Best way to handle (large) chemical reactions


#1

Hi,

I am wondering what is the best way to handle chemical reactions for SSA simulations. For example, given a set of chemical reactions, I want to extract the transition matrix and rate function in order to use Gillespie.jl. One could use the python package of Stochpy or pyxlr8, but I was thinking about a “julian” compact way of doing this.

Thank you for your help / sharing your code,

Best regards


#2

I think you need to say how the chemical reactions are specified.


#3

Well you probably don’t want to use a transition matrix for a large sparse set of reactions. DifferentialEquations does it all using a sparse representation so that should do better on large networks for a small cost on smaller networks.

There is also an undocumented DSL for handling this.

There’s also BioSimulator.jl to consider:

I do plan on wrapping these all onto the DiffEq API if they keep developing. If there’s something else you’re looking for like some file parsing, feel free to suggest in DiffEqBiological.jl. I am unaware of a common format and if we should support it.


#4

Thank you for these links, it is very helpful.