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

Summary 13C-based metabolic flux analysis (13C-MFA) 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 provided at https://jugit.fz-juelich.de/IBG-1/ModSim/Fluxomics/13CFLUX, and scripts to replicate SI results at https://github.com/JuBiotech/Supplement-to-Stratmann-et-al.-Bioinformatics-2025. Supplementary information Supplementary data are available at Bioinformatics online.