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.
We need to find an actively maintained / developed graph plotting library to switch to though. [GraphMakie.jl](https://github.com/JuliaPlots/GraphMakie.jl) seems active, but that would pull in Makie (unless we split out the...
Specfically in the symbolic interface.
- [ ] Scaling to large reaction networks: handling parallelism and sparsity - [ ] Choosing jump equation simulators - [ ] File I/O and reading in reaction networks -...
Just an idea, could be fun, and shouldn't affect current functionality. Enable stuff like: ```julia @reaction_network begin (k1,k2), X1 -> X2 -> X3 (k1,k2,k3), X Y --> Z (k1,k2,k3,k4), A...
Some API functions will need to get updated for non-integer stoichiometry, or have it documented that they won't work with floats or syms.
https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008952
It'd be nice to isolate the reaction expression parser for use in, e.g., loading reactions from a file. This is simple to do: One can overload `get_reactions` as in `get_reactions(exs::Vector{Expr},...
ODESystems allow you to do ```julia open("mwe.jl", "w") do io write(io, sys) end ``` this fails on ReactionSystems with ```julia ERROR: type Reaction has no field lhs Stacktrace: [1] getproperty...
Hello, I'm very grateful that you've developed such a useful tool, and I'm now trying to build a counter-application that has some problems. In general, the chemical equation needs to...
Is there a way we can store volumes in `ReactionSystem` (i.e. every species is associated with a volume/compartment it resides in)? This would allow us to optionally divide any simulation...
