Friday, August 26, 2016

SBOL at IWBDA 2016

At the start of this year’s International Workshop on Bio-Design Automation, we ran a workshop to teach people about SBOL, the Synthetic Biology Open Language.  As you may remember from previous things that I have written, SBOL is a way of describing biological designs: beyond the “marked up DNA” model supported by older standards like GenBank, SBOL supports the needs of engineering by allowing descriptions of how subsystems are stitched together into a design, as well as the behavior of these components as they interact.  In short, it’s a good rendezvous point for tying together all of the different aspects of a biological design.

Unlike some of the education events we’ve done in the past, this one was focused on developers rather than users.  So after a brief introduction, we got deep down into the weeds of the data model and the code libraries.  There were several dozen people there, mostly from across the UK and Europe, and by the end of the afternoon folks had generally managed to get the libraries and demonstration projects effectively running on their machines and start putting together some complex representations with code.  Some will be even probably be able to bring this back effectively to their universities and companies and start making use of it in their own projects.  All told then, a nice success, and building on this success, we’re hoping to run it in more places, as well as to supply the materials to anybody else who wants to run tutorials.

Challenge problem from the SBOL tutorial: representing a CRISPR repressor system.

SBOL also got some nice mentions in the main track of the workshop: in addition to some “core SBOL” talks, I was very pleased to see it mentioned in a large number of the other talks from the whole community, either as something they’d already taken advantage of in their work, or else something they were aiming to integrate with in the near future.

Standardization is not simple, easy or glamorous.  Bit by bit, however, we are laying the groundwork for a nicely integrated world of biological engineering tools.
Post a Comment