Sam Isaacson

- [x] conservation laws - [ ] constant and BC species (explore network API interactions) - [x] events - [x] constraints - [x] Showing how to use elimination of conservation...

Add Downstream tests?

2

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?

events, constant and boundary condition species for SDEs and Jumps

4

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...

Drop Graphviz and requires

5

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.

Update API functions for non-integer stoichiometry

5

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.

Many tests currently assume a certain ordering of species and rates coming from the DSL. We need to update these to use `varmap_to_vars`. This was, for example, causing me issues...

alias elimination

1

Ideally we would have a way to eliminate algebraic coupling constraints so users could define couplings like ``` sys1.A ~ sys2.B ``` and we can then eliminate one of those...

For CME type equations as in https://github.com/SciML/Catalyst.jl/pull/417, it might be worthwhile to look at some of the reachability analysis methods in the literature. One recent example: https://match.pmf.kg.ac.rs/electronic_versions/Match81/n3/match81n3_705-736.pdf

TODO per discussion of 11/25

29

- [x] Eliminate `@reaction_func` and how Hill functions work. (Niklas) - [x] Fix ReactionNetworkImporters. (Sam) - [x] Fix BCR loading and update BCR benchmarks. (Sam) - [x] Work towards previous...