isodesign 2.0.0

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 identify the optimal isotopic composition of labeled substrates in :sup:13\ C-fluxomics experiments.

It is one of the routine tools that we use at the MetaToul platform and MetaSys team of the Toulouse Biotechnology Institute. IsoDesign has been developed in collaboration with the Math cell of TBI, with the continuous support of MetaboHUB.

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

This documentation is available on Read the Docs.

Key features

• users can define all isotopic forms to consider for each substrate,
• account for the substrate price to keep the cost of the experiment reasonable,
• design of both (isotopic) stationary and non-stationary :sup:13\ C-fluxomics experiments
• diverse scoring criteria to finely analyse flux resolution at reaction-, pathway- and network-levels to identify the optimal label input according to the biological question,
• scoring criteria can be combined to find the optimal balance between different objectives (e.g., the highest flux resolution at a minimal cost),
• visual representation of the design results to support the decision-making process,
• increased computational performance through parallel computing,
• shipped as a library with a graphical user interface,
• open-source, free and easy to install everywhere where Python and R run,
• biologist-friendly.

Quick-start

IsoDesign runs on all platforms and requires Python (3.10 or higher) and R (3.4.0 or higher). Please check the documentation for complete installation and usage instructions.

Installation with conda (recommended)

This is the recommended installation procedure. If you have a version of conda (such as miniconda or Anaconda), you can install IsoDesign with the following command:

$ conda install isodesign -c bioconda

This will install IsoDesign and all its dependencies.

Installation with pip

If you don't have any version of conda (neither miniconda nor Anaconda) but do have Python3 and R installed on your system, you can install IsoDesign with pip.

$ pip install isodesign

This will install IsoDesign and most of its dependencies. To use IsoDesign, you will need some additional R dependencies (necessary for 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 documentation.

Start IsoDesign

Then, start the graphical user interface with:

$ isodesign

IsoDesign is also available directly from command-line and as a Python library.

Have a look to our tutorial for details on IsoDesign usage.

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]