Tutorial on working with SBOL Data Model

[PiotrZakrzewski]

Based on https://github.com/SynBioDex/SBOL-Notebooks/blob/main/iwbda_2023_examples.ipynb

The intention is to provide a set of concrete examples on how to create and modify different SBOL data structures.

[PiotrZakrzewski]

@jakebeal Could you help me with this draft? Are there any stylistic conventions I should adapt to? What content do you think this tutorial should have at the minimum?

[jakebeal]

If you're willing, it would be great to start by just mapping the whole thing over, as is. The style that you've got is looking good in the test build: https://pysbol3--449.org.readthedocs.build/en/449/sbol_data_model.html

With regards to the Range content that you are contributing, it would be nice to have it be actually executable in combination with the rest of the code in the document. For example, you might use the Range to make a SequenceFeature in e0040 that marks the start codon of its e0040_sequence

Finally: don't worry about the build error that's there right now -- that is a different issue that showed up on the main branch too, due to a chance in pylint standards, and I've just filed issue #450 for dealing with that.

[PiotrZakrzewski]

@jakebeal I pushed the draft of mapping the Jupyter tutorial as-is, without the Range part. Once this is merged I will make another PR just for the Range part.

I will fix some small formatting issues and proof read the draft tomorrow before I remove the Draft label, but feel free to leave some remarks already.

[PiotrZakrzewski]

@jakebeal ready

[tcmitchell]

@PiotrZakrzewski thank you, this looks great to me. @jakebeal will need to review it as well. Thanks very much for the contribution!

[tcmitchell]

@jakebeal it would be nice to have you review the document before merging. If you think it's fine without review please add a comment and I'll go ahead and merge. Thanks!

[jakebeal]

Apologies for the delay in review. I have finally had a chance to go carefully end-to-end. I found a couple of typos, but other than that it looks goof to go!