Other SBML related Julia packages

There are currently three additional SBML related packages in Julia. SBML.jl wraps a subset of the libSBML functionality and is used by SBMLImporter and other SBML related packages for parsing SBML models. COBREXA.jl is designed for constraint-based metabolic modeling. Constraint-based models, which are often referred to as flux-balance analysis (FBA) models, are not supported by SBMLImporter., thus for FBA models we recommend COBREXA.

Lastly, SBMLToolkit.jl similarly to SBMLImporter imports dynamic models into a ReactionSystem. However, we recommend SBMLImporter due to the following key differences:

• SBMLToolkit works with (and transforms) species to be in amount. SBMLImporter supports species units to be either amount or concentration.

• SBMLImporter has wider event support, including events with directionality. It further processes events without species in the trigger into a DiscreteCallback, making simulations more efficient.

• SBMLImporter rewrites SBML piecewise expressions to callbacks if possible instead of using ifelse, this improves simulation stability and reduces simulation runtime.

• When possible, SBMLImporter converts reactions to so-called MassActionJumps. This greatly improve performance for most Jump simulations.

• SBMLImporter has more extensive SBML support, passing more tests in the SBML test-suite. It is further the SBML importer for PEtab.jl, which regularly tests against several published models of various sizes.