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 of cells and extracellular substrates and products. PhysioFit is shipped with some common growth models, and additional tailor-made models can be implemented by users.
PhysioFit includes the following features:
- calculation of growth rate and extracellular (uptake and production) fluxes,
- a set of steady-state and dynamic models are shipped with PhysioFit,
- tailor-made models can be constructed by users,
- 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 a command line interface,
- open-source, free and easy to install everywhere where Python 3 and pip run,
- biologist-friendly.
It is one of the routine tools that we use at the MetaSys team and MetaToul platform to calculate fluxes.
The code is open-source, and available on GitHub under a GPLv3 license <license>.
This documentation is available on Read the Docs (https://physiofit.readthedocs.io) and can be downloaded as a PDF file.
installation.rst quickstart.rst method.rst usage.rst models.rst cite.rst
librairy.rst faq.rst license.rst
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