Ecosyste.ms: Awesome
An open API service indexing awesome lists of open source software.
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
JSON representation
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
Awesome Lists containing this project
README

# Reconstructing phycospheric metabolic networks
[](https://www.repostatus.org/#active)



[](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.