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https://github.com/earmingol/cobra_utils

Utility to simplify obtaining information from genome-scale models as well as their manipulation. This implementation is available only for working with COBRApy.
https://github.com/earmingol/cobra_utils

biochemistry bioinformatics cobra cobrapy computational-biology metabolic-models metabolic-network metabolic-reconstruction modeling modeling-tool python systems-biology

Last synced: 23 days ago
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Utility to simplify obtaining information from genome-scale models as well as their manipulation. This implementation is available only for working with COBRApy.

Host: GitHub
URL: https://github.com/earmingol/cobra_utils
Owner: earmingol
License: mit
Created: 2019-06-07T09:40:24.000Z (over 5 years ago)
Default Branch: master
Last Pushed: 2020-03-13T07:12:17.000Z (over 4 years ago)
Last Synced: 2024-01-30T07:55:59.581Z (9 months ago)
Topics: biochemistry, bioinformatics, cobra, cobrapy, computational-biology, metabolic-models, metabolic-network, metabolic-reconstruction, modeling, modeling-tool, python, systems-biology
Language: Jupyter Notebook
Homepage:
Size: 1.66 MB
Stars: 1
Watchers: 2
Forks: 1
Open Issues: 0
Metadata Files:
- Readme: README.md
- License: LICENSE

Awesome Lists containing this project

README

        # COBRA utils

[![PyPI version](https://badge.fury.io/py/cobra-utils.svg)](https://pypi.org/project/cobra-utils/)

[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3470217.svg)](https://doi.org/10.5281/zenodo.3470217)

This is a series of utilities to use together with [COBRApy](https://github.com/opencobra/cobrapy).

The goal of this tool is to make easier the usage of COBRApy.

## Installation

To install this package from a Unix OS, run:

```

pip install cobra-utils

```

To install this package from Windows, run:

```

python -m pip install cobra-utils

```

In case you downloaded the source code, in a Unix OS run:

```

pip install -e .

```

or in Windows:

```

python -m pip install -e .

```

## Examples

* [Loading a model and retrieving reactions information](./notebooks/Ecoli_Rxn_Information.ipynb)

* [Reporter metabolites and pathways from differential expression in two strains of *E. coli*](./notebooks/Ecoli_Reporter_Metabolites_Pathways.ipynb)