13CFLUX is a universal software toolkit for isotope-based metabolic flux analysis. Relying on a metabolic network specification with corresponding atom transitions included, measured uptake and secretion rates as well as measured isotopic labeling patterns the method allows for a detailed quantification of in-vivo reaction rates under metabolic steady-state conditions.

Functionality of 13CFLUX:

  • Flexible network specification
  • Syntax and consistency checking
  • Parameter fitting with
    • Evolutionary algorithms
    • Gradient-based SQP methods
  • Statistical analysis
  • Experimental design facility
  • Example networks are included


See our references page.


13CFLUX is developed under Linux. Due to their static linkage x86 binaries are running under any Linux operating system on Intel compatible systems.


13CFLUX can be obtained in three different ways:

  1. A trial version with a restricted number of fluxes and isotopomers is available from this internet server (see Trial Software Download below) together with a reference manual.
  2. For non-commercial usage at universities and research institutes the fully functioning system can be obtained for free from the authors provided that a contract is signed which excludes commercial usage (see Academic Usage below).
  3. For commercial usage the software will be sold by
    METabolic EXplorer S.A.
    Biopôle Clermont-Limagne
    63360 Saint-Beauzire


Currently, a re-implementation of 13CFLUX is actively promoted. Maintenance for previous versions of 13CFLUX is thus expired. For support questions you might send an email.

The new 13CFLUX software will be designed to fulfil requirements from state-of-the-art techniques:

  • powerful code to simulate really large networks fast and an
  • automated workflows handling series of experimental data from high-throughput experiments.

Software Download

  • Trial version restricted to 17 fluxes.
    Some documentation is also included in the Tar Archive.
    Trial version download page
  • Full Version for Academic Usage
    Download of Agreement:
    • Please download and send a signed copy of the agreement and your electronic mail address to the following address:

      Prof. Wolfgang Wiechert
      Institute of Bio- and Geosciences
      IBG-1: Biotechnology
      Forschungszentrum Jülich GmbH
      52425 Jülich
    The agreement will be signed by METabolic EXplorer S.A. and Prof. Wiechert and a copy will be sent back to you. As soon as the contract is approved we will let you know a link to the unrestricted executable files. You may then download the software. If you'd rather would like a CDROM with the academic version give us a short notice while sending the agreement.

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