13CFLUX

13CFLUX is a simulator for 13C metabolic flux analysis (13C-MFA), the state-of-the-art method for quantifying metabolic reaction rates from isotope labeling data in systems biology, metabolic engineering and biomedicine. The software has evolved over three generations, now with a modern architecture and substantially improved performance across isotopically stationary and non-stationary (INST) workflows. Originally developed in an academic setting and since further advanced at Forschungszentrum Jülich, it is designed to support demanding fluxomics studies on microbial, plant and mammalian systems.

The 13CFLUX ecosystem consists of the 13CFLUX(v3) simulation engine, the universal modeling language FluxML, and the MCMC sampling toolbox hopsy. FluxML provides an implementation-independent XML-based language for specifying 13C-MFA models, including metabolic networks, atom mappings and measurement configurations, enabling standardized model description. 13CFLUX builds directly on FluxML, integrating a C++17 backend with a high-level Python API to simulate arbitrary labeling states, support multi-experiment and multi-tracer analyses, and interface with modern numerical libraries. For advanced uncertainty quantification and Bayesian inference, 13CFLUX connects to hopsy, a flexible open-source platform for polytope-restricted MCMC sampling implemented as a Python package atop a high-performance C++ core.

13CFLUX is open-source software released under the GNU AGPL-3.0, with source code and containers provided via a GitLab instance. The project adheres to modern research software engineering practices, including unit testing and continuous integration. To lower the barrier of entry, API documentation is provided alongside working examples to develop new analysis workflows and reproduce existing ones. Together, the simulator, FluxML, and hopsy form a FAIR-oriented toolkit for building modern interoperable 13C-MFA and fluxomics pipelines, running everywhere from laptops to HPC environments.