Catalyst.jl
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SciML
Chemical reaction network and systems biology interface for scientific machine learning (SciML). High performance, GPU-parallelized, and O(1) solvers in open source software.
Currently I believe we generate CLE models using ODE ratelaws, but in some cases one might actually want to use the underlying propensity functions. We should both document this more...
Now that the DSL supports ODEs we should update the HH model example to build the whole system at once using the DSL.
And note we currently need to have users call `collect(vec_symbolic_variable)` before passing to `ReactionSystem`.
In this function: ```julia function Latexify.infer_output(env, rs::ReactionSystem, args...) env in [:arrows, :chem, :chemical, :arrow] && return chemical_arrows error("The environment $env is not defined.") latex_function = Latexify.get_latex_function(rs, args...) return latex_function end...
This pull request sets the compat entry for the `GLMakie` package to `0.10` for package docs. This keeps the compat entries for earlier versions. Note: I have not tested your...
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Due to: https://github.com/JuliaSymbolics/Symbolics.jl/issues/1314 This is just to track that.
Catalyst exports a lot of stuff currently, and some of it could be moved to sub-modules (or libraries) to clean up and reduce the default exports (network analysis functionality beyond...
There seems to be an issue with format checks from JuliaFormatter not just causing large reformattings suddenly, but also now leading to bugs in the formatted code: https://github.com/domluna/JuliaFormatter.jl/issues/878 Once this...
Once https://github.com/SciML/ModelingToolkit.jl/pull/3114/files is merged, and updated to include rational functions, we should probably remove the Catalyst HomotopyContinuation extension and instead have users go via MTK.
Needs https://github.com/SciML/ModelingToolkit.jl/pull/3123 and an MTK release.