SBMLToolkit

SBMLToolkit.jl is a lightweight tool to import models specified in the Systems Biology Markup Language (SBML) into the Julia SciML ecosystem. More specifically, SBMLToolkit.jl extracts reactions, initial conditions and parameter values from SBML files. Events, Rules and several other SBML components are not yet supported. For details on support of SBML test suite cases, please refer to the SBML Test-Suite Results Tracker. There are multiple ways to specify the same model in SBML. Please help us improving SBMLToolkit.jl by creating a GitHub issue if you experience errors when converting your SBML model.

SBMLToolkit uses the SBML.jl wrapper of the libSBML library to lower dynamical SBML models into dynamical systems. If you are interested in constrained-based modelling please have a look at COBREXA.jl.

Installation

SBMLToolkit.jl is available on the Julia package managing system. To install SBMLToolkit run the following in the REPL:

]add SBMLToolkit

Tutorial

SBML models can be simulated with the following steps (note that sol is in absolute quantities rather than concentrations):

using SBMLToolkit, ModelingToolkit

SBMLToolkit.checksupport("my_model.xml")
mdl = readSBML("my_model.xml", doc -> begin
    set_level_and_version(3, 2)(doc)
    convert_simplify_math(doc)
end)
rs = ReactionSystem(mdl)
odesys = convert(ODESystem, rs)

tspan = [0., 1.]
prob = ODEProblem(odesys, [], tspan, [])
sol = solve(prob, Tsit5())

License

The package is released under the MIT license.

Development team

This package was developed by Paul F. Lang at the University of Oxford, UK and Anand Jain at the University of Chicago, USA.

Questions and comments

Please contact Paul F. Lang or Anand Jain with any questions or comments.