https://github.com/robaina/phycogem

Modeling phycospheric metabolic interactions in python
https://github.com/robaina/phycogem

bioinformatics genome-scale-metabolic-model marine-microbial-ecology metagenomics phycosphere

Last synced: 11 days ago
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Modeling phycospheric metabolic interactions in python

• Host: GitHub
• URL: https://github.com/robaina/phycogem
• Owner: Robaina
• License: apache-2.0
• Created: 2023-08-20T09:17:36.000Z (over 1 year ago)
• Default Branch: main
• Last Pushed: 2024-06-27T11:20:26.000Z (8 months ago)
• Last Synced: 2025-02-05T09:28:47.481Z (14 days ago)
• Topics: bioinformatics, genome-scale-metabolic-model, marine-microbial-ecology, metagenomics, phycosphere
• Language: Python
• Homepage:
• Size: 48 MB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 9
• Metadata Files:
  • Readme: README.md

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README

        
![logo](notebooks/images/phycogem_logo.png)




# Reconstructing phycospheric metabolic networks

[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)

![license](https://img.shields.io/github/license/Robaina/Pynteny)

![Contributor Covenant](https://img.shields.io/badge/Contributor%20Covenant-v2.0%20adopted-ff69b4)

![python](https://img.shields.io/badge/Python-3.11-blue)

[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)

Updating CarveME's universe curation pipeline in [this fork](https://github.com/Robaina/carveme_expanded_universe)

# :bulb: About

This repo contains Python code and Jupyter Notebooks aimed at facilitating the reconstruction and analysis of community genome-scale models reconstructed from genome data.

## :wrench: Installation

To install the package, first clone the repo and create the conda environment. We recomend using [mamba](https://mamba.readthedocs.io/en/latest/user_guide/mamba.html) instead of conda to speed up the process:

```bash

git clone https://github.com/Robaina/Phycogem.git

cd Phycogem

mamba env create -f envs/phycogem-dev.yml

conda activate phycogem-dev

```

Then build and install the package:

```bash

poetry build

pip install dist/phycogem*.whl

```

## :rocket: Usage

To use the package, activate the Conda environment:

```bash

conda activate phycogem-dev

```

This environment includes a Jupyter Notebook ipykernel, so the package can be used in a notebook as well.

## :notebook_with_decorative_cover: Notebooks

This repo contains several Notebooks to exemply the use of the package. They can be found within the `notebooks` folder.