events, constant and boundary condition species for SDEs and Jumps

[isaacsas]

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 --> A + B or 0 --> B with rate k*A. The problem with the first is that A is treated as a variable internally. SBML includes an explicit "constant" tag for species, so this is something commonly used in models. Along those lines we could

1. Have a way of marking A in a DSL reaction as a constant species. The Antimony DSL would have one write $A --> B to indicate it is constant. If we had something like that in the DSL we could then move it to being a parameter before actually generating the corresponding Reaction.
2. Use the metadata system to indicate a variable is constant. Not making it a parameter internally though would mean a lot of the current codebase would have to have special cases added to handle a constant state appropriately. So I think just modifying the DSL to allow tagging a species as constant would make more sense.

[isaacsas]

I guess where this would get tricky is something like 2A + B --> C with A constant and a rate k. Should this be rewritten to B --> C with rate k*A^2/2 or k*A*(A-1)/2, or something else. This would be dependent on whether the reaction is being interpreted deterministically or stochastically.

Using metadata to tag it as constant would let us keep A around as a species until model conversion, when we could resolve this, but as I mentioned above would complicate some stuff (like network analysis).

[isaacsas]

Also need to consider boundary condition species (which do not get ODEs from reactions, but may have constraint equations or events).

[isaacsas]

Closed by #514

[isaacsas]

Reopening as I realized this won't work beyond ODESystems and NonlinearSystems until if/when events and/or constraints can be supported with SDESystems and/or JumpSystems.

Needed components in MT:

• discrete events, or continuous events for SDEs / mixed systems.
• constraints to make sense for SDEs and/or jumps. (For SDEs probably means being able to extend with nonlinear or ODE systems).

As these are added in MT we can add support for this in Catalyst.

[isaacsas]

We've had these for a while now.