A notebook that creates an example of an SBOL2 Component#33
A notebook that creates an example of an SBOL2 Component#33Yehuda-Binik wants to merge 15 commits intomainfrom
Conversation
…a-component_definition
Yehuda-Binik
requested review from
LukasBuecherl,
PrashantVaidyanathan,
cjmyers and
jakebeal
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "Create a plasmid `Sequence` object and add it to the document" |
There was a problem hiding this comment.
I think all the "plasmid" statements here should be "promoter"
| "example_gene_component_definition.addRole(sbol2.SO_GENE)\n", | ||
| "example_gene_component_definition.addRole(sbol2.SO_PROMOTER)\n", | ||
| "doc.addComponentDefinition(example_gene_component_definition)\n", | ||
| "example_gene_component_definition.components.add(promoter_component)" |
There was a problem hiding this comment.
If you put in a CDS and an ordering constraint, then you can also demonstrate how pySBOL2 lets you calculate a sequence for the containing ComponentDefinition, using the ComponentDefinition.compile method.
There was a problem hiding this comment.
I feel that this functionality can be shown off in the sequence_constraint notebook. Since that is where sequence constraints are going to be shown off in full
There was a problem hiding this comment.
That's reasonable if you want to keep this simple.
I would suggest leaving a comment in here that points to that notebook, though.
fixed typos Co-authored-by: Jacob Beal <jakebeal@gmail.com>
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "Now we will add a `role` and a `roleIntegration` to the cds_component" |
There was a problem hiding this comment.
In this part of the notebook, I would like to have an example of a component that has its role property set along with a roleIntegration of OverrideRoles. However, I do not know what example scenario to use to demonstrate this functionality. I was thinking perhaps I could use an activator ComponentDefinition that is actually being used as a repressor. However, I'm not sure if this example makes sense. In addition, there does not seem to be predefined pysbol constants of Activator and Repressor so I think I would have to find the relevant ontology and create my own URI. How would I go about doing this? Is this the path I should be going down? Any assistance would be appreciated.
There was a problem hiding this comment.
The overrideRoles value is very rarely used, and I'm not sure we have many good examples. I don't think that I've ever used it myself.
@cjmyers , do you have a good example here?
2 participants
Addresses #15. Notebook does not include examples for both MapsTo and measures properties, as those should be shown in their respective Notebooks.