isodesign 2.0.0b2

Facilitates the choice of the optimal isotopic composition of labeled substrates in 13C-fluxomics experiments.

IsoDesign

What is IsoDesign ?

IsoDesign is a scientific tool designed to optimize the choice of the optimal isotopic composition of labeled substrates in 13C fluxomic labelling experiments. Simulated labeling is calculated using the influx_si software, distributed with IsoDesign.

It is one of the routine tools that we use at the Mathematics cell of TBI and MetaToul platform.

The code is open-source, and available under a GPLv3 license.

Detailed documentation can be found online at Read the Docs (https://isodesign.readthedocs.io/).

Key features

• user can define lower and upper bounds (between 0 and 100) and define the desired number of intervals for each isotopic form to be included,
• substrate pricing can be entered, which will be incorporated into the scoring criteria,
• simulation of all possible combinations of isotopic forms in a single run,
• ability to simulate stationary or instationary labeling,
• multiple scoring criteria are available and can be applied simultaneously to assess simulation results,
• the results of the scoring criteria are displayed using a table for detailed values and a bar plot for visual representation,
• shipped as a library with a graphical interface,
• open-source, free and easy to install everywhere where Python 3 and pip run,
• biologist-friendly.

Quick-start

IsoDesign requires Python 3.10 or higher and run on all platforms. Please check the documentation for complete installation and usage instructions.

Installation with pip

If you have Python3 and R installed on your system, you can install IsoDesign from Pypi with pip :

$ pip install isodesign

To use IsoDesign, you will need to some R dependencies (necessary for the simulation part with influx_si). Once you installed IsoDesign, you can install these dependencies by running the following command:

$ influx_s --install_rdep

For more information on the installation of R dependencies, please refer to influx_si software documentation.

Then, start the graphical interface with:

$ isodesign

IsoDesign 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 IsoDesign please submit a new issue to our GitHub issue tracker.

Developers guide

Contributions

Contributions are very welcome! :heart:

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/isodesign 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.

Authors

Rochelle KOUAKOU, Loic LE GREGAM

Contacts

:email: [e-mail], [e-mail]