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,

• 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,

• calculation of the Akaike information criterion to guide users to identify the most appropriate model,

• 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

• Installation
  • Installation
  • Alternatives & updates
• Quick start
  • Graphical user interface
  • Command line interface
  • Online use (W4M)
  • Library
• Method
  • Overview
  • Models
  • Flux calculation
  • Sensitivity analysis
  • Goodness-of-fit evaluation
  • Model comparison and selection
• Tutorial
  • Required input data file
  • Configuration file (yaml)
  • Flux calculation parameters
  • Output files
• Models
  • Models shipped with PhysioFit
  • User-made models
• How to cite

Miscellaneous

• Library documentation
  • API reference
• 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?
  • Which model should I use?
  • How can I check if my data has been fitted correctly?
  • My data hasn’t been correctly fitted. Why?
  • I cannot start PhysioFit graphical user interface, can you help me?
  • I have trouble finding PhysioFit on the Workflow4Metabolomics Galaxy instance
  • I have develop a new model, can you include it in PhysioFit distribution?
  • How using PhysioFit programmatically?
  • I would like a new feature.
• License

• Search Page