.. IsoDesign documentation master file, created by
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.. image:: _static/IsoDesign_logo.png
   :align: left
   :scale: 48%


Welcome to IsoDesign documentation !
====================================

IsoDesign is a scientific tool designed to identify the optimal
isotopic composition of labeled substrates in :sup:`13`\ C-fluxomics
experiments.

Intracellular fluxes and associated statistics are estimated using the
`influx_si software <https://influx-si.readthedocs.io/en/latest/index.html>`_.

**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**,
   * 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
<https://mth-metatoul.com/>`_ and `MetaSys team <http://www
.toulouse-biotechnology-institute
.fr/en/research/molecular-physiology-and-metabolism/metasys.html>`_ of the
`Toulouse Biotechnology Institute <http://www
.toulouse-biotechnology-institute.fr/en/>`_.
IsoDesign has been developed in collaboration with the `Math cell of TBI
<https://www.toulouse-biotechnology-institute
.fr/en/plateformes-plateaux/cellule-mathematiques/>`_, with the continuous
support of `MetaboHUB <https://www.metabohub.fr/home.html>`_.

The code is open-source, and available on `GitHub <https://github
.com/MetaboHUB-MetaToul-FluxoMet/IsoDesign/>`_ under a
:ref:`GPLv3 license <license>`.

This documentation is available on Read the Docs (`https://isodesign
.readthedocs.io <https://isodesign.readthedocs.io/>`_)
and can be downloaded as a `PDF file <https://readthedocs
.org/projects/isodesign/downloads/pdf/latest/>`_.


.. toctree::
   :maxdepth: 2
   :caption: User documentation

   installation.rst
   quickstart.rst
   tutorial.rst


.. toctree::
   :maxdepth: 2
   :caption: Miscellaneous

   library_doc.rst
   license.rst