Saturday, December 05, 2015

SBOL Visual

We have just published what I believe is a very important paper, "SBOL Visual: A Graphical Language for Genetic Designs."  You can read it online for free, from PLOS Biology.  This is the culmination of a long and slow process (as most standards work tends to be) of looking at the different ways that people make diagrams explaining genetic designs and trying to boil it all down into a simple common language for communicating.

Diagram languages for communicating designs are practically universal, in any area of human endeavor where we need to talk about making complicated things.  Whether you're building electronic circuits or houses, writing software or maintaining a sewer system, sewing from patterns or folding origami, there are standard ways of drawing diagrams in order to communicate ideas and minimize confusion.  So of course we need them for engineering biological organisms as well, and thus, SBOL Visual.

The basic idea is quite simple, and can be captured in a simple image of genetic constructs organized along a DNA or RNA sequence "backbone":

The current set of icons covers a lot of the constructs that people engineer, though by no means all.  If you've got another thing to put on a diagram, you can use any icon you want, as long as it doesn't conflict with an existing SBOL Visual icon. To let SBOL Visual expand and become more universal, however, there's an open community process for adding more icons, with a number of icons slowly working their way through the process.
Current SBOL visual icons
Finally, although we provide "standard" icons, there is actually a great deal of flexibility in how you can style them, which makes it easy to use these icons in anything from scribbling on a whiteboard to computerized design software to figures in scientific publications.
All of these diagrams follow the SBOL visual standard.
In some ways, this is a very simple thing.  It is, however, extremely important to get these simple thing right, in order to reduce the amount of friction, frustration, and mistakes we make when we work together and communicate about the things we do.  SBOL Visual is an important step in getting that "less wrong" in the engineering of biology, and I'm glad that it's officially become published now as well.
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