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.
@article{arxiv.2509.23847,
title = {13CFLUX -- Third-generation high-performance engine for isotopically (non)stationary 13C metabolic flux analysis},
author = {Anton Stratmann and Martin Beyß and Johann F. Jadebeck and Wolfgang Wiechert and Katharina Nöh},
journal= {arXiv preprint arXiv:2509.23847},
year = {2025}
}