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SynBioDex / SBOL-Notebooks

A repository containing Jupyter Notebooks for SBOL
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Create a SBOL 2 example of Component using pySBOL2 #15

Open PrashantVaidyanathan opened 1 month ago

Yehuda-Binik commented 1 month ago

@jakebeal @tcmitchell @cjmyers

Does anyone understand the difference between SequenceAnnotation and sourceLocations? I mean, I have read the documentation multiple times and understand from an abstract point of view the differences, but I just don't get what their different uses are in practice. When would you use one vs another? It seems important to me to include the sourceLocations property in the Component NoteBook, however I am having trouble. In the MarkDown, I want to explain why or why not one would use a sourceLocation. However, I don't quite have an answer to this myself. Any assistance would be greatly appreciated.

jakebeal commented 1 month ago

The key idea is that sourceLocation is used to say when only a portion of a ComponentDefinition is included.

For example, let's say that you've got a plasmid that is the RBS BBa_B0034 in a pSB1C3 backbone. If you do a BioBrick assembly to extract BBa_B0034 and insert it into another plasmid in front of the GFP coding sequence BBa_E0040 to make a composite ComponentDefinition, then you would use sourceLocation to express that the only the BBa_B0034 bit of your original plasmid is what got included in your composite. The SequenceAnnotation, on the other hand, will say where the BBa_B0034 goes in the composite.