Quick start

In this section we will explain how to launch your first job once PhysioFit has been installed onto your system.

See also

  • If you have already used PhysioFit and are looking for a more in-depth tutorial, check out the Tutorial section.

Graphical user interface

To open the Graphical User Interface, type in a terminal (e.g. Anaconda Prompt if installed on Windows):

physiofit

If you have installed the package in a specific environment, make sure to activate this environment before starting PhysioFit.

PhysioFit interface will open in a new browser window:

_images/interface.jpg

Select an input file (which can be a tsv file containing the data or a yaml configuration file containing the run parameters and a path towards the data, see Tutorial for more details), select a model, modify the calculation parameters according to your data, and click on Run flux calculation. PhysioFit proceeds automatically to the flux calculation and display its progress and possibly important messages such as errors. The output of the calculations (i.e. fluxes and associated statistics) will be written in a text file as will the statistical test results, while plots will be generated individually for each metabolite (svg files) and combined in a multi-page pdf file. If multiple experiments were included in the input data, a summary (csv file) will also be generated. See Output files for more details.

Command line interface

To process your data, type in a terminal:

physiofit [command line options]

Here after the available options with their full names are enumerated and detailed.

usage: physiofit [-h] [-d DATA] [-c CONFIG] [-m MODEL] [-g] [--list] [-v]
                 [-op OUTPUT_PDF] [-of OUTPUT_FLUXES] [-os OUTPUT_STATS]
                 [-oc OUTPUT_CONFIG] [-or OUTPUT_RECAP] [-oz OUTPUT_ZIP]

Named Arguments

-d, --data

Path to data file in tabulated format (txt or tsv)

-c, --config

Path to config file in yaml format

-m, --model

Which model should be chosen. Useful only if generating related config file

-g, --galaxy

Is the CLI being used on the galaxy platform

Default: False

--list

Return the list of models in model folder

Default: False

-v, --debug_mode

Activate the debug logs

Default: False

-op, --output_pdf

Path to output the pdf file containing plots

-of, --output_fluxes

Path to output the flux results

-os, --output_stats

Path to output the khi² test

-oc, --output_config

Path to output the yaml config file

-or, --output_recap

Path to output the summary

-oz, --output_zip

Path to export zip file

Library

PhysioFit is also available as a library (a Python module) that you can import directly in your Python scripts:

import physiofit

See also

Have a look at our API if you are interested in this feature.