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paulflang authored Dec 13, 2023
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SBMLToolkit.jl is a lightweight tool to import models specified in the Systems Biology Markup Language (SBML) into the Julia SciML ecosystem. There are multiple ways to specify the same model in SBML. Please help us improving SBMLToolkit.jl by creating a GitHub issue if you experience errors when converting your SBML model.

SBMLToolkit uses the [SBML.jl](https://github.com/LCSB-BioCore/SBML.jl) wrapper of the [libSBML](https://model.caltech.edu/software/libsbml/) library to lower dynamical SBML models into dynamical systems. If you would like to import BioNetGen models use the `writeSBML()` export function or import the `.net` file with [ReactionNetworkImporters.jl](https://github.com/SciML/ReactionNetworkImporters.jl). For constrained-based modeling, please have a look at [COBREXA.jl](https://github.com/LCSB-BioCore/COBREXA.jl).
SBMLToolkit uses the [SBML.jl](https://github.com/LCSB-BioCore/SBML.jl) wrapper of the [libSBML](https://model.caltech.edu/software/libsbml/) library to lower dynamical SBML models into dynamical systems. If you would like to import BioNetGen models use the `writeSBML()` export function or import the `.net` file with [ReactionNetworkImporters.jl](https://github.com/SciML/ReactionNetworkImporters.jl). For constrained-based modeling, please have a look at [COBREXA.jl](https://github.com/LCSB-BioCore/COBREXA.jl). We also recommend trying [SBMLImporter.jl](https://github.com/sebapersson/SBMLImporter.jl) (Pros: respects directionality of events, outputs concentrations instead of amounts. Cons: imports ODESystems, i.e. does not interface with Catalyst).

## Installation

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