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.
I recently came across the package `Catalyst.jl` (and I am very impressed with/ excited about it!). I need many samples (in the order of 10^5) from the Gillespie simulation of...
I have a biological model that has a few explicit delays that mean I need to use the DDE functionality of JuliaDiffEq. I checked on the gitter.im and was told...
I still have some old stuff to finish up in Cambridge, but the next step, which I think is relatively low hanging, would be to enable good support for spatial...
From https://discourse.julialang.org/t/read-in-network-does-not-match-hard-coded-network/81997/5 ```julia rx = @reaction k, A+A --> B @parameters k @variables t A(t) B(t) rx2 = Reaction(k, [A,A], [B], [1,1], [1]) rx != rx2 # true ``` We...
Sometimes a user might know a conservation law and have a specific notation they want to use for the constant (along with knowing which species they'd want to eliminate). We...
- [x] conservation laws - [ ] constant and BC species (explore network API interactions) - [x] events - [x] constraints - [x] Showing how to use elimination of conservation...
Hello, I have a system of chemical reactions that describe the thermodynamic equilibrium of a system. It is described as a system of reactions, and each reaction has an equilibrium...
I guess we should at least add SBMLToolkit once it is considered stable and ReactionNetworkImporters. @paulflang what do you think? Any other packages that make sense?
It would be nice if the macro `@reaction_network` could infer the parameters and the chemical species directly from the model without the need to declare the parameters after `end`.
We've had several requests in the past for constant species, and my general advice was if one wanted `A` to be constant don't write `A --> B` but write `A...