13CFLUX - third-generation high-performance engine for isotopically (non)stationary 13C metabolic flux analysis

Bioinformatics, vol. 41

Abstract

SUMMARY: 13C-based metabolic flux analysis is a cornerstone of quantitative systems biology, yet its increasing data complexity and methodological diversity place high demands on simulation software. We introduce 13CFLUX(v3), a third-generation simulation platform that combines a high-performance C++ engine with a convenient Python interface. The software delivers substantial performance gains across isotopically stationary and nonstationary analysis workflows, while remaining flexible to accommodate diverse labeling strategies and analytical platforms. Its open-source availability facilitates seamless integration into computational ecosystems and community-driven extension. By supporting multi-experiment integration, multi-tracer studies, and advanced statistical inference such as Bayesian analysis, 13CFLUX provides a robust and extensible framework for modern fluxomics research. AVAILABILITY AND IMPLEMENTATION: Sources and containers are provided at https://jugit.fz-juelich.de/IBG-1/ModSim/Fluxomics/13CFLUX, and scripts to replicate results in the supplementary data at https://github.com/JuBiotech/Supplement-to-Stratmann-et-al.-Bioinformatics-2025.

Authors 5

1. Anton Stratmann Aachen Computational Systems Biotechnology

   Forschungszentrum Jülich · RWTH Aachen University

   Affiliation as printed

   Computational Systems Biotechnology (AVT.CSB), RWTH Aachen University , 52062 Aachen,

   Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH , 52425 Jülich,

   Forschungszentrum Jülich GmbH Institute of Bio- and Geosciences, IBG-1: Biotechnology, , Jülich, 52425,

   RWTH Aachen University Computational Systems Biotechnology (AVT.CSB), , Aachen, 52062,

2. Martin Beyß Aachen Computational Systems Biotechnology

   Forschungszentrum Jülich · RWTH Aachen University

   Affiliation as printed

   Computational Systems Biotechnology (AVT.CSB), RWTH Aachen University , 52062 Aachen,

   Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH , 52425 Jülich,

   Forschungszentrum Jülich GmbH Institute of Bio- and Geosciences, IBG-1: Biotechnology, , Jülich, 52425,

   RWTH Aachen University Computational Systems Biotechnology (AVT.CSB), , Aachen, 52062,

3. Johann F. Jadebeck Aachen Computational Systems Biotechnology

   Forschungszentrum Jülich · RWTH Aachen University

   Affiliation as printed

   Computational Systems Biotechnology (AVT.CSB), RWTH Aachen University , 52062 Aachen,

   Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH , 52425 Jülich,

   Forschungszentrum Jülich GmbH Institute of Bio- and Geosciences, IBG-1: Biotechnology, , Jülich, 52425,

   RWTH Aachen University Computational Systems Biotechnology (AVT.CSB), , Aachen, 52062,

4. Wolfgang Wiechert Aachen Computational Systems Biotechnology

   Forschungszentrum Jülich · RWTH Aachen University

   Affiliation as printed

   Computational Systems Biotechnology (AVT.CSB), RWTH Aachen University , 52062 Aachen,

   Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH , 52425 Jülich,

   Forschungszentrum Jülich GmbH Institute of Bio- and Geosciences, IBG-1: Biotechnology, , Jülich, 52425,

   RWTH Aachen University Computational Systems Biotechnology (AVT.CSB), , Aachen, 52062,

5. Katharina Nöh corresponding

   Forschungszentrum Jülich

   Affiliation as printed

   Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH , 52425 Jülich,

   Forschungszentrum Jülich GmbH Institute of Bio- and Geosciences, IBG-1: Biotechnology, , Jülich, 52425,