API

load_SBML(path_SBML::AbstractString;
          ifelse_to_callback::Bool=true,
          inline_assignment_rules::Bool=false,
          write_to_file::Bool=false,
          model_as_string::Bool=false)

Parse an SBML model into a ParsedReactionNetwork and convert SBML events/piecewise to callbacks.

For information on simulating the ParsedReactionNetwork, as a JumpProblem, a SDEProblem, or an ODEProblem see the documentation.

path_SBML can be the model as a string if model_as_string=true.

Arguments

• path_SBML: File path to a valid SBML file (level 2 or higher).
• ifelse_to_callback=true: Whether to rewrite ifelse (piecewise) expressions to callbacks; recommended for performance.
• inline_assignment_rules=true: Whether to inline assignment rules into model equations. Recommended for model import speed, however, it will not be possible to access the rule-variable via sol[:var].
• write_to_file=false: Whether to write the parsed SBML model to a Julia file in the same directory as the SBML file.
• model_as_string=false: Whether or not the model (path_SBML) is provided as a string.

Returns

• parsed_rn: A ParsedReactionNetwork struct that can be converted into a JumpProblem, a SDEProblem, or an ODEProblem
• cbset: Callbackset (events, piecewise etc...) for the model.

Examples

# Import and simulate model as a JumpProblem
using SBMLImporter, JumpProcesses
prnbng, cb = load_SBML(path_SBML)
tspan = (0.0, 10.0)
dprob = DiscreteProblem(prnbng.rn, prnbng.u₀, tspan, prnbng.p)
jprob = JumpProblem(prnbng.rn, dprob, Direct())
sol = solve(jprob, SSAStepper(), callback=cb)

# Import and simulate model as a SDE
using SBMLImporter, StochasticDiffEq
prnbng, cb = load_SBML(path_SBML)
tspan = (0.0, 10.0)
sprob = SDEProblem(prnbng.rn, prnbng.u₀, tspan, prnbng.p)
sol = solve(sprob, LambaEM(), callback=cb)

# Import and simulate model as an ODE
using SBMLImporter, ModelingToolkit, OrdinaryDiffEq
prnbng, cb = load_SBML(path_SBML)
sys = convert(ODESystem, prnbng.rn)
oprob = ODEProblem(sys, prnbng.u₀, tspan, prnbng.p, jac=true)
sol = solve(oprob, Rodas5P(), callback=cb)