SBOL Editors Weekly Update - Apr. 11th

[Tramy Nguyen]

HARMONY:

Oxford, UK on Jun. 18th - 22nd

INFORMATION   REGISTRATION Closing June 3rd

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. 

SBOL will have breakout sessions at this meeting and are currently collecting topics of interest to plan for HARMONY.

If the community has suggestions on what topics that they would like to be discussed at the meeting, please e-mail the editors (sbol-e...@googlegroups.com) and let us know.

Here is a list of proposed topics that we will be considering:

• Discuss SBOL visual 2.1 for visualizing ModuleDefinitions and Interactions
• Discuss SBOL data model 2.2.1 that will address minor revisions and errors to the spec.
• Discuss best practices for encoding experimental data
• Hold a hacking session to write papers for sboljs, combinatorial designs, and experimental data
• Discuss merging ComponentDefnition and ModuleDefinition classes
• Discussion on what SBOL tools that need to work with SBOL

Please let the SBOL editors know in advance if you would like to attend these breakout sessions remotely so we can have equipments prepared.

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.

• Parametric SVG as a flexible format for Synthetic Biology Open Language Visual (SBOLv) symbols
• Integrating CAD and CAM tools for automating a synthetic biology workflow
• Beautiful rendering of complex genetic designs in Python with DNAplotlib and the Synthetic Biology Open Language (SBOL)
• Add SBOL Import and Export Capabilities to the Synthetic Biology Tool TinkerCell

More information about this program can be found here. 

News from this program are posted here.

A full timeline of this years 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  libsbol-team@googlegroups.com.

SBOL Visual:

Does your software tool support SBOL Visual 2.0.0 glyphs?

If so, let us know by e-mailing the SBOL Editors (sbol-e...@googlegroups.com).

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. 

SBOL Visual 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 also 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