Like the propagation delay and threshold value parameters in electronic circuits, does SBOL format support any such parameters/glyph to represent the propagation delay (time to trigger the output protein once the input is provided) and threshold value (minimum input concentration required to trigger the model’s output) of genetic models?
If currently not supported, can these parameters be incorporated in the SBOL visual representation which would give reader an idea (just by looking at the schematic diagram) about the timing behavior of a model?
Note: I will use SBOL3 in my descriptions; the answer can be equivalently translated to SBOL2
At present, SBOL doesn't have any explicit recommendations for how to represent these types of timing parameters. This is because there is not yet a clear scientific consensus on whether or not such parameters are a good way to represent genetic circuits.
That said, one of the advantages of using SBOL is that its extensible RDF-based model allows additional information like this to be added into a model. Two good ways of doing so are:
Measureobject with appropriate units and type. For example, if you have biological devices with a 90 minute propagation delay, then on the
Componentrepresenting the device you can add a
Measurewith numerical value 90, units of
om:minute. You'd likely want two types, one of
SBO:0000225 (Delay), and a custom type for your own notion of propagation delay, since I don't think that's included in any ontology yet.
This becomes more complicated if you want to talk about behavior in different environmental contexts, but the basic principles are still the same.
Finally, as for SBOL visual: again, there's no explicit representation, but the model is extensible, and this information can be added as any sort of text or custom glyph as long as it doesn't conflict with ones already in the standard.
Correct answer by jakebeal on May 9, 2021
2 Asked on August 21, 2021
1 Asked on August 21, 2021 by najeha-mohamed
1 Asked on August 21, 2021 by mariam
2 Asked on August 21, 2021 by felipe-almeida
1 Asked on August 21, 2021 by ace8910
1 Asked on August 19, 2021
4 Asked on August 19, 2021 by jameshfisher
2 Asked on August 19, 2021 by clove444
1 Asked on August 19, 2021 by ophelia-vallee
2 Asked on August 19, 2021
0 Asked on August 18, 2021 by sasam
0 Asked on August 17, 2021 by unicorn
1 Asked on August 15, 2021
1 Asked on August 13, 2021
Get help from others!