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.

SBOL Data

SBOL Enhancement Proposals
https://github.com/SynBioDex/SEPs
10 forks.
2 stars.
32 open issues.
Recent commits:

SBOL Visual

Repository for the SBOL Visual image files.
https://github.com/SynBioDex/SBOL-visual
6 forks.
11 stars.
28 open issues.
Recent commits:

Social Media
Weekly Update

Weekly Update

Posted: October 25, 2017 | 0 comments

July 25th, 2018

SBOL Editor Election:

The SBOL Editor election has officially started. If you are apart of the SBOL community, please help our community elect the next SBOL editor. We have 5 great candidates that are running for the editor position.
Voting will close on Friday, July 27th. The result of the election will be announce in the next weekly update.

SBOL Workshop @ IWBDA:

Berkeley, CA on Jul. 31st – Aug. 3rd
IWBDA is about to start in the next of few days. We have an SBOL workshop prepared for those who are in the area and are curious to attend.
[SBOL Workshop Agenda]

New SEP for SBOL Visual:

We have a new SEP submitted to SBOL visual. If you are curious to read and contribute to the current discussion, follow the links below.
SEP 14: Modules and MapsTo [Info] [Discussion]

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]

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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