Welcome to PhysioFit documentation!
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.
This documentation is available on Read the Docs (https://physiofit.readthedocs.io) and can be downloaded as a PDF file.
User documentation
Miscellaneous
- Library documentation
- Frequently asked questions (FAQ)
- How are fluxes calculated?
- How many measurements should I use to calculate fluxes?
- Can I calculate fluxes in case of missing values?
- What units should be used for input data?
- What are the flux units?
- An error has been raised. What should I do?
- What parameters values should I use?
- How can I check if my data have been fitted correctly?
- What is a χ² test?
- My data hasn’t been correctly fitted. Why?
- I cannot start PhysioFit graphical user interface, can you help me?
- I have develop a new model, can you include it in PhysioFit distribution?
- I would like a new feature.
- License