Torkel Loman

In the case we go down the separate package routes, maybe it would make more sense to simply have a single package, CatalystExtended, which contains minor and tangential functionality like...

> Keep in mind we don't need separate repos for them. They can all live in sub-folders of a lib folder in Catalyst. So it would all still be in...

No worries @PBrdng . In this case the error was entirely independent of HC (it had to do with how I had written the tests). Part of the discussion is...

I think we had some discussion about compartments and volumes at some point a while ago. I don't remember exactly how it went, but I thin the conclusion was "This...

I thinkl one thing we discussed was how this ties into hierarchical reaction systems. I.e. it would make sense to enforce a single reaction system to be maximally one compartment,...

I have a decent chunk of thoughts on compartments, but am travelling and mostly on my phone. Will write something when I get back home.

So, generally, I think it makes most sense for compartmental models to be separate `ReactionSystem` models, which are then composed together to from the final, full model. Here, to specific...

Yes, that approach should work fine, e.g. ``` @reaction_network begin @compartment nucleus begin @species nuc_prot(t) (p,d), 0 X end @compartment cytosol begin d, X --> 0 end k*nucleus.nuc_prot, nucleus.X -->...

I think you get the same ids/names in Catalyst, but this is a nice way to reference them. I think this is nice since it someone how include the concept...

Some related docs https://docs.sciml.ai/Catalyst/stable/model_creation/compositional_modeling/ https://docs.sciml.ai/Catalyst/stable/model_creation/reactionsystem_content_accessing/#model_accessing_hierarchical