x3cflux 3.1.0

13CFLUX is a high-performance simulator for isotopically stationary and non-stationary simulation of isotope labeling experiments. It is build on highly optimized C++ code, made available in Python through pybind11. It comprises the following main functions:

• Read metabolic models and labeling data from standardized FluxML
• Simulation of labeling distributions and data residuals given fluxes and metabolite concentrations
• Fitting and statistical analysis (Frequentist and Bayesian) of ¹³C labeling experiments

13CFLUX is being developed by the Modelling and Simulation group under the supervision of Katharina Nöh at the IBG-1, Forschungszentrum Jülich, Germany.

Data formats

Models and labeling data are read from FluxML, a standardized XML format for 13C metabolic flux analysis shared across the 13CFLUX tool family (see the FluxML paper and the libFluxML documentation for the full schema).

Results (fluxes, residuals, covariances, sampling output, etc.) are returned as plain numpy arrays and Python objects rather than written to a fixed file format, so they can be persisted or post-processed with whatever tooling fits your pipeline, e.g.:

import numpy as np
np.savetxt("fluxes.csv", fluxes, delimiter=",")

Installation

The recommended way for practitioners to install 13CFLUX is via pip from the Python Package Index (PyPI). It is recommended to do this in a Python environment. Before installation, you should make sure to have ipopt installed (either directly or by installing cyipopt via conda). Then just run

pip install x3cflux

To verify the installation:

python -c "import x3cflux; print(x3cflux.__version__)"

To run the test suite and confirm the software produces correct results, clone the repository and run:

pip install ".[test]"
cd src/test
pytest python

Alternatively, a container image with 13CFLUX pre-installed (built and pushed automatically from every main commit) is available and requires no local build toolchain:

docker run --rm -it jugit-registry.fz-juelich.de/ibg-1/modsim/fluxomics/13cflux:latest

This drops you into a Python shell with x3cflux ready to import.

Documentation

We provide a Read The Docs documentation. Check it out!

Getting help and contributing

For questions, troubleshooting, and modelling discussions, visit the 13CFLUX forum. Some categories are currently restricted and require free registration for full access.

Development takes place on JuGit, where we have access to powerful continuous integration and a Docker registry. Please report issues and request features only on JuGit.

Contributions are welcome. CONTRIBUTING.md covers how to get a JuGit account, how to build and test from source, the branching model, and the formatting and metadata checks that run on every commit. Participation is governed by our Code of Conduct, and contributions are accepted under a Contributor License Agreement.

Versioning

13CFLUX follows Semantic Versioning (MAJOR.MINOR.PATCH). Pre-releases (e.g. towards a new major version) are tagged with an aN suffix, e.g. 3.0.0a0. The package version is not set manually; it is derived automatically from the git tag of a release via setuptools_scm.

There are no long-term-support (LTS) branches; only the latest release receives fixes (see SECURITY.md). Every release has an entry in CHANGELOG.md. How releases are prepared and cut is described in CONTRIBUTING.md.

Citation

Every release is also archived on Zenodo. The concept DOI below always resolves to the latest version; see CITATION.cff for how to cite a specific version:

If you use this software, please also cite the paper describing it:

@article{Stratmann2025,
    author = {Stratmann, Anton and Beyß, Martin and Jadebeck, Johann F and Wiechert, Wolfgang and Nöh, Katharina},
    title = {13CFLUX — Third-generation high-performance engine for isotopically (non)stationary 13C metabolic flux analysis},
    journal = {Bioinformatics},
    pages = {btaf630},
    year = {2025},
    issn = {1367-4811},
    doi = {10.1093/bioinformatics/btaf630},
    url = {https://doi.org/10.1093/bioinformatics/btaf630},
}