physiofit's Introduction

PhysioFit

What is PhysioFit?

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.

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,
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.

Quick-start

PhysioFit requires Python 3.9 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! ❤️

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

PhysioFit: a software to quantify cell growth parameters and extracellular fluxes. Le Grégam L., Guitton Y., Bellvert F., Jourdan F., Portais J.C., Millard P. bioRxiv preprint, doi: 10.1101/2023.10.12.561695

Authors

Loïc Le Grégam, Pierre Millard

Contact

📧 [email protected], [email protected]

physiofit's People

Stargazers

Watchers

physiofit's Issues

crossprod error

Hello @pierremillard,

I've been trying to play with PhysioFit and I got an unexpected traceback with the following code:

source("./PhysioFit-master/physio_fit.R", chdir=TRUE)

res = physio_fit(datfile="example.txt")

(I use a copy of PhysioFit extracted from the archive on the master branch. The example file is a copy of the file shipped in the example folder.)

console + traceback:

Initialize the system...
Estimate fluxes...
it=0	res=2.600188e+14
it=1	res=260033830	normstep=1.414212	btk=1
it=2	res=95666376	normstep=0.05244889	btk=1
it=3	res=35196044	normstep=0.05289034	btk=1
it=4	res=12948900	normstep=0.05288783	btk=1
it=5	res=4764008	normstep=0.05244526	btk=1
it=6	res=1752665	normstep=0.05235102	btk=1
it=7	res=644720.1	normstep=0.05211036	btk=1
it=8	res=237067.3	normstep=0.05147469	btk=1
it=9	res=87071.05	normstep=0.04980738	btk=1
it=10	res=31877.28	normstep=0.04568199	btk=1

 Error in crossprod(res, ap) : non-conformable arguments 
3.
crossprod(res, ap) at nlsic.R#262
2.
nlsic(sys$params[sys$to_est], Cost, u = sys$u, co = sys$co, control = list(errx = 1e-06, 
    maxit = 50, trace = 1, ci = list(report = T), history = F, 
    adaptbt = T), e = NULL, eco = NULL, flsi = lsi_ln, sys$data_meas, 
    sys, sim_fun) at physio_fit.R#502
1.
physio_fit(datfile = "example.txt")

metasys-lisbp / physiofit Goto Github PK