isodesign 2.0.0b1

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 in functional studies of metabolic systems.

Detailed documentation can be found online at Read the Docs ().

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

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]