Metadata-Version: 2.1
Name: physiofit
Version: 2.2.3
Summary: Calculate extracellular fluxes from metabolite concentrations and biomass data
Home-page: https://github.com/MetaSys-LISBP/PhysioFit
Author: Loïc Le Grégam
Author-email: legregam@insa-toulouse.fr
Project-URL: Bug Tracker, https://github.com/MetaSys-LISBP/PhysioFit/issues
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: GNU General Public License (GPL)
Classifier: Operating System :: OS Independent
Requires-Python: >=3.7
Description-Content-Type: text/markdown
License-File: LICENSE

# PhysioFit

[![PyPI version](https://badge.fury.io/py/physiofit.svg)](https://badge.fury.io/py/physiofit)
[![PyPI pyversions](https://img.shields.io/pypi/pyversions/physiofit.svg)](https://pypi.python.org/pypi/physiofit/)
[![Documentation Status](https://readthedocs.org/projects/physiofit/badge/?version=latest)](http://physiofit.readthedocs.io/?badge=latest)


## What is PhysioFit?
PhysioFit is a scientific tool designed to i) quantify exchange (production and consumption) fluxes and  ii) cell growth rate during (batch) cultivations of microorganisms.

Fluxes are estimated from time-course measurements of extracellular metabolites and biomass concentrations. PhysioFit has been designed to calculate fluxes in batch experiments, assuming cells are in metabolic (pseudo) steady-state (i.e. fluxes are constant during the experiment).

It is one of the routine tools that we use at the [MetaSys team](http://www.lisbp.fr/en/research/molecular-physiology-and-metabolism/metasys.html) and [MetaToul platform](http://www.metatoul.fr) 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](https://doi.org/10.1128/aem.00768-19).

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

## Key features
* **calculation of growth rate and extracellular (uptake and production) fluxes**.
* if cell growth has some **lag** (e.g. due to adaptation to a novel environment), lag can be taken into account and lag time estimated.
* **non-enzymatic degradation** of some metabolites (e.g. DHA or glutamine) can be estimated and taken into account when calculating fluxes.
* sensitivity analyses are performed 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 3.7 or higher and run on all platforms.
Please check [the documentation](https://physiofit.readthedocs.io/en/latest/quickstart.html) for complete
installation and usage instructions.

Use `pip` to **install PhysioFit from PyPi**:

```bash
$ pip install physiofit
```

Then, start the graphical interface with:

```bash
$ 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](https://github.com/MetaSys-LISBP/PhysioFit/issues).


## Developers guide
### Contributions
Contributions are very welcome! :heart:

Please work on your own fork,
follow [PEP8](https://www.python.org/dev/peps/pep-0008/) 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:

```bash
$ 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
Peiro C., Millard P., de Simone A., Cahoreau E., Peyriga L., Enjalbert B., and Heux S. Chemical and metabolic controls on dihydroxyacetone metabolism lead to suboptimal growth of *Escherichia coli*. Appl Environ Microbiol, 2019, [doi: 10.1128/AEM.00768-19](https://doi.org/10.1128/AEM.00768-19)

## Authors
Loïc Le Grégam, Pierre Millard

## Contact
:email: legregam@insa-toulouse.fr, millard@insa-toulouse.fr
