I have a library of biological implementations (i.e. plasmids) of genetic circuits and their experimental data associated. I want to implement an in silico version with SBOL, but to be consistent with what I have I'm my freezer, I need to identify not only the genetic circuit but also the biological replicate (i.e. the different colonies picked), as they have their own associated experimental data.


Support for distinguishing replicates was added in SBOL 2.2, along with other support for linking data throughout the experiment cycle. I will explain this in terms of SBOL 3, which is simpler, then give the SBOL 2 translation at the end.

For SBOL 3, all designs, including those for a plasmid, a strain, etc, are specified in terms of the Component class. This is just a "paper" design, however, and may or may not actually exist. When you have a real physical aliquot that you want to talk about, this is represented by an Implementation object: this is your biological replicate.

The Implementation doesn't really have any content of its own; its nature is defined by linking back to the intended design with a prov:wasDerivedFrom link. If you've verified that what you got is what you intended, you can supplement that with a built link as well.

One additional note, however: when you're representing a colony, you're probably not actually representing just a plasmid, but rather are representing a particular strain that has been transformed by a plasmid. The actual data you have may then be one level further removed, since the data has been gathered from a sample under particular growth conditions. SBOL can represent that as well, by describing the sample as a mixture of particular media, inducers, etc., with a transformed strain, which is itself a cell type containing your plasmid.

Here is an example diagram showing just this sort of relationship, of data associated with three replicates of a sample.

SBOL representation of three replicates of a sample

You can find this example in the SBOL3 tutorial from COMBINE 2020.

Finally, in SBOL 2, this works exactly the same way, except that instead of a Component your implementation points to a ComponentDefinition or a ModuleDefinition, depending on the nature of the design you're representing. I won't go into that distinction, because it was a bad idea and there's a reason we got rid of it for SBOL 3.

  • $\begingroup$ Indeed, as @jakebeal says, the "colony" is a strain transformed with a plasmid, and then this Implementation can be used in experiments with different media and inducers. $\endgroup$ – Alejandro Vignoni Mar 16 at 21:17
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    $\begingroup$ Exactly, @AlejandroVignoni: you can end up with trees of replicate derivation. I personally value that quite a bit, because the "flat" notion of "biological replicate" vs "technical replicate" often ends up obscuring these relationships. $\endgroup$ – jakebeal Mar 16 at 21:18

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