Reconstructing phycospheric metabolic networks

Updating CarveME's universe curation pipeline in this fork

💡 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.

🔧 Installation

To install the package, first clone the repo and create the conda environment. We recomend using mamba instead of conda to speed up the process:

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:

poetry build
pip install dist/phycogem*.whl

🚀 Usage

To use the package, activate the Conda environment:

conda activate phycogem-dev

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

📔 Notebooks

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