A notebook that creates an example of an SBOL2 Generic Location

[PrashantVaidyanathan]

This addresses #26

[jakebeal]

I think this isn't very informative yet, because it isn't concrete enough to really show the value of the representation.
How about instead having this show a Cre-Lox recombination applied to activate a not-yet-selected coding sequence by un-reversing it?

That would be a little more complicated, but I think a lot more compelling. The total representation would be:

• Two Component objects, for the Cre-Lox sites
• One SequenceAnnotation for the unknown CDS
• One Range (first recombination site) and two GenericLocation (CDS and second site)
• Two SequenceConstraint objects.

[PrashantVaidyanathan]

@jakebeal - I agree with your comment there and I like the idea.
I have mixed feelings about including this example just for Generic Location because this has a lot more SBOL classes in it.

How about we have a simpler notebook that just shows Generic Location. But we can also add another notebook showing a Cre-Lox recombination? I've added another notebook (outside the CreatingSBOL2Objects folder).

Happy to hear your thoughts.

[PrashantVaidyanathan]

We can also add a note pointing users to the Cre-Lox example (or perhaps a ReadMe in the sbol2 folder)

[jakebeal]

I think there's no point in using GenericLocation without this level of complexity.

I would thus suggest that instead of making a low-content GenericLocation, that we have this notebook's documentation point to the notebooks for SequenceConstraint, SequenceAnnotation, etc. as prerequisites

[PrashantVaidyanathan]

I've modified the Generic Location notebook to reflect your comments. I've also added a link to the Cre-Lox notebook while providing users with a simpler code snippet to understand how to create a Generic Location.

[jakebeal]

Some of my comments are "nice to haves", but I think it's important to avoid duplicating the loxP component and not add a sequence to the unknown CDS.

[PrashantVaidyanathan]

Some of my comments are "nice to haves", but I think it's important to avoid duplicating the loxP component and not add a sequence to the unknown CDS.

@jakebeal - I've addressed these comments in the latest commit. If you are happy with the changes, please feel free to merge this PR.