SciMLTutorials.jl
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SciML
DiffEqBiological packages outdated
The tutorials https://tutorials.sciml.ai/html/models/03-diffeqbio_I_introduction.html and following are outdated. They still refer to DiffEqBiological instead of Catalyst. On my system, I started to fix the tutorials and I came across several issues, some of which I could fix. I will try to create a comprehensive list of errors if you are interested in keeping these tutorials. In my opinion this would make sense, because the examples in the Catalyst docs are by far not as detailed.
I just found that for Update Catalyst bifurcation tutorial #370 there is already a pull request which would fix this for https://tutorials.sciml.ai/html/models/04b-diffeqbio_III_steadystates.html
This is what I came up so far: https://github.com/rlars/SciMLTutorials.jl/commit/366b2c4da585e88ef50cb22755d7ce700578a967
These should probably just be removed; the first two tutorials are basically covered in Catalyst doc tutorials, as is a basic example of bifurcations with BifurcationKit. The steady-state calculations via homotopycontinuation are not currently supported in an explicit way, but I think @TorkelE had been looking into it for adding to ModelingToolkit in general.
@rlars what do you feel is missing from the current Catalyst tutorials?
It would be nice if we could easily sync the Catalyst doc tutorials into Weave ones here somehow to allow a Notebook version. @ChrisRackauckas is there any tooling for syncing from there here or vice-versa?
I guess we could convert the Catalyst tutorials to Weave markdown ones here, and then just link to them in the Catalyst docs.
@rlars what do you feel is missing from the current Catalyst tutorials?
Ah, I see, I compared https://catalyst.sciml.ai/dev/tutorials/basic_examples/ to the DiffEqBiological tutorials. If I look at https://catalyst.sciml.ai/dev/tutorials/using_catalyst/, I can find what I missed.