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PhysioFit is a scientific tool designed to quantify cell growth parameters and uptake & production fluxes

Fluxes are estimated using mathematical models by fitting time-course measurements of the concentration ofcells and extracellular substrates and products. PhysioFit is shipped with some common growth models, andadditional tailor-made models can be implemented by users.

It is one of the routine tools that we use at theMetaSys teamandMetaToul platform in functional studies of metabolic systems.

The code is open-source, and available under a GPLv3 license. Additional information can be found in the followingpublication.

Detailed documentation can be found online at Read the Docs(https://physiofit.readthedocs.io/).

• calculation of growth rate and extracellular (uptake and production) fluxes,
• a set ofsteady-state and dynamic models,
• tailor-made models can be constructed by users,
• Monte-Carlo sensitivity analysis toestimate the precision of the calculated fluxes,
• evaluation of the goodness of fit and visual inspection of the fitted curves,
• calculation of the Akaike information criterion toguide users to identify the most appropriate model,
• shipped as alibrary with both agraphical and acommand line interface,
• open-source, free and easy to install everywhere where Python 3 and pip run,
• biologist-friendly.

PhysioFit requires Python 3.9 or higher and run on all platforms.Please checkthe documentation for completeinstallation and usage instructions.

Usepip toinstall PhysioFit from PyPi:

$ pip install physiofit

Then, start the graphical interface with:

$ physiofit

PhysioFit is also available directly from command-line and as a Python library.

If you have an idea on how we could improve PhysioFit please submit a newissuetoour GitHub issue tracker.

Contributions are very welcome! ❤️

Please work on your own fork,followPEP8 style guide,and make sure you pass all the tests before a pull request.

In development mode, do apip install -e /path/to/PhysioFit to installlocally the development version.

Build the HTML documentation with:

$cd doc$ make html

The PDF documentation can be built locally by replacinghtml bylatexpdfin the command above. You will need a recent latex installation.

PhysioFit: a software to quantify cell growth parameters and extracellular fluxes.Le Grégam L., Guitton Y., Bellvert F., Jourdan F., Portais J.C., Millard P.bioRxiv preprint,doi: 10.1101/2023.10.12.561695

Loïc Le Grégam, Pierre Millard

📧legregam@insa-toulouse.fr,millard@insa-toulouse.fr