API

SBML_to_ODESystem(path_SBML::AbstractString;
                  ifelse_to_callback::Bool=true,
                  write_to_file::Bool=false, 
                  verbose::Bool=true, 
                  return_all::Bool=false, 
                  model_as_string::Bool=false)

Parse an SBML model into a ModelingToolkit ODESystem and potentially convert events/piecewise to callbacks.

By default, structurally_simplified is called on the ODESystem before it is returned.

For information on simulating the ODESystem, refer to the documentation.

For testing 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.
• write_to_file=false: Whether to write the parsed SBML model to a Julia file in the same directory as the SBML file.
• verbose=true: Whether or not to display information on the number of return arguments.
• return_all=true: Whether or not to return all possible arguments (see below), regardless of whether the model has events.
• model_as_string=false : Whether or not the model (path_SBML) is provided as str, mainly for testing.

Returns

• ode_system: A ModelingToolkit ODESystem that can be converted into an ODEProblem and solved.
• specie_map: A species map setting initial values; together with the ODESystem, it can be converted into an ODEProblem.
• parameter_map A parameter map setting parameter values; together with the ODESystem, it can be converted into an ODEProblem.
• cbset - only for models with events/piecewise expressions: Callbackset (events) for the model.
• get_tstops- Only for models with events/piecewise expressions: Function computing time stops for discrete callbacks in the cbset.
• ifelse_t0 - Only for models with time-dependent ifelse (piecewise) expressions: Functions checking and adjusting for callback-rewritten piecewise expressions that are active at t=t0.

Examples

# Import and simulate model without events
using SBMLImporter
sys, specie_map, parameter_map = SBML_to_ODESystem(path_SBML)

using OrdinaryDiffEq
tspan = (0, 10.0)
prob = ODEProblem(sys, specie_map, tspan, parameter_map, jac=true)
# Solve ODE with Rodas5P solver
sol = solve(prob, Rodas5P())

# Import a model with events
using SBMLImporter
sys, specie_map, parameter_map, cb, get_tstops = SBML_to_ODESystem(path_SBML)

using OrdinaryDiffEq
tspan = (0, 10.0)
prob = ODEProblem(sys, specie_map, tspan, parameter_map, jac=true)
# Compute event times
tstops = get_tstops(prob.u0, prob.p)
sol = solve(prob, Rodas5P(), tstops=tstops, callback=callbacks)