Supported SBML Features

SBMLImporter supports many SBML features for models of level 2 or higher. Currently, excluding FBA models it successfully passes 1257 out of 1785 test cases. The failed test cases cover features currently not supported. Key features supported include:

  • Events.
  • Rate rules.
  • Assignment rules.
  • Algebraic rules.
  • Dynamic compartment size.
  • Species and model conversion factors.

Species can be specified in either concentrations or amounts. The unit is determined as follows:

  • If initialConcentration is set for a species, its unit will be set to concentration.
  • If initialAmount is set for a species, it will be treated as being in amount.
  • If neither is set, and the substanceUnits of the species is "substance," it is treated as being in amounts.

Currently SBMLImporter does not support the following features:

  • Models with empty SBML reactions.
  • Delay (creating a delay-differential-equations).
  • Events with delay.
  • Events with priority.
  • Hierarchical models.
  • Fast reactions.
  • Parameter or species names corresponding to Julia constants (pi, Inf, NaN, true, false).
  • Certain uncommon math expressions, such as lt with three arguments, implies etc...

Import might also fail for complicated nested piecewise expressions inside SBML functions.

Support for additional features

If SBMLImporter lacks support for a feature you would like to have, please file an issue on GitHub.