Catalyst.jl
Catalyst.jl copied to clipboard
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.
- [ ] Linear Noise Approximation (https://tanhevg.github.io/GpABC.jl/latest/overview-lna/, https://arxiv.org/pdf/1509.00612.pdf, https://arxiv.org/pdf/1608.06582.pdf) - [ ] Minimal continuous-time Markov chains (https://www.researchgate.net/publication/317716528_A_Minimal_Continuous-Time_Markov_Pharmacometric_Model) - [ ] Master Equation (as a set of ODEs) - [ ]...
This pull request changes the compat entry for the `ModelingToolkit` package from `8.47` to `8.47, 9` for package docs. This keeps the compat entries for earlier versions. Note: I have...
![github-actions[bot] avatar](https://avatars.githubusercontent.com/in/15368?v=4 "github-actions[bot] avatar"){kind=avatar}
This pull request changes the compat entry for the `ModelingToolkit` package from `8.73` to `8.73, 9`. This keeps the compat entries for earlier versions. Note: I have not tested your...
Changes mentions of "states" to "unknowns". Changes `get_states` (and similar functions) to `get_unknowns` (and similar functions. I have tried to go through the full repo, and ensure that states such...
In v9, MTK creates default time and differential variables. This PRs make Catalyst use these (throughout tests and documentation). I.e. instead of ```julia @variables t D = Differential(t) ``` we...
For MTK v9 all inputs to various systems have to be complete. Which means we must either add `complete(::ReactionSystem)` wherever these are required, or make them complete by default. Since...
A very large number of examples throughout the docs now error due to using `Symbol`s in ways that are no longer supported / work so we are going to have...
This is not complete yet, but I will initiate the PR so that I can summarise what I have lined up for the internal update of the `LatticeReactionStructure`. The idea...
One of the more niche features is the ability to (linearly) scale the noise magnitude in the CEL: https://docs.sciml.ai/Catalyst/stable/catalyst_applications/advanced_simulations/#Scaling-the-noise-magnitude-in-the-chemical-Langevin-equations. The current interface was a bit "clanky". New new interface (as...
New version of: https://github.com/SciML/Catalyst.jl/pull/730 (rebasing was a mess) Enables computation of stability of steady states. Conservation laws should be accounted for. Simple example: ```julia using Catalyst import HomotopyContinuation rs =...