Sam Isaacson

Results 329 comments of Sam Isaacson

Not at the moment, but this is certainly a feature we could think about.

Let's keep this open so this stays on our radar.

To use SSAStepper you need to describe your system as a collection of (constant rate) jumps, not as the derivative function you give the ODEs. It can't take an arbitrary...

I don't think there is any single convention that is always followed, but many ODE models replace `S-1` with `S` in my experience (especially if they are working in units...

Isn't losing the "-1" consistent with the rigorous mean-field limit of the stochastic model? If we assume the stochastic rate law is `k*A*(A-1)/2` which we agree on, the large-population mean-field...

Also, this has been a long weekend and I'm a bit out of it, so if any of that is confusing feel-free to let me know!

It also looks like we use `combinatoric_ratelaws` in an analogous manner for the jump rate laws, allowing users to indicate they don't want the constant factorial terms (perhaps because they...

Let me move this over to Catalyst, and keep it open there. I think generalizing our scalings to handle the three options I mentioned above is worth thinking about longer-term...

Yeah, that's a definite possibility. I feel like I might have seen some package using that kind of triangle logo before though. I'll have to see if I can remember...

Ideally we'd represent the full (possibly infinite) system of equations for the chemical master equation symbolically, but then specialize to a concrete system based on the initial condition or a...