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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

To install SBMLImporter.jl in the Julia REPL enter

julia> ] add SBMLImporter

or alternatively

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

SBMLImporter is compatible with Julia version 1.10 and above. For best performance we strongly recommend using the latest Julia version.

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 believe you have encountered unexpected behavior or a bug, please open an issue on GitHub.