ODE, SDE, and Discrete Problem dispatches for `ParsedReactionNetwork`

SciML / ReactionNetworkImporters.jl

Julia Catalyst.jl importers for various reaction network file formats like BioNetGen and stoichiometry matrices

https://docs.sciml.ai/ReactionNetworkImporters/stable/

MIT License

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ODE, SDE, and Discrete Problem dispatches for `ParsedReactionNetwork` #105

Open TorkelE opened 9 months ago

TorkelE commented 9 months ago

Since these contain initial conditions and parameter values, would it make sense to create dispatches to e.g. do

using ReactionNetworkImporters
BCR = loadrxnetwork(BNGNetwork(), "BCR.net")
tspan = (0.0,1000.0)
oprob = ODEProblem(BCR, tspan)

isaacsas commented 9 months ago

The generated ReactionSystem has u0 and p added as defaults via metadata. See the README. You shouldn’t need to pass them in.

TorkelE commented 9 months ago

You mean using

oprob = ODEProblem(rn, Float64[], (0.0, tf), Float64[])

I thought this was slightly different, as I do not give the actual ParsedReactionNetwork, and utilise the default values in its contained ReactionSystem?