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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.
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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 completed 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/COBREXA/COBREXA.jl). We also recommend trying [SBMLImporter.jl](https://github.com/sebapersson/SBMLImporter.jl). While SBMLToolkit.jl has a slightly cleaner interface, SBMLImporter.jl respects directionality of events, can output concentrations in addition to amounts, and provides better simulation performance for models including time-triggered events and SBML `piecewise` expressions. If you are an experienced SBML user and interested if SBMLToolkit supports certain (SBML test suite)[https://github.com/sbmlteam/sbml-test-suite] cases, you can download the logs from the latest CI run of the [SBMLToolkitTestSuite](https://github.com/SciML/SBMLToolkitTestSuite.jl/actions/workflows/CI.yml).
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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 completed 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/COBREXA/COBREXA.jl). We also recommend trying [SBMLImporter.jl](https://github.com/sebapersson/SBMLImporter.jl). While SBMLToolkit.jl has a slightly cleaner interface, SBMLImporter.jl respects directionality of events, can output concentrations in addition to amounts, and provides better simulation performance for models including time-triggered events and SBML `piecewise` expressions.
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If you are an experienced SBML user and interested if SBMLToolkit supports certain [SBML test suite](https://github.com/sbmlteam/sbml-test-suite) cases, you can download the logs from the latest CI run of the [SBMLToolkitTestSuite](https://github.com/SciML/SBMLToolkitTestSuite.jl/actions/workflows/CI.yml).
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## Installation
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