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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 1 year ago

TorkelE commented 1 year 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 1 year 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 1 year 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?