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 scientists 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 SBOL Enhancement Proposal (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

July 18th, 2018

Governance:

We have some potential candidates that have been nominated to run for SBOL editor and we are waiting for confirmation. For those who would like to nominate a member from the SBOL community or for those who would like to volunteer themselves, please e-mail the SBOL Editors the candidate’s name and their contact information. We will accept nomination until Friday, July 20th and will begin the voting process on Monday, July 23rd.

Information about the role of an SBOL Editor can be found here.

SBOL Data Model v2.2.1 Release:

We have finalized a rough draft for the SBOL data model v2.2.1 specification release. We would like to welcome the community to provide feedback on the specification before making the final release for v2.2.1 on July 31st.

Link to the paper can be found here.
Corrections to the paper should be reported on the GitHub issue tracker here.

SEP for Data Model:

We have some ongoing discussions about proposing features to the SBOL data model. If you are interested about the topics listed below, feel free to add to the discussions before they are moved to a vote. The voting process will determine whether these features will be accepted or rejected for the upcoming SBOL data model specification release.

Data Model 2.3 Feature Request:
SEP 13: Sequence insertion and replacement [INFO] [DISCUSSION] Voting will be released soon!
SEP 21: Experiments and experimental data [INFO] [DISCUSSION]
SEP 26: Adding a link from Location to Sequence [INFO] [DISCUSSION]

Data Model 3.0 Feature Request:
SEP 22: Rename displayId to id [INFO] [DISCUSSION]
SEP 25: Merge ComponentDefinition and ModuleDefinition [INFO] [DISCUSSION]
SEP 27: Adding a type field to Activity class [INFO] [DISCUSSION]

IWBDA:

Berkeley, CA on Jul. 31st – Aug. 3rd
SBOL will be holding a workshop at this year’s IWBDA conference. At this workshop, we will be presenting talks and leading a hands-on session for SBOL developers. If you are interested to see how you can support SBOL, we welcome everyone in the community. A tentative schedule for the SBOL workshop can be found here.

Note that to register for the SBOL workshop, be sure to check the SBOL workshop tick box when registering for the IWBDA workshop. The SBOL workshop tick box will be visible at the checkout stage of the registration process. An e-mail from the IWBDA organizing committee was sent to those who have signed up for the early bird registration to inform them if they are interested on attending the workshop session. If you fall under this category, please check your inbox for the notification.

[INFORMATION] [LATE IWBDA REGISTRATION] After July 18th!

COMBINE:

Boston, MA on Oct. 8th – 12th

Join the SBOL community at COMBINE to hear and discuss about the different data standards and their ongoing efforts.

[INFORMATION]
[ABSTRACT SUBMISSION] Due August 3rd
[TRAVEL SCHOLARSHIP] Due August 3rd

Tramy Nguyen
Nic Roehner
Curtis Madsen
Angel Goñi Moreno
Zach Palchick



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