Metadata-Version: 2.1
Name: isodesign
Version: 2.0.0b2
Summary: Facilitates the choice of the optimal isotopic composition of labeled substrates in 13C-fluxomics experiments.
Author: rkouakou
Author-email: kouakou@insa-toulouse.fr>, llegregam <legregam@insa-toulouse.fr
Requires-Python: >=3.10,<3.13
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Requires-Dist: influx-si (>=7.0.3,<8.0.0)
Requires-Dist: numpy (>=1.24.0,<2.0.0)
Requires-Dist: openpyxl (>=3.1.5,<4.0.0)
Requires-Dist: pandas (>=2.1.4,<3.0.0)
Requires-Dist: plotly (>=5.23.0,<6.0.0)
Requires-Dist: sess-i (>=0.1.0,<0.2.0)
Requires-Dist: streamlit (>=1.36.0,<2.0.0)
Description-Content-Type: text/markdown

# IsoDesign

[![PyPI version](https://badge.fury.io/py/isodesign.svg)](https://badge.fury.io/py/isodesign)
[![Documentation Status](https://readthedocs.org/projects/isodesign/badge/?version=latest)](https://isodesign.readthedocs.io/en/latest/?badge=latest)

## 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](https://influx-si.readthedocs.io/en/latest/index.html), distributed with IsoDesign. 

It is one of the routine tools that we use at the [Mathematics cell of TBI](https://www.toulouse-biotechnology-institute.fr/en/plateformes-plateaux/cellule-mathematiques/) 
and [MetaToul platform](https://www.metabohub.fr/home.html).

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/](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](https://isodesign.readthedocs.io/en/latest/quickstart.html) 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 :

```bash
$ 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:

```bash
$ influx_s --install_rdep
```

For more information on the installation of R dependencies, please refer to [influx_si software](https://influx-si.readthedocs.io/en/latest/install.html#r-dependencies) documentation.


Then, start the graphical interface with:

```bash
$ 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](https://github.com/MetaboHUB-MetaToul-FluxoMet/IsoDesign/issues).


## Developers guide
### Contributions
Contributions are very welcome! :heart:

Please work on your own fork,
follow [PEP8](https://www.python.org/dev/peps/pep-0008/) 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:

```bash
$ 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: kouakou@insa-toulouse.fr, legregam@insa-toulouse.fr



