Metadata-Version: 2.4
Name: x3cflux
Version: 3.0.2
Summary: Python interface for 13CFLUX
Keywords: 13C-MFA,MFA,mass-spectrometry,HPC
Author-Email: Anton Stratmann <info@13cflux.net>, Martin Beyss <info@13cflux.net>, Katharina Noeh <info@13cflux.net>
License-Expression: AGPL-3.0-only
License-File: LICENSE
Classifier: Development Status :: 5 - Production/Stable
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Classifier: Programming Language :: Python :: 3.14
Classifier: Operating System :: POSIX :: Linux
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Project-URL: documentation, https://x3cflux.readthedocs.io
Project-URL: homepage, https://13cflux.net
Project-URL: repository, https://jugit.fz-juelich.de/IBG-1/ModSim/Fluxomics/13CFLUX
Requires-Python: >=3.9
Requires-Dist: numpy
Requires-Dist: scipy
Requires-Dist: joblib
Requires-Dist: cvxpy
Requires-Dist: cyipopt
Requires-Dist: hopsy>=1.6.1
Provides-Extra: test
Requires-Dist: pytest; extra == "test"
Requires-Dist: pytest-cov; extra == "test"
Description-Content-Type: text/markdown

<img src="https://jugit.fz-juelich.de/IBG-1/ModSim/Fluxomics/13CFLUX/-/raw/main/docs/source/images/banner.png" width=350>

[![Pipeline Status](https://jugit.fz-juelich.de/IBG-1/ModSim/Fluxomics/13CFLUX/badges/main/pipeline.svg)](https://jugit.fz-juelich.de/IBG-1/ModSim/Fluxomics/13CFLUX/-/pipelines?scope=all&page=1&ref=main)
[![Coverage Report](https://jugit.fz-juelich.de/IBG-1/ModSim/Fluxomics/13CFLUX/badges/main/coverage.svg)](https://jugit.fz-juelich.de/IBG-1/ModSim/Fluxomics/13CFLUX/-/commits/main)
[![Latest Release](https://jugit.fz-juelich.de/IBG-1/ModSim/Fluxomics/13CFLUX/-/badges/release.svg)](https://jugit.fz-juelich.de/IBG-1/ModSim/Fluxomics/13CFLUX/-/releases)

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 <sup>13</sup>C 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.

## 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](https://coin-or.github.io/Ipopt/INSTALL.html) or by installing
[cyipopt via conda](https://cyipopt.readthedocs.io/en/stable/install.html)). Then just run

```shell
pip install x3cflux
```

## Documentation

We provide a [Read The Docs documentation](https://x3cflux.readthedocs.io). Check it out!

## Development

The development of *13CFLUX* primarily takes place on
[JuGit](https://jugit.fz-juelich.de/IBG-1/ModSim/Fluxomics/13CFLUX), where we have access to powerful continuous
integration and a Docker registry. **Please report issues and request features only JuGit.**

## Citation

```
@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},
}
```

## Further links

- PyPI: https://pypi.org/project/x3cflux/
- Github Mirror: https://github.com/JuBiotech/13CFLUX