FLUXIBLE: Making 13C-Metabolic Flux Analysis More Accessible

ScienceServe FZJ Recipient: Katharina Nöh, IBG-1

Metabolism is the engine of life. Inside every living cell, countless biochemical reactions run in parallel, converting nutrients into energy and biomass, and helping cells adapt to changing environments. The rates of these metabolic reactions – called fluxes – are key to understanding how cells function, respond to stress, or can be engineered for becoming efficient biotechnological production hosts.

One of the most powerful tools to quantify these fluxes is ¹³C Metabolic Flux Analysis (¹³C-MFA). In ¹³C-MFA, cells are fed with nutrients that carry a stable carbon isotope (e.g. ¹³C, ¹⁵N or combinations). Using isotope labelling experiments, biochemical network models and advanced statistical methods, researchers can reconstruct how carbon or nitrogen flows through cellular metabolic networks and quantify intracellular fluxes that cannot be measured directly.

Despite its enormous value in biotechnology, ecology and medicine, ¹³C-MFA is still mostly limited to a small number of specialist labs. The reasons are clear: the methodology is complex, the software landscape is fragmented, and workflows are often tailored to individual groups rather than broadly reusable.

What FLUXIBLE Wants to Change?

The FLUXIBLE project tackles this barrier by transforming the 13CFLUX software developed at IBG-1: Biotechnology into a more user-friendly, FAIR-compliant and community-driven platform. Concretely, the project aims to:

• Publish the 13CFLUX ecosystem with rich metadata and persistent identifiers, packaged in containerized environments so that users can easily find, install and run the software in a reproducible way.
• Modularize the FluxML modelling language into an independent Python package, with a versioned schema and a formal governance process, making it easier to extend, maintain and integrate with other tools.
• Develop training materials and run a hands-on workshop to empower users who want to apply ¹³C-MFA in their own research.

These measures will increase the visibility, accessibility and reusability of 13CFLUX and help expand the use of ¹³C-MFA within the Helmholtz Association and beyond.

FLUXIBLE is a joint effort of Forschungszentrum Jülich, IBG-1: Biotechnology, Helmholtz-Zentrum für Umweltforschung (UFZ), Department of Microbial Biotechnology and Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Department of Chemical and Biological Engineering. Together, these teams combine expertise in ¹³C-MFA, isotope labelling experiments, and advanced analytics to make this key technology more widely usable for the scientific community.