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SBMLImporter.jl

SBMLImporter is a Julia package for importing dynamic Systems Biology Markup Language (SBML) models into either a JumpProblem for Gillespie simulations, a SDEProblem for chemical Langevin simulations, or an ODEProblem for deterministic simulations.

Major highlights

  • Imports an SBML models into a Catalyst.jl ReactionSystem. This allows for easy conversion to a JumpProblem, a SDEProblem, or an ODEProblem.
  • Support for a majority of SBML features, such as dynamic compartments, events, rules, piecewise (ifelse) expressions, and units. An extensive feature list can be found here.
  • Thoroughly tested against both the SBML test suite and a large collection of published models.
  • Integrates with PEtab.jl for fitting SBML models to data.
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Installation

SBMLImporter.jl is an officially registered Julia package, tested and supported on Linux, macOS and Windows. The easiest way to install it is via the Julia package manager. In the Julia REPL, enter:

julia> ] add SBMLImporter

or alternatively

julia> using Pkg; Pkg.add("SBMLImporter")

SBMLImporter is compatible with Julia 1.10 and above. For best performance, we strongly recommend using the latest Julia version, which can be most reliably installed using juliaup.

If you encounter installation issues, please consult the troubleshooting guide.

Getting help

If you have any problems using SBMLImporter, here are some helpful tips:

  • Read the FAQ section in the online documentation.
  • Post your questions in the #sciml-sysbio channel on the Julia Slack.
  • If you have encountered unexpected behavior or a bug, please open an issue on GitHub.