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sybila / biodivine-lib-param-bn

Rust library for working with parametrised Boolean networks.
MIT License
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Error message when loading "normal" SBML #19

Closed daemontus closed 2 years ago

daemontus commented 3 years ago

When opening a "normal" SBML model, the error is "not found list of qualitative species". Ideally, we should warn that the model is not SBML-qual, just SBML.

Another option would be to opportunistically import a regulatory graph from the original SBML model. We might want to consider this in the future.

daemontus commented 2 years ago

For now, this is fixed in c94317aafde141f89afa94245b2bb9245a3f532a by adding a more helpful error message.

Automatic parsing of non-qual SBML models is currently out of scope (there are other tools that can do the conversion to a BN though: maybe integrate these?)

xtrojak commented 2 years ago

Maybe CASQ is related work for you, although it works for CellDesigner files (which something even more general than SBML).

daemontus commented 2 years ago

Yes, also this. But for that, users can probably run the tool separately, at least for now nobody is going to re-implement that into this library.