SBMLToolkit
SBMLToolkit.jl is a lightweight tool to import models specified in the Systems Biology Markup Language (SBML) into the Julia SciML ecosystem. There are multiple ways to specify the same model in SBML. Please help us improve 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 would like to import BioNetGen models, use the writeSBML() export function or import the .net file with ReactionNetworkImporters.jl. For constrained-based modeling, please have a look at COBREXA.jl.
Installation
To install SBMLToolkit.jl, use the Julia package manager:
using Pkg
Pkg.add("SBMLToolkit")Contributing
Please refer to the SciML ColPrac: Contributor's Guide on Collaborative Practices for Community Packages for guidance on PRs, issues, and other matters relating to contributing to SciML.
See the SciML Style Guide for common coding practices and other style decisions.
There are a few community forums:
- The #diffeq-bridged and #sciml-bridged channels in the Julia Slack
- The #diffeq-bridged and #sciml-bridged channels in the Julia Zulip
- On the Julia Discourse forums
- See also SciML Community page
Tutorial
SBML models can be simulated with the following steps (note that sol is in absolute quantities rather than concentrations):
using SBMLToolkit, ModelingToolkit, OrdinaryDiffEq
SBMLToolkit.checksupport_file("my_model.xml")
mdl = readSBML("my_model.xml", doc -> begin
set_level_and_version(3, 2)(doc)
convert_promotelocals_expandfuns(doc)
end)
rs = ReactionSystem(mdl) # If you want to create a reaction system
odesys = convert(ODESystem, rs) # Alternatively: ODESystem(mdl)
tspan = (0.0, 1.0)
prob = ODEProblem(odesys, [], tspan, [])
sol = solve(prob, Tsit5())SBMLToolkit also provides the following convenience functions to import SBML.Models, Catalyst.ReactionSystems and ModelingToolkit.ODESystems:
mdl = readSBML(sbmlfile, DefaultImporter())
rs = readSBML(sbmlfile, ReactionSystemImporter())
odesys = readSBML(sbmlfile, ODESystemImporter())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 use GitHub issues, the #sciml-sysbio channel in the Julia Slack workspace or email Paul F. Lang or Anand Jain with any questions or comments.
Reproducibility
The documentation of this SciML package was built using these direct dependencies,
Status `~/work/SBMLToolkit.jl/SBMLToolkit.jl/docs/Project.toml`
[e30172f5] Documenter v1.10.1
[86080e66] SBMLToolkit v0.1.31 `~/work/SBMLToolkit.jl/SBMLToolkit.jl`and using this machine and Julia version.
Julia Version 1.11.5
Commit 760b2e5b739 (2025-04-14 06:53 UTC)
Build Info:
Official https://julialang.org/ release
Platform Info:
OS: Linux (x86_64-linux-gnu)
CPU: 4 × AMD EPYC 7763 64-Core Processor
WORD_SIZE: 64
LLVM: libLLVM-16.0.6 (ORCJIT, znver3)
Threads: 1 default, 0 interactive, 1 GC (on 4 virtual cores)A more complete overview of all dependencies and their versions is also provided.
Status `~/work/SBMLToolkit.jl/SBMLToolkit.jl/docs/Manifest.toml`
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Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m`You can also download the manifest file and the project file.