Welcome to IsoDesign documentation !
IsoDesign is a scientific tool designed to identify the optimal isotopic composition of labeled substrates in 13C-fluxomics experiments.
Intracellular fluxes and associated statistics are estimated using the influx_si software.
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 13C-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,
usable as a library with a graphical user interface,
open-source, free and easy to install everywhere where Python and R run,
biologist-friendly.
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 on GitHub under a GPLv3 license.
This documentation is available on Read the Docs (https://isodesign .readthedocs.io) and can be downloaded as a PDF file.
User documentation
Miscellaneous