sbmlode

An SBML model describes a system of ordinary differential equations (ODEs), but it is not written as one: the equations follow from the reactions, rules, events and units of the model. sbmlode derives this system once and writes it

• as code which simulates the model: python (numpy and scipy), julia (OrdinaryDiffEq.jl) and R (deSolve), verified against libroadrunner over the SBML test suite;
• as documents which describe the model: typst, LaTeX and markdown;
• as typed data for an application which lays out the equations itself, such as SBML4Humans, see Typed target.

sbmlode depends on python-libsbml and jinja2 only. It is the ODE export of sbmlutils 0.14 as a package of its own, which sbmlutils re-exports as sbmlutils.converters.ode.

Installation

pip install sbmlode               # the export
pip install "sbmlode[simulate]"   # with numpy, pandas and scipy, which the python code runs with

Quick start

from sbmlode import OdeSystem

system = OdeSystem.from_sbml("model.xml")

code: str = system.render("python")  # the code or document as a string
system.write("model.jl")  # the format from the suffix of the file
system.write("model.md", standalone=False)  # with the options of the format

The Guide describes the formats, their options, the supported SBML and the verification, the API reference the classes and functions.

License

sbmlode is open source under the MIT license. Please open an issue for a question or a problem.