Thermo-Flux

Tools for flux balance anlysis with thermodynamic constraints.

Full documentation on ReadTheDocs (https://thermo-flux.readthedocs.io/en/latest/) and accompanying protocol at doi:10.1101/2025.11.20.689566.

Installation

Requirements

• Python >= 3.11
• Gurobi 11.0

1. To avoid dependency conflicts it is reccomended to use a python environment e.g:

   conda create -n thermoflux python=3.11

   conda activate thermoflux

Installation using pip

2a. Now thermo_flux can be safely installed using pip.. python -m pip install thermo-flux

Local installation

2b. Otherwise thermo_flux can be installed locally, from a cloned repository. Clone the thermo_flux repository and navigate to the thermo_flux directory:

```git clone https://github.com/molecular-systems-biology/thermo-flux```

```cd thermo_flux```

3b. Run the installation command below - for development use the -e flag (for an editable install) :

```python -m pip install -e .``` 

Getting gurobi optimizer

4. For thermodynamic optimisations, ensure a Gurobi license is installed correctly (free for academics):

   conda install -c gurobi gurobi

Examples

Example usage notebooks can be found in the examples directory.

Cite us

If you use Thermo-Flux please cite our protocol paper at:

Smith EN, Fargier N, Pedro J & Heinemann M (2025) Thermo-Flux: generation and analysis of comprehensive thermodynamic-stoichiometric metabolic network models. 2025.11.20.689566 doi:10.1101/2025.11.20.689566 [PREPRINT]

Thermo-Flux relies on eQuilibrator for underlying thermodynamic calculations so please also cite the eQuilibrator database:

M. E. Beber, M. G. Gollub, D. Mozaffari, K. M. Shebek, A. I. Flamholz, R. Milo, and E. Noor, eQuilibrator 3.0: a database solution for thermodynamic constant estimation Nucleic Acids Research (2021), DOI:10.1093/nar/gkab1106

Acknowledgments

Thanks to Yusuke Himeoka, Moritz Beber, Elad Noor and Mattia Gollub for helpful discussions and advice.