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), the 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

Dec. 6th, 2017

Google Summer of Code 2018:

The editors are collecting SBOL project ideas for GSoC 2018.
If the community have projects that they would like to propose, please contact the SBOL Editors
Here are a list of SBOL project ideas that have been requested so far:

Support SBOL2 in TinkerCell
Support SBOL2 and SBOLv2 in DNAPlotlib
Improving the ICE DNA sequence data model to be compatible with SBOL2

SBOL Data:

Votes are in for SEP 18: Attachment [Info] ACCEPTED!

There are two experimental design SEPs that have been proposed:
SEP 19 : Using SBOL to model the Design-Build-Test Learn Cycle [Info] [Discussion]
SEP 20: Linking experimental results with Biological clones and replicates [Info] [Discussion]

With the recent discussions that have been going on for these two SEPs, the community is ready to bring these two SEPs to a vote.
Voting forms for these two SEPs will be released on Dec. 7th for a two day discussion period.
Nicholas Roehner will be sending out the voting form so stay tune for the announcement.

The SBOL developers for the libSBOLj library are implementing support for experimental data, prov-o, and combinatorial design. If you are interested in these features, you can track the progress here.

SBOL Visual:

We are planning the next release of SBOL Visual 2.0.
Here are all the SBOL Visual SEPs that were accepted for this release.

SEP V001 : Bounding box, interior, backbone alignment, and relative scale [Info]
SEP V002 : Alternative Glyphs [Info]
SEP V003 : Distinguishing Unknown [Info]
SEP V004: Non-Coding RNA Gene Glyph [Info]
SEP V005: Ambiguities and Variants [Info]
SEP V006: No Glyph Assigned [Info]
SEP V007 : Stem-Top Glyphs [Info]
SEP V008 : Functional Component Glyphs [Info]
SEP V009: Engineering Region vs. Composite [Info]
SEP V010 : Arrows [Info]

SBOL 2018 Workshops:

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

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

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

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

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

iGEM: Boston, MA on Oct 24th – 28th

Robert Sidney Cox III
James McLaughlin
Tramy Nguyen
Nic Roehner
Curtis Madsen



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