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.
It might be possible to make a `ReactionSystem`s additional arguments when `OptimizationProblems` are created from `OptimizationFunction`s. If so, that might be used to permit symbolic maps and indexing in input...
We should have an option for setting the value of `t` when nonlinear systems are created. Next, e.g `Bifurcationproblem` and `hc_steady_states` could use this functionality to permit the user to...
A tutorial on how to carry out global sensitivity on Catalyst models. I'm a little bit wary of using an infectious disease model as an example (since they are not...
Added a short tutorial on DynamicalSystems.jl It shows: - How to compute Basins of attraction. - Lyapunov exponents. A third purpose is to demonstrate the DynamicalSystems.jl package generally, so that...
Rebased on new master. Adds a tutorial for how to use SciML/Optimization to find a parameter set that optimise a behaviour. Primarily this shows of how SciML/Optimization can be used...
To avoid rebasing hell this is simply a new version of https://github.com/SciML/Catalyst.jl/pull/663. You might have some input on simpler ways to compute the (non-spatial) mass action Jumps @isaacsas, but otherwise,...
Basically, we have a couple of standard models that we use recurringly throughout tutorials. I expanded the basic model examples doc page (also renaming it to "Library of Basic Chemical...
It seems like the only thing we are missing for compositional modeling to work smoothly is a notion of connections between systems, which here would really just mean aliasing that...
We have just discussed this on Slack. See https://docs.sciml.ai/Catalyst/stable/faqs/#How-to-index-solution-objects-using-symbolic-variables-and-observables?
Are there plans to support symbolic coefficients in stoichiometry matrix construction? For example, I have a birth-death process where $M$ is produced in bursts that are geometrically distributed: ``` @register_symbolic...
