1.0.0, version 2.0 was expanded to include not only nucleic acid components but also molecular species and functional interactions as well.
To view and download SBOL Visual 2.0 glyphs, click here.
We provide sample visual glyphs supported in PDF, SVG, and PNG.
There is a Quick Introduction to SBOL Visual 2.0 that is provided here.

SBOL 2018 Workshops:

Mark your calendar! Here are a couple of workshops and conferences that we are planning on attending for this year.

SEED: Scottsdale, AZ on Jun. 3rd – 7th

HARMONY: Oxford, UK on Jun. 18th – 22nd

IWBDA: Berkeley, CA on Jul. 31st – Aug. 3rd

COMBINE: Boston, MA on Oct. 8th – 12th

iGEM: Boston, MA on Oct 24th – 28th

Tramy Nguyen
Nic Roehner
Curtis Madsen
Angel Goñi Moreno
Zach Palchick



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