The Synthetic Biology Open Language is an open representational standard for encoding biological designs. As this community has been growing, it has been trying to figure out a better way than FAQs to compile ongoing Q&A expert knowledge about how to use the standard for representing designs.
As a long-standing contributor on Academia.SE, it seems to me that Biology.SE might be a good place to start building up such a Q&A compilation, adding tags, etc. We would only want to do so if this community would find it to be on topic.
Examples of questions that might be asked would be:
- How should I represent growth media in SBOL?
- In SBOL, how do you distinguish a circular plasmid from linear DNA?
- How do I represent a sequence deletion in SBOL?
- Do I need to include intermediate gene products like mRNA in order to express a gene regulatory relationship in SBOL?
A slightly fuller example might be:
How should I represent growth media in SBOL?
Our lab is doing an experiment comparing growth in M9 media and LB. M9 is a mixture of several different chemicals, see: cshprotocols.cshlp.org/content/2010/8/pdb.rec12295.short
How do I represent that in SBOL?"
The recommended best practice for representing mixtures (including media) in SBOL 2 is as a ModuleDefinition, with a FunctionalComponent for each ingredient and a Measure specifying the amount of each in the mixture.
I believe that Biology.SE would be a better place for this than StackOverflow because the questions are more about structuring knowledge than about programming. I believe this would be a better place than Bioinformatics because it is more stable and broader in scope.
Bottom line: would Biology.SE be receptive to an influx of SBOL practitioners asking an answering questions about this topic?