physiofit 3.2.0

Calculate extracellular fluxes from metabolite concentrations and biomass data

PhysioFit

What is PhysioFit?

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

Fluxes are estimated using various mathematical models by fitting time-course measurements of the concentration of cells and extracellular substrates and products. PhysioFit v3 includes by default the most common growth models, and additional models can be implemented by users.

It is one of the routine tools that we use at the MetaSys team and MetaToul 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 following publication.

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

Key features

• calculation of growth rate and extracellular (uptake and production) fluxes,
• default models for quantifying parameters in steady-state conditions (with and without lag & metabolite degradation over time),
• user-defined growth models,
• Monte-Carlo sensitivity analysis to estimate the precision of the calculated fluxes,
• evaluation of the goodness of fit and visual inspection of the fitted curves,
• shipped as a library with both a graphical and command line interface,
• open-source, free and easy to install everywhere where Python 3 and pip run,
• biologist-friendly.

Quick-start

PhysioFit requires Python 3.8 or higher and run on all platforms. Please check the documentation for complete installation and usage instructions.

Use pip to install PhysioFit from PyPi:

$ pip install physiofit

Use conda to install from conda:

$ conda install physiofit -c bioconda

Then, start the graphical interface with:

$ physiofit

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

Bug and feature requests

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

Developers guide

Contributions

Contributions are very welcome! :heart:

Please work on your own fork, follow PEP8 style guide, and make sure you pass all the tests before a pull request.

Local install with pip

In development mode, do a pip install -e /path/to/PhysioFit to install locally the development version.

Build the documentation locally

Build the HTML documentation with:

$ cd doc
$ make html

The PDF documentation can be built locally by replacing html by latexpdf in the command above. You will need a recent latex installation.

How to cite

PhysioFit: quantifying cell growth parameters and uptake and production fluxes. Le Grégam L., Guitton Y., Bellvert F., Jourdan F., Portais J.C., Millard P. In preparation for publication

Authors

Loïc Le Grégam, Pierre Millard

Contact

:email: [e-mail], [e-mail]