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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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Error with importing functions from .NET files #92

Open NikosMemmos opened 1 year ago

NikosMemmos commented 1 year ago

Hi all,

I am using BioNetGen to generate my reaction network and define some rate laws, different from the standard ones, as functions in the BioNetGen file. However, while the import works perfectly when I try to solve I receive an error that the function for the rate law is not defined (see attached image). Is there anything wrong with the way I am importing the .NET file?

Thank you for your time!

error_network_importer

isaacsas commented 1 year ago

Can you share the .net file? We don’t fully support custom functions but I can take a look at what is going on.

An alternative is to export the file as SBML and use SBMLToolkit to load it into Catalyst.

NikosMemmos commented 1 year ago

Hi @isaacsas , I hope you are doing well. Is there any update on the issue? I keep facing the same error.

isaacsas commented 1 year ago

Sorry, I haven't had a chance to look into this -- one of the issues is that I am unaware of any official Bionetgen documentation on how a function block works. If you know of any please feel free to link it.

You are also welcome to make a PR adding support for function blocks if you want! You can see the current parser for .net files at:

https://github.com/SciML/ReactionNetworkImporters.jl/blob/master/src/parsing_routines_bngnetworkfiles.jl

Presumably anything handling function blocks would be parsed in a similar way.