Calculate extracellular fluxes from metabolite concentrations and biomass data
Project description
PhysioFit
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 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.
- 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 for complete installation and usage instructions.
Use pip to install 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.
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
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
Authors
Loïc Le Grégam, Pierre Millard
Contact
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