Metadata-Version: 2.4
Name: fungem
Version: 0.1.0
Summary: fungem: Testing of metabolic functions that should be performed by a genome-scale model
Home-page: https://forgemia.inra.fr/metexplore/theses-postdocs/thesis_koloina/toolbox-python/
Author: Koloina Rabemanantsoa, Nathalie Poupin
Author-email: koloina.rabemanantsoa@inrae.fr, nathalie.poupin@inrae.fr
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
Classifier: Operating System :: OS Independent
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: <3.12,>=3.7
Description-Content-Type: text/markdown
License-File: LICENSE.md
Requires-Dist: pandas
Requires-Dist: cobra
Requires-Dist: openpyxl
Requires-Dist: joblib
Requires-Dist: pytest
Dynamic: license-file

# fungem - a framework to assess feasible metabolic functions in a genome scale model

## What is fungem

**fungem is a scientific software dedicated to the analysis of metabolic functions a metabolic network model is able to perform**.

A metabolic function is defined as the ability of a metabolic network to produce a specific set of output metabolites when only a limited set of inputs are allowed.
e.g.: production of ATP from glucose, ADP, Pi and H20.

INSERT image

The output of fungem is a file summarizing the results of the metabolic functions analysis.


## Key features
* **metabolic functions testing from a limited set of inputs**,
* **metabolic functions testing from a defined medium**,
* contains functions to compare which metabolic functions are possible in different models and conditions

## Local install with pip

```bash
git clone https://forgemia.inra.fr/metexplore/theses-postdocs/thesis_koloina/toolbox-python.git
pip install -e /path/to/toolbox-python
```

You can then run metabolic function tests as done in the [notebooks](https://forgemia.inra.fr/metexplore/theses-postdocs/thesis_koloina/toolbox-python/-/tree/dev/doc?ref_type=heads)

## Bug and feature requests
If you have an idea on how we could improve IsoCor please submit a new *issue*
to [our GitHub issue tracker](https://forgemia.inra.fr/metexplore/theses-postdocs/thesis_koloina/toolbox-python/-/issues)

## Authors
Koloina Rabemanantsoa, Nathalie Poupin

## Contact
koloina.rabemanantsoa@inrae.fr, nathalie.poupin@inrae.fr
