SBMLImporter.jl

Julia Importer for Dynamic Models in the SBML Format

SBMLImporter.jl is a Julia importer for dynamic models specified in the Systems Biology Markup Language (SBML) into a Catalyst ReactionSystem - which allows for model simulations with stochastic (Gillespie, SDE) or deterministic (ODE) simulators. It supports many SBML features, such as events, rate-, assignment-, algebraic-rules, dynamic compartment size, and conversion factors. For a detailed list of supported features, see below.

To perform parameter estimation for a SBML model, see PEtab.jl.

A list of differences compared to SBMLToolkit is provided below. For constraint-based modeling, see COBREXA.jl.

Installation

SBMLImporter.jl can be installed via the Julia package manager:

julia> ] add SBMLImporter

Alternatively, you can use:

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

Quick Start

Importing an SBML model is straightforward. Given the path to a SBML file to import into a ReactionSystem do:

using SBMLImporter
rn, specie_map, parameter_map = SBML_to_ReactionSystem(path_SBML)

Here, rn is the ReactionSystem that for example can be converted into an ODESystem or a SDESystem, specie_map is a mapping for the initial values, and parameter_map is a mapping/values for the model parameters. To simulate the model with an ODE-solver, construct an ODEProblem and solve it using any ODE solver from OrdinaryDiffeq:

using OrdinaryDiffEq
sys = convert(ODESystem, rn)
tspan = (0, 10.0)
prob = ODEProblem(sys, specie_map, tspan, parameter_map, jac=true)
sol = solve(prob, Rodas5P())

Alternatively, the model can be imported directly into an ODESystem with:

sys, specie_map, parameter_map = SBML_to_ODESystem(path_SBML)

To import more advanced models with events and/or piecewise (ifelse) expressions, see the documentation.

Differences compared to SBMLToolkit

The key differences between SBMLToolkit and SBMLImporter are:

SBMLToolkit works with (and transforms) species to be in amount. SBMLImporter supports species in amount and/or concentration.
SBMLToolkit has a cleaner interface, as it performs all model processing via Symbolics.jl.
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 integration stability and reduces runtime.
SBMLImporter has more extensive SBML support, passing more tests in the test-suite. It is further the SBML importer for PEtab.jl, which regularly tests against several published models of various sizes.

Supported SBML Features

SBMLImporter supports many SBML features for SBML models (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. If SBMLImporter lacks support for a feature you would like, please file an issue on GitHub. The features not supported are:

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, 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.

Citation